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Sample records for direct phenotypic comparison

  1. A Direct Comparison of Remote Sensing Approaches for High-Throughput Phenotyping in Plant Breeding.

    PubMed

    Tattaris, Maria; Reynolds, Matthew P; Chapman, Scott C

    2016-01-01

    Remote sensing (RS) of plant canopies permits non-intrusive, high-throughput monitoring of plant physiological characteristics. This study compared three RS approaches using a low flying UAV (unmanned aerial vehicle), with that of proximal sensing, and satellite-based imagery. Two physiological traits were considered, canopy temperature (CT) and a vegetation index (NDVI), to determine the most viable approaches for large scale crop genetic improvement. The UAV-based platform achieves plot-level resolution while measuring several hundred plots in one mission via high-resolution thermal and multispectral imagery measured at altitudes of 30-100 m. The satellite measures multispectral imagery from an altitude of 770 km. Information was compared with proximal measurements using IR thermometers and an NDVI sensor at a distance of 0.5-1 m above plots. For robust comparisons, CT and NDVI were assessed on panels of elite cultivars under irrigated and drought conditions, in different thermal regimes, and on un-adapted genetic resources under water deficit. Correlations between airborne data and yield/biomass at maturity were generally higher than equivalent proximal correlations. NDVI was derived from high-resolution satellite imagery for only larger sized plots (8.5 × 2.4 m) due to restricted pixel density. Results support use of UAV-based RS techniques for high-throughput phenotyping for both precision and efficiency.

  2. A Direct Comparison of Remote Sensing Approaches for High-Throughput Phenotyping in Plant Breeding

    PubMed Central

    Tattaris, Maria; Reynolds, Matthew P.; Chapman, Scott C.

    2016-01-01

    Remote sensing (RS) of plant canopies permits non-intrusive, high-throughput monitoring of plant physiological characteristics. This study compared three RS approaches using a low flying UAV (unmanned aerial vehicle), with that of proximal sensing, and satellite-based imagery. Two physiological traits were considered, canopy temperature (CT) and a vegetation index (NDVI), to determine the most viable approaches for large scale crop genetic improvement. The UAV-based platform achieves plot-level resolution while measuring several hundred plots in one mission via high-resolution thermal and multispectral imagery measured at altitudes of 30–100 m. The satellite measures multispectral imagery from an altitude of 770 km. Information was compared with proximal measurements using IR thermometers and an NDVI sensor at a distance of 0.5–1 m above plots. For robust comparisons, CT and NDVI were assessed on panels of elite cultivars under irrigated and drought conditions, in different thermal regimes, and on un-adapted genetic resources under water deficit. Correlations between airborne data and yield/biomass at maturity were generally higher than equivalent proximal correlations. NDVI was derived from high-resolution satellite imagery for only larger sized plots (8.5 × 2.4 m) due to restricted pixel density. Results support use of UAV-based RS techniques for high-throughput phenotyping for both precision and efficiency. PMID:27536304

  3. The spatial patterns of directional phenotypic selection.

    PubMed

    Siepielski, Adam M; Gotanda, Kiyoko M; Morrissey, Michael B; Diamond, Sarah E; DiBattista, Joseph D; Carlson, Stephanie M

    2013-11-01

    Local adaptation, adaptive population divergence and speciation are often expected to result from populations evolving in response to spatial variation in selection. Yet, we lack a comprehensive understanding of the major features that characterise the spatial patterns of selection, namely the extent of variation among populations in the strength and direction of selection. Here, we analyse a data set of spatially replicated studies of directional phenotypic selection from natural populations. The data set includes 60 studies, consisting of 3937 estimates of selection across an average of five populations. We performed meta-analyses to explore features characterising spatial variation in directional selection. We found that selection tends to vary mainly in strength and less in direction among populations. Although differences in the direction of selection occur among populations they do so where selection is often weakest, which may limit the potential for ongoing adaptive population divergence. Overall, we also found that spatial variation in selection appears comparable to temporal (annual) variation in selection within populations; however, several deficiencies in available data currently complicate this comparison. We discuss future research needs to further advance our understanding of spatial variation in selection.

  4. Direct Comparison of a Natural Loss-Of-Function Single Nucleotide Polymorphism with a Targeted Deletion in the Ncf1 Gene Reveals Different Phenotypes

    PubMed Central

    Sareila, Outi; Hagert, Cecilia; Rantakari, Pia; Poutanen, Matti; Holmdahl, Rikard

    2015-01-01

    The genetic targeting of mouse models has given insight into complex processes. However, phenotypes of genetically targeted mice are susceptible to artifacts due to gene manipulation, which may lead to misinterpretation of the observations. To directly address these issues, we have compared the immunological phenotypes of Ncf1 knockout mice with Ncf1m1J mice possessing a naturally occurring intronic loss-of-function SNP in their Ncf1 gene. Neutrophil cytosolic factor 1 (NCF1) is the key regulatory component of the phagocytic NADPH oxidase 2 (NOX2) complex. Defects in NCF1 lead to lower production of reactive oxygen species (ROS) associated with autoimmune diseases in humans. In mice, collagen induced arthritis (CIA) and psoriatic arthritis are autoimmune disorders known to be regulated by Ncf1, and they were utilized in the present study to compare the Ncf1 knockout with Ncf1m1J mice. Targeted Ncf1 knockout mice were generated on a pure C57BL/6N genetic background, and thereafter crossed with B10.Q.Ncf1m1J mice. The targeting silenced the Ncf1 gene as intended, and both the B6N;B10.Q.Ncf1m1J mice as well as the knockout littermates had reduced ROS production compared to wild type mice. Both also exhibited enhanced STAT1 (signal transducer and activator of transcription 1) protein expression as an indicator of pronounced interferon signature reported recently for Ncf1 deficient mice. Surprisingly, female Ncf1 knockout mice were protected from CIA whereas the Ncf1m1J females developed severe disease. Ovariectomization retrieved the susceptibility of Ncf1 knockout females pointing to a sex hormone regulated protection against CIA in these mice. The data partly explains the discrepancy of the phenotypes reported earlier utilizing the Ncf1m1J mice or Ncf1 knockout mice. These observations indicate that even a targeted knockout mutation may lead to a different biological outcome in comparison to the natural loss-of-function mutation of the same gene. PMID:26528554

  5. Direct Comparison of Mice Null for Liver or Intestinal Fatty Acid-binding Proteins Reveals Highly Divergent Phenotypic Responses to High Fat Feeding*

    PubMed Central

    Gajda, Angela M.; Zhou, Yin Xiu; Agellon, Luis B.; Fried, Susan K.; Kodukula, Sarala; Fortson, Walter; Patel, Khamoshi; Storch, Judith

    2013-01-01

    The enterocyte expresses two fatty acid-binding proteins (FABP), intestinal FABP (IFABP; FABP2) and liver FABP (LFABP; FABP1). LFABP is also expressed in liver. Despite ligand transport and binding differences, it has remained uncertain whether these intestinally coexpressed proteins, which both bind long chain fatty acids (FA), are functionally distinct. Here, we directly compared IFABP−/− and LFABP−/− mice fed high fat diets containing long chain saturated or unsaturated fatty acids, reasoning that providing an abundance of dietary lipid would reveal unique functional properties. The results showed that mucosal lipid metabolism was indeed differentially modified, with significant decreases in FA incorporation into triacylglycerol (TG) relative to phospholipid (PL) in IFABP−/− mice, whereas LFABP−/− mice had reduced monoacylglycerol incorporation in TG relative to PL, as well as reduced FA oxidation. Interestingly, striking differences were found in whole body energy homeostasis; LFABP−/− mice fed high fat diets became obese relative to WT, whereas IFABP−/− mice displayed an opposite, lean phenotype. Fuel utilization followed adiposity, with LFABP−/− mice preferentially utilizing lipids, and IFABP−/− mice preferentially metabolizing carbohydrate for energy production. Changes in body weight and fat may arise, in part, from altered food intake; mucosal levels of the endocannabinoids 2-arachidonoylglycerol and arachidonoylethanolamine were elevated in LFABP−/−, perhaps contributing to increased energy intake. This direct comparison provides evidence that LFABP and IFABP have distinct roles in intestinal lipid metabolism; differential intracellular functions in intestine and in liver, for LFABP−/− mice, result in divergent downstream effects at the systemic level. PMID:23990461

  6. RNA Directed Modulation of Phenotypic Plasticity in Human Cells

    PubMed Central

    Burdach, Jon; Morris, Kevin V.

    2016-01-01

    Natural selective processes have been known to drive phenotypic plasticity, which is the emergence of different phenotypes from one genome following environmental stimulation. Long non-coding RNAs (lncRNAs) have been observed to modulate transcriptional and epigenetic states of genes in human cells. We surmised that lncRNAs are governors of phenotypic plasticity and drive natural selective processes through epigenetic modulation of gene expression. Using heat shocked human cells as a model we find several differentially expressed transcripts with the top candidates being lncRNAs derived from retro-elements. One particular retro-element derived transcripts, Retro-EIF2S2, was found to be abundantly over-expressed in heat shocked cells. Over-expression of Retro-EIF2S2 significantly enhanced cell viability and modulated a predisposition for an adherent cellular phenotype upon heat shock. Mechanistically, we find that this retro-element derived transcript interacts directly with a network of proteins including 40S ribosomal protein S30 (FAU), Eukaryotic translation initiation factor 5A (EIF5A), and Ubiquitin-60S ribosomal protein L40 (UBA52) to affect protein modulated cell adhesion pathways. We find one motif in Retro-EIF2S2 that exhibits binding to FAU and modulates phenotypic cell transitions from adherent to suspension states. The observations presented here suggest that retroviral derived transcripts actively modulate phenotypic plasticity in human cells in response to environmental selective pressures and suggest that natural selection may play out through the action of retro-elements in human cells. PMID:27082860

  7. RNA Directed Modulation of Phenotypic Plasticity in Human Cells.

    PubMed

    Trakman, Laura; Hewson, Chris; Burdach, Jon; Morris, Kevin V

    2016-01-01

    Natural selective processes have been known to drive phenotypic plasticity, which is the emergence of different phenotypes from one genome following environmental stimulation. Long non-coding RNAs (lncRNAs) have been observed to modulate transcriptional and epigenetic states of genes in human cells. We surmised that lncRNAs are governors of phenotypic plasticity and drive natural selective processes through epigenetic modulation of gene expression. Using heat shocked human cells as a model we find several differentially expressed transcripts with the top candidates being lncRNAs derived from retro-elements. One particular retro-element derived transcripts, Retro-EIF2S2, was found to be abundantly over-expressed in heat shocked cells. Over-expression of Retro-EIF2S2 significantly enhanced cell viability and modulated a predisposition for an adherent cellular phenotype upon heat shock. Mechanistically, we find that this retro-element derived transcript interacts directly with a network of proteins including 40S ribosomal protein S30 (FAU), Eukaryotic translation initiation factor 5A (EIF5A), and Ubiquitin-60S ribosomal protein L40 (UBA52) to affect protein modulated cell adhesion pathways. We find one motif in Retro-EIF2S2 that exhibits binding to FAU and modulates phenotypic cell transitions from adherent to suspension states. The observations presented here suggest that retroviral derived transcripts actively modulate phenotypic plasticity in human cells in response to environmental selective pressures and suggest that natural selection may play out through the action of retro-elements in human cells.

  8. Phenotype Sequencing: Identifying the Genes That Cause a Phenotype Directly from Pooled Sequencing of Independent Mutants

    PubMed Central

    Harper, Marc A.; Chen, Zugen; Toy, Traci; Machado, Iara M. P.; Nelson, Stanley F.; Liao, James C.; Lee, Christopher J.

    2011-01-01

    Random mutagenesis and phenotype screening provide a powerful method for dissecting microbial functions, but their results can be laborious to analyze experimentally. Each mutant strain may contain 50–100 random mutations, necessitating extensive functional experiments to determine which one causes the selected phenotype. To solve this problem, we propose a “Phenotype Sequencing” approach in which genes causing the phenotype can be identified directly from sequencing of multiple independent mutants. We developed a new computational analysis method showing that 1. causal genes can be identified with high probability from even a modest number of mutant genomes; 2. costs can be cut many-fold compared with a conventional genome sequencing approach via an optimized strategy of library-pooling (multiple strains per library) and tag-pooling (multiple tagged libraries per sequencing lane). We have performed extensive validation experiments on a set of E. coli mutants with increased isobutanol biofuel tolerance. We generated a range of sequencing experiments varying from 3 to 32 mutant strains, with pooling on 1 to 3 sequencing lanes. Our statistical analysis of these data (4099 mutations from 32 mutant genomes) successfully identified 3 genes (acrB, marC, acrA) that have been independently validated as causing this experimental phenotype. It must be emphasized that our approach reduces mutant sequencing costs enormously. Whereas a conventional genome sequencing experiment would have cost $7,200 in reagents alone, our Phenotype Sequencing design yielded the same information value for only $1200. In fact, our smallest experiments reliably identified acrB and marC at a cost of only $110–$340. PMID:21364744

  9. The transition of smooth muscle cells from a contractile to a migratory, phagocytic phenotype: direct demonstration of phenotypic modulation

    PubMed Central

    Sandison, Mairi E.; Dempster, John

    2016-01-01

    Key points Smooth muscle cell (SMC) phenotypic conversion from a contractile to a migratory phenotype is proposed to underlie cardiovascular disease but its contribution to vascular remodelling and even its existence have recently been questioned.Tracking the fate of individual SMCs is difficult as no specific markers of migratory SMCs exist.This study used a novel, prolonged time‐lapse imaging approach to continuously track the behaviour of unambiguously identified, fully differentiated SMCs.In response to serum, highly‐elongated, contractile SMCs initially rounded up, before spreading and migrating and these migratory cells displayed clear phagocytic activity.This study provides a direct demonstration of the transition of fully contractile SMCs to a non‐contractile, migratory phenotype with phagocytic capacity that may act as a macrophage‐like cell. Abstract Atherosclerotic plaques are populated with smooth muscle cells (SMCs) and macrophages. SMCs are thought to accumulate in plaques because fully differentiated, contractile SMCs reprogramme into a ‘synthetic’ migratory phenotype, so‐called phenotypic modulation, whilst plaque macrophages are thought to derive from blood‐borne myeloid cells. Recently, these views have been challenged, with reports that SMC phenotypic modulation may not occur during vascular remodelling and that plaque macrophages may not be of haematopoietic origin. Following the fate of SMCs is complicated by the lack of specific markers for the migratory phenotype and direct demonstrations of phenotypic modulation are lacking. Therefore, we employed long‐term, high‐resolution, time‐lapse microscopy to track the fate of unambiguously identified, fully‐differentiated, contractile SMCs in response to the growth factors present in serum. Phenotypic modulation was clearly observed. The highly elongated, contractile SMCs initially rounded up, for 1–3 days, before spreading outwards. Once spread, the SMCs became motile and

  10. Molecular signatures of mammalian hibernation: comparisons with alternative phenotypes

    PubMed Central

    2013-01-01

    Background Mammalian hibernators display phenotypes similar to physiological responses to calorie restriction and fasting, sleep, cold exposure, and ischemia-reperfusion in non-hibernating species. Whether biochemical changes evident during hibernation have parallels in non-hibernating systems on molecular and genetic levels is unclear. Results We identified the molecular signatures of torpor and arousal episodes during hibernation using a custom-designed microarray for the Arctic ground squirrel (Urocitellus parryii) and compared them with molecular signatures of selected mouse phenotypes. Our results indicate that differential gene expression related to metabolism during hibernation is associated with that during calorie restriction and that the nuclear receptor protein PPARα is potentially crucial for metabolic remodeling in torpor. Sleep-wake cycle-related and temperature response genes follow the same expression changes as during the torpor-arousal cycle. Increased fatty acid metabolism occurs during hibernation but not during ischemia-reperfusion injury in mice and, thus, might contribute to protection against ischemia-reperfusion during hibernation. Conclusions In this study, we systematically compared hibernation with alternative phenotypes to reveal novel mechanisms that might be used therapeutically in human pathological conditions. PMID:23957789

  11. Comparison of Liver Cell Models Using the Basel Phenotyping Cocktail

    PubMed Central

    Berger, Benjamin; Donzelli, Massimiliano; Maseneni, Swarna; Boess, Franziska; Roth, Adrian; Krähenbühl, Stephan; Haschke, Manuel

    2016-01-01

    Currently used hepatocyte cell systems for in vitro assessment of drug metabolism include hepatoma cell lines and primary human hepatocyte (PHH) cultures. We investigated the suitability of the validated in vivo Basel phenotyping cocktail (caffeine [CYP1A2], efavirenz [CYP2B6], losartan [CYP2C9], omeprazole [CYP2C19], metoprolol [CYP2D6], midazolam [CYP3A4]) in vitro and characterized four hepatocyte cell systems (HepG2 cells, HepaRG cells, and primary cryopreserved human hepatocytes in 2-dimensional [2D] culture or in 3D-spheroid co-culture) regarding basal metabolism and CYP inducibility. Under non-induced conditions, all CYP activities could be determined in 3D-PHH, CYP2B6, CYP2C19, CYP2D6, and CYP3A4 in 2D-PHH and HepaRG, and CYP2C19 and CYP3A4 in HepG2 cells. The highest non-induced CYP activities were observed in 3D-PHH and HepaRG cells. mRNA expression was at least four-fold higher for all CYPs in 3D-PHH compared to the other cell systems. After treatment with 20 μM rifampicin, mRNA increased 3- to 50-fold for all CYPs except CYP1A2 and 2D6 for HepaRG and 3D-PHH, 4-fold (CYP2B6) and 17-fold (CYP3A4) for 2D-PHH and four-fold (CYP3A4) for HepG2. In 3D-PHH at least a two-fold increase in CYP activity was observed for all inducible CYP isoforms while CYP1A2 and CYP2C9 activity did not increase in 2D-PHH and HepaRG. CYP inducibility assessed in vivo using the same phenotyping probes was also best reflected by the 3D-PHH model. Our studies show that 3D-PHH and (with some limitations) HepaRG are suitable cell systems for assessing drug metabolism and CYP induction in vitro. HepG2 cells are less suited to assess CYP induction of the 2C and 3A family. The Basel phenotyping cocktail is suitable for the assessment of CYP activity and induction also in vitro. PMID:27917125

  12. Phenotypic and evolutionary consequences of social behaviours: interactions among individuals affect direct genetic effects.

    PubMed

    Trubenová, Barbora; Hager, Reinmar

    2012-01-01

    Traditional quantitative genetics assumes that an individual's phenotype is determined by both genetic and environmental factors. For many animals, part of the environment is social and provided by parents and other interacting partners. When expression of genes in social partners affects trait expression in a focal individual, indirect genetic effects occur. In this study, we explore the effects of indirect genetic effects on the magnitude and range of phenotypic values in a focal individual in a multi-member model analyzing three possible classes of interactions between individuals. We show that social interactions may not only cause indirect genetic effects but can also modify direct genetic effects. Furthermore, we demonstrate that both direct and indirect genetic effects substantially alter the range of phenotypic values, particularly when a focal trait can influence its own expression via interactions with traits in other individuals. We derive a function predicting the relative importance of direct versus indirect genetic effects. Our model reveals that both direct and indirect genetic effects can depend to a large extent on both group size and interaction strength, altering group mean phenotype and variance. This may lead to scenarios where between group variation is much higher than within group variation despite similar underlying genetic properties, potentially affecting the level of selection. Our analysis highlights key properties of indirect genetic effects with important consequences for trait evolution, the level of selection and potentially speciation.

  13. The behavioral phenotype in MECP2 duplication syndrome: A comparison to idiopathic autism

    PubMed Central

    Peters, Sarika U.; Hundley, R. J.; Wilson, A.K.; Warren, Z.; Vehorn, A.; Carvalho, C.; Lupski, J.R.; Ramocki, M.B.

    2012-01-01

    Alterations in the X-linked gene MECP2 encoding the methyl-CpG-binding protein 2 (MeCP2) have been linked to autism spectrum disorders (ASD). Most recently, data suggest that overexpression of MECP2 may be related to ASD. To better characterize the relevance of MECP2 overexpression to ASD-related behaviors, we compared the core symptoms of ASD in MECP2 duplication syndrome to nonverbal-mental-age-matched boys with idiopathic ASD. Within the MECP2 duplication group we further delineated aspects of the behavioral phenotype, and also examined how duplication size and gene content corresponded to clinical severity. We compared 10 males with MECP2 duplication syndrome (ages 3–10) to a chronological and mental age-matched sample of 9 nonverbal males with idiopathic ASD. Our results indicate that boys with MECP2 duplication syndrome share the core behavioral features of ASD (e.g. social affect, restricted/repetitive behaviors). Direct comparisons of ASD profiles revealed that a majority of boys with MECP2 duplication syndrome are similar to idiopathic ASD; they have impairments in social affect (albeit to a lesser degree than idiopathic ASD) and similar severity in restricted/repetitive behaviors. Nonverbal mental age did not correlate with severity of social impairment or repetitive behaviors. Within the MECP2 duplication group, breakpoint size does not predict differences in clinical severity. In addition to social withdrawal and stereotyped behaviors, we also found that hyposensitivity to pain/temperature are part of the behavioral phenotype of MECP2 duplication syndrome. Our results illustrate that overexpression/increased dosage of MECP2 is related to core features of ASD. PMID:23169761

  14. Dark matter directional detection: comparison of the track direction determination

    NASA Astrophysics Data System (ADS)

    Couturier, C.; Zopounidis, J. P.; Sauzet, N.; Naraghi, F.; Santos, D.

    2017-01-01

    Several directional techniques have been proposed for a directional detection of Dark matter, among others anisotropic crystal detectors, nuclear emulsion plates, and low-pressure gaseous TPCs. The key point is to get access to the initial direction of the nucleus recoiling due to the elastic scattering by a WIMP. In this article, we aim at estimating, for each method, how the information of the recoil track initial direction is preserved in different detector materials. We use the SRIM simulation code to emulate the motion of the first recoiling nucleus in each material. We propose the use of a new observable, D, to quantify the preservation of the initial direction of the recoiling nucleus in the detector. We show that in an emulsion mix and an anisotropic crystal, the initial direction is lost very early, while in a typical TPC gas mix, the direction is well preserved.

  15. Direct functional assessment of the composite phenotype through multivariate projection strategies.

    PubMed

    Conesa, Ana; Bro, Rasmus; García-García, Francisco; Prats, José Manuel; Götz, Stefan; Kjeldahl, Karin; Montaner, David; Dopazo, Joaquín

    2008-12-01

    We present a novel approach for the analysis of transcriptomics data that integrates functional annotation of gene sets with expression values in a multivariate fashion, and directly assesses the relation of functional features to a multivariate space of response phenotypical variables. Multivariate projection methods are used to obtain new correlated variables for a set of genes that share a given function. These new functional variables are then related to the response variables of interest. The analysis of the principal directions of the multivariate regression allows for the identification of gene function features correlated with the phenotype. Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches.

  16. A comparison of phenylketonuria with attention deficit hyperactivity disorder: do markedly different aetiologies deliver common phenotypes?

    PubMed

    Stevenson, M; McNaughton, N

    2013-10-01

    Phenylketonuria (PKU) is a well-defined metabolic disorder arising from a mutation that disrupts phenylalanine metabolism and so produces a variety of neural changes indirectly. Severe cognitive impairment can be prevented by dietary treatment; however, residual symptoms may be reported. These residual symptoms appear to overlap a more prevalent childhood disorder: Attention Deficit/Hyperactivity Disorder (ADHD). However, the aetiology of ADHD is a vast contrast to PKU: it seems to arise from a complex combination of genes; and it has a substantial environmental component. We ask whether these two disorders result from two vastly different genotypes that converge on a specific core phenotype that includes similar dysfunctions of Gray's (Gray, 1982) Behavioural Inhibition System (BIS), coupled with other disorder-specific dysfunctions. If so, we believe comparison of the commonalities will allow greater understanding of the neuropsychology of both disorders. We review in detail the aetiology, treatment, neural pathology, cognitive deficits and electrophysiological abnormalities of PKU; and compare this with selected directly matching aspects of ADHD. The biochemical and neural pathologies of PKU and ADHD are quite distinct in their causes and detail; but they result in the disorder in the brain of large amino acid levels, dopamine and white matter that are very similar and could explain the overlap of symptoms within and between the PKU and ADHD spectra. The common deficits affect visual function, motor function, attention, working memory, planning, and inhibition. For each of PKU and ADHD separately, a subset of deficits has been attributed to a primary dysfunction of behavioural inhibition. In the case of ADHD (excluding the inattentive subtype) this has been proposed to involve a specific failure of the BIS; and we suggest that this is also true of PKU. This accounts for a substantial proportion of the parallels in the superficial symptoms of both disorders and

  17. Direct Field and Reverberant Chamber Acoustic Test Comparisons

    NASA Technical Reports Server (NTRS)

    OConnell, Michael

    2007-01-01

    Reverberant and direct acoustic test comparisons were analyzed in this viewgraph presentation. The acoustic test data set includes: 1) CloudSat antenna subjected to PF reverberant chamber acoustic test; 2) CloudSat subjected to a PF direct speaker acoustic test; and 3) DAWN flight spacecraft subjected to PF direct speaker and a workmanship reverberant chamber acoustic test.

  18. HOXA10 Controls Osteoblastogenesis by Directly Activating Bone Regulatory and Phenotypic Genes▿

    PubMed Central

    Hassan, Mohammad Q.; Tare, Rahul; Lee, Suk Hee; Mandeville, Matthew; Weiner, Brian; Montecino, Martin; van Wijnen, Andre J.; Stein, Janet L.; Stein, Gary S.; Lian, Jane B.

    2007-01-01

    HOXA10 is necessary for embryonic patterning of skeletal elements, but its function in bone formation beyond this early developmental stage is unknown. Here we show that HOXA10 contributes to osteogenic lineage determination through activation of Runx2 and directly regulates osteoblastic phenotypic genes. In response to bone morphogenic protein BMP2, Hoxa10 is rapidly induced and functions to activate the Runx2 transcription factor essential for bone formation. A functional element with the Hox core motif was characterized for the bone-related Runx2 P1 promoter. HOXA10 also activates other osteogenic genes, including the alkaline phosphatase, osteocalcin, and bone sialoprotein genes, and temporally associates with these target gene promoters during stages of osteoblast differentiation prior to the recruitment of RUNX2. Exogenous expression and small interfering RNA knockdown studies establish that HOXA10 mediates chromatin hyperacetylation and trimethyl histone K4 (H3K4) methylation of these genes, correlating to active transcription. HOXA10 therefore contributes to early expression of osteogenic genes through chromatin remodeling. Importantly, HOXA10 can induce osteoblast genes in Runx2 null cells, providing evidence for a direct role in mediating osteoblast differentiation independent of RUNX2. We propose that HOXA10 activates RUNX2 in mesenchymal cells, contributing to the onset of osteogenesis, and that HOXA10 subsequently supports bone formation by direct regulation of osteoblast phenotypic genes. PMID:17325044

  19. A Comparison of State Advance Directive Documents

    ERIC Educational Resources Information Center

    Gunter-Hunt, Gail; Mahoney, Jane E.; Sieger, Carol E.

    2002-01-01

    Purpose: Advance directive (AD) documents are based on state-specific statutes and vary in terms of content. These differences can create confusion and inconsistencies resulting in a possible failure to honor the health care wishes of people who execute health care documents for one state and receive health care in another state. The purpose of…

  20. Exome sequencing and directed clinical phenotyping diagnose cholesterol ester storage disease presenting as autosomal recessive hypercholesterolemia

    PubMed Central

    Stitziel, Nathan O.; Fouchier, Sigrid W.; Sjouke, Barbara; Peloso, Gina M.; Moscoso, Alessa M.; Auer, Paul L.; Goel, Anuj; Gigante, Bruna; Barnes, Timothy A.; Melander, Olle; Orho-Melander, Marju; Duga, Stefano; Sivapalaratnam, Suthesh; Nikpay, Majid; Martinelli, Nicola; Girelli, Domenico; Jackson, Rebecca D.; Kooperberg, Charles; Lange, Leslie A.; Ardissino, Diego; McPherson, Ruth; Farrall, Martin; Watkins, Hugh; Reilly, Muredach P.; Rader, Daniel J.; de Faire, Ulf; Schunkert, Heribert; Erdmann, Jeanette; Samani, Nilesh J.; Charnas, Lawrence; Altshuler, David; Gabriel, Stacey; Kastelein, John J.P.; Defesche, Joep C.; Nederveen, Aart J.; Kathiresan, Sekar; Hovingh, G. Kees

    2014-01-01

    Objective Autosomal recessive hypercholesterolemia (ARH) is a rare inherited disorder characterized by extremely high total and low-density lipoprotein cholesterol levels that has been previously linked to mutations in LDLRAP1. We identified a family with ARH not explained by mutations in LDLRAP1 or other genes known to cause monogenic hypercholesterolemia. The aim of this study was to identify the molecular etiology of ARH in this family. Approach and Results We used exome sequencing to assess all protein coding regions of the genome in three family members and identified a homozygous exon 8 splice junction mutation (c.894G>A, also known as E8SJM) in LIPA that segregated with the diagnosis of hypercholesterolemia. Since homozygosity for mutations in LIPA is known to cause cholesterol ester storage disease (CESD), we performed directed follow-up phenotyping by non-invasively measuring hepatic cholesterol content. We observed abnormal hepatic accumulation of cholesterol in the homozygote individuals, supporting the diagnosis of CESD. Given previous suggestions of cardiovascular disease risk in heterozygous LIPA mutation carriers, we genotyped E8SJM in >27,000 individuals and found no association with plasma lipid levels or risk of myocardial infarction, confirming a true recessive mode of inheritance. Conclusions By integrating observations from Mendelian and population genetics along with directed clinical phenotyping, we diagnosed clinically unapparent CESD in the affected individuals from this kindred and addressed an outstanding question regarding risk of cardiovascular disease in LIPA E8SJM heterozygous carriers. PMID:24072694

  1. Comparison of directed self-assembly integrations

    NASA Astrophysics Data System (ADS)

    Somervell, Mark; Gronheid, Roel; Hooge, Joshua; Nafus, Kathleen; Rincon Delgadillo, Paulina; Thode, Chris; Younkin, Todd; Matsunaga, Koichi; Rathsack, Ben; Scheer, Steven; Nealey, Paul

    2012-03-01

    Directed Self-Assembly (DSA) is gaining momentum as a means for extending optical lithography past its current limits. There are many forms of the technology, and it can be used for creating both line/space and hole patterns.1-3 As with any new technology, adoption of DSA faces several key challenges. These include creation of a new materials infrastructure, fabrication of new processing hardware, and the development of implementable integrations. Above all else, determining the lowest possible defect density remains the industry's most critical concern. Over the past year, our team, working at IMEC, has explored various integrations for making 12-14nm half-pitch line/space arrays. Both grapho- and chemo-epitaxy implementations have been investigated in order to discern which offers the best path to high volume manufacturing. This paper will discuss the manufacturing readiness of the various implementations by comparing the process margin for different DSA processing steps and defect density for the entirety of the flow. As part of this work, we will describe our method for using programmed defectivity on reticle to elucidate the mechanisms that drive self-assembly defectivity on wafer.

  2. Mouse models of frontotemporal dementia: A comparison of phenotypes with clinical symptomatology.

    PubMed

    Ahmed, Rebekah M; Irish, Muireann; van Eersel, Janet; Ittner, Arne; Ke, Yazi D; Volkerling, Alexander; van der Hoven, Julia; Tanaka, Kimi; Karl, Tim; Kassiou, Michael; Kril, Jillian J; Piguet, Olivier; Götz, Jürgen; Kiernan, Matthew C; Halliday, Glenda M; Hodges, John R; Ittner, Lars M

    2017-03-01

    Frontotemporal dementia (FTD) is the second most common cause of young onset dementia. It is increasingly recognized that there is a clinical continuum between FTD and amyotrophic lateral sclerosis (ALS). At a clinical, pathological and genetic level there is much heterogeneity in FTD, meaning that our understanding of this condition, pathophysiology and development of treatments has been limited. A number of mouse models focusing predominantly on recapitulating neuropathological and molecular changes of disease have been developed, with most transgenic lines expressing a single specific protein or genetic mutation. Together with the species-typical presentation of functional deficits, this makes the direct translation of results from these models to humans difficult. However, understanding the phenotypical presentations in mice and how they relate to clinical symptomology in humans is essential for advancing translation. Here we review current mouse models in FTD and compare their phenotype to the clinical presentation in patients.

  3. Pseudomonas aeruginosa in Dairy Goats: Genotypic and Phenotypic Comparison of Intramammary and Environmental Isolates

    PubMed Central

    Scaccabarozzi, Licia; Leoni, Livia; Ballarini, Annalisa; Barberio, Antonio; Locatelli, Clara; Casula, Antonio; Bronzo, Valerio; Pisoni, Giuliano; Jousson, Olivier; Morandi, Stefano; Rapetti, Luca; García-Fernández, Aurora; Moroni, Paolo

    2015-01-01

    Following the identification of a case of severe clinical mastitis in a Saanen dairy goat (goat A), an average of 26 lactating goats in the herd was monitored over a period of 11 months. Milk microbiological analysis revealed the presence of Pseudomonas aeruginosa in 7 of the goats. Among these 7 does, only goat A showed clinical signs of mastitis. The 7 P. aeruginosa isolates from the goat milk and 26 P. aeruginosa isolates from environmental samples were clustered by RAPD-PCR and PFGE analyses in 3 genotypes (G1, G2, G3) and 4 clusters (A, B, C, D), respectively. PFGE clusters A and B correlated with the G1 genotype and included the 7 milk isolates. Although it was not possible to identify the infection source, these results strongly suggest a spreading of the infection from goat A. Clusters C and D overlapped with genotypes G2 and G3, respectively, and included only environmental isolates. The outcome of the antimicrobial susceptibility test performed on the isolates revealed 2 main patterns of multiple resistance to beta-lactam antibiotics and macrolides. Virulence related phenotypes were analyzed, such as swarming and swimming motility, production of biofilm and production of secreted virulence factors. The isolates had distinct phenotypic profiles, corresponding to genotypes G1, G2 and G3. Overall, correlation analysis showed a strong correlation between sampling source, RAPD genotype, PFGE clusters, and phenotypic clusters. The comparison of the levels of virulence related phenotypes did not indicate a higher pathogenic potential in the milk isolates as compared to the environmental isolates. PMID:26606430

  4. Comparison of phenotypic and virulence genes characteristics in human and chicken isolates of Proteus mirabilis.

    PubMed

    Barbour, Elie K; Hajj, Zahi G; Hamadeh, Shadi; Shaib, Houssam A; Farran, Mohamad T; Araj, George; Faroon, Obaid; Barbour, Kamil E; Jirjis, Faris; Azhar, Esam; Kumosani, Taha; Harakeh, Steve

    2012-10-01

    The objective of this work is to compare the phenotypic and virulence genes characteristics in human and chicken isolates of Proteus mirabilis. The bacterial examination of 50 livers of individual broilers, marketed by four major outlets, revealed a high recovery of P. mirabilis (66%), and a low recovery frequency of Salmonella spp. (4%), Serratia odorifera (2%), Citrobacter brakii (2%), and Providencia stuartii (2%). The phenotypic biochemical characterization of the recovered 33 chicken isolates of P. mirabilis were compared to 30 human isolates (23 urinary and six respiratory isolates). The comparison revealed significant differences in the presence of gelatinase enzyme (100% presence in chicken isolates versus 91.3 and 83.3% presence in human urinary and respiratory isolates, respectively, P,0.05). The H(2)S production occurred in 100% of chicken isolates versus 95.6 and 66.7% presence in human urinary and respiratory isolates, respectively, P,0.05). The other 17 biochemical characteristics did not differ significantly among the three groups of isolates (P.0.05). Two virulence genes, the mrpA and FliL, were having a typical 100% presence in randomly selected isolates of P. mirabilis recovered from chicken livers (N510) versus isolates recovered from urinary (N55) and respiratory specimens of humans (N55) (P.0.05). The average percentage similarity of mrpA gene nucleotide sequence of poultry isolates to human urinary and respiratory isolates was 93.2 and 97.5-%, respectively. The high similarity in phenotypic characteristics, associated with typical frequency of presence of two virulence genes, and high similarity in sequences of mrpA gene among poultry versus human P. mirabilis isolates justifies future investigations targeting the evaluation of adaptable pathogenicity of avian Proteus mirabilis isolates to mammalian hosts.

  5. Comparison of phenotypic and virulence genes characteristics in human and chicken isolates of Proteus mirabilis

    PubMed Central

    Barbour, Elie K; Hajj, Zahi G; Hamadeh, Shadi; Shaib, Houssam A; Farran, Mohamad T; Araj, George; Faroon, Obaid; Barbour, Kamil E; Jirjis, Faris; Azhar, Esam; Kumosani, Taha; Harakeh, Steve

    2012-01-01

    The objective of this work is to compare the phenotypic and virulence genes characteristics in human and chicken isolates of Proteus mirabilis. The bacterial examination of 50 livers of individual broilers, marketed by four major outlets, revealed a high recovery of P. mirabilis (66%), and a low recovery frequency of Salmonella spp. (4%), Serratia odorifera (2%), Citrobacter brakii (2%), and Providencia stuartii (2%). The phenotypic biochemical characterization of the recovered 33 chicken isolates of P. mirabilis were compared to 30 human isolates (23 urinary and six respiratory isolates). The comparison revealed significant differences in the presence of gelatinase enzyme (100% presence in chicken isolates versus 91.3 and 83.3% presence in human urinary and respiratory isolates, respectively, P<0.05). The H2S production occurred in 100% of chicken isolates versus 95.6 and 66.7% presence in human urinary and respiratory isolates, respectively, P<0.05). The other 17 biochemical characteristics did not differ significantly among the three groups of isolates (P>0.05). Two virulence genes, the mrpA and FliL, were having a typical 100% presence in randomly selected isolates of P. mirabilis recovered from chicken livers (N = 10) versus isolates recovered from urinary (N = 5) and respiratory specimens of humans (N = 5) (P>0.05). The average percentage similarity of mrpA gene nucleotide sequence of poultry isolates to human urinary and respiratory isolates was 93.2 and 97.5-%, respectively. The high similarity in phenotypic characteristics, associated with typical frequency of presence of two virulence genes, and high similarity in sequences of mrpA gene among poultry versus human P. mirabilis isolates justifies future investigations targeting the evaluation of adaptable pathogenicity of avian Proteus mirabilis isolates to mammalian hosts. PMID:23182140

  6. The equine alveolar macrophage: Functional and phenotypic comparisons with peritoneal macrophages☆

    PubMed Central

    Karagianni, Anna E.; Kapetanovic, Ronan; McGorum, Bruce C.; Hume, David A.; Pirie, Scott R.

    2013-01-01

    Alveolar macrophages (AMs) constitute the first line of defence in the lung of all species, playing a crucial role in the regulation of immune responses to inhaled pathogens. A detailed understanding of the function and phenotype of AMs is a necessary pre-requisite to both elucidating their role in preventing opportunistic bacterial colonisation of the lower respiratory tract and developing appropriate preventative strategies. The purpose of the study was to characterise this important innate immune cell at the tissue level by making functional and phenotypic comparisons with peritoneal macrophages (PMs). We hypothesised that the tissue of origin determines a unique phenotype of AMs, which may constitute an appropriate therapeutic target for certain equine respiratory diseases. Macrophages isolated from the lung and the peritoneal cavity of 9 horses were stimulated with various toll like receptor (TLR) ligands and the production of nitrite, tumour necrosis factor alpha (TNFα), interleukin (IL) 10 and indoleamine 2,3-dioxygenase (IDO) were measured by the Griess reaction and enzyme linked immunosorbent assay (ELISA) and/or quantitative polymerase chain reaction, respectively. Cells were also compared on the basis of phagocytic-capacity and the expression of several cell surface markers. AMs, but not PMs, demonstrated increased TNFα release following stimulation with LPS, polyinosinic polycytidylic acid (Poly IC) and heat-killed Salmonella typhinurium and increased TNFα and IDO mRNA expression when stimulated with LPS. AMs showed high expression of the specific macrophage markers cluster of differentiation (CD) 14, CD163 and TLR4, whereas PMs showed high expression of TLR4 only. AMs, but not PMs, demonstrated efficient phagocytic activity. Our results demonstrate that AMs are more active than PMs when stimulated with various pro-inflammatory ligands, thus supporting the importance of the local microenvironment in the activation status of the macrophage. This

  7. The equine alveolar macrophage: functional and phenotypic comparisons with peritoneal macrophages.

    PubMed

    Karagianni, Anna E; Kapetanovic, Ronan; McGorum, Bruce C; Hume, David A; Pirie, Scott R

    2013-10-01

    Alveolar macrophages (AMs) constitute the first line of defence in the lung of all species, playing a crucial role in the regulation of immune responses to inhaled pathogens. A detailed understanding of the function and phenotype of AMs is a necessary pre-requisite to both elucidating their role in preventing opportunistic bacterial colonisation of the lower respiratory tract and developing appropriate preventative strategies. The purpose of the study was to characterise this important innate immune cell at the tissue level by making functional and phenotypic comparisons with peritoneal macrophages (PMs). We hypothesised that the tissue of origin determines a unique phenotype of AMs, which may constitute an appropriate therapeutic target for certain equine respiratory diseases. Macrophages isolated from the lung and the peritoneal cavity of 9 horses were stimulated with various toll like receptor (TLR) ligands and the production of nitrite, tumour necrosis factor alpha (TNFα), interleukin (IL) 10 and indoleamine 2,3-dioxygenase (IDO) were measured by the Griess reaction and enzyme linked immunosorbent assay (ELISA) and/or quantitative polymerase chain reaction, respectively. Cells were also compared on the basis of phagocytic-capacity and the expression of several cell surface markers. AMs, but not PMs, demonstrated increased TNFα release following stimulation with LPS, polyinosinic polycytidylic acid (Poly IC) and heat-killed Salmonella typhinurium and increased TNFα and IDO mRNA expression when stimulated with LPS. AMs showed high expression of the specific macrophage markers cluster of differentiation (CD) 14, CD163 and TLR4, whereas PMs showed high expression of TLR4 only. AMs, but not PMs, demonstrated efficient phagocytic activity. Our results demonstrate that AMs are more active than PMs when stimulated with various pro-inflammatory ligands, thus supporting the importance of the local microenvironment in the activation status of the macrophage. This

  8. Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins.

    PubMed

    Risso, Valeria A; Gavira, Jose A; Gaucher, Eric A; Sanchez-Ruiz, Jose M

    2014-06-01

    Consensus-sequence engineering has generated protein variants with enhanced stability, and sometimes, with modulated biological function. Consensus mutations are often interpreted as the introduction of ancestral amino acid residues. However, the precise relationship between consensus engineering and ancestral protein resurrection is not fully understood. Here, we report the properties of proteins encoded by consensus sequences derived from a multiple sequence alignment of extant, class A β-lactamases, as compared with the properties of ancient Precambrian β-lactamases resurrected in the laboratory. These comparisons considered primary sequence, secondary, and tertiary structure, as well as stability and catalysis against different antibiotics. Out of the three consensus variants generated, one could not be expressed and purified (likely due to misfolding and/or low stability) and only one displayed substantial stability having substrate promiscuity, although to a lower extent than ancient β-lactamases. These results: (i) highlight the phenotypic differences between consensus variants and laboratory resurrections of ancestral proteins; (ii) question interpretations of consensus proteins as phenotypic proxies of ancestral proteins; and (iii) support the notion that ancient proteins provide a robust approach toward the preparation of protein variants having large numbers of mutational changes while possessing unique biomolecular properties.

  9. De Lange syndrome: subjective and objective comparison of the classical and mild phenotypes.

    PubMed Central

    Allanson, J E; Hennekam, R C; Ireland, M

    1997-01-01

    Classical de Lange syndrome presents with a striking face, pronounced growth and mental retardation, and variable limb deficiencies. Over the past five years, a mild variant has been defined, with less significant psychomotor retardation, less marked pre- and postnatal growth deficiency, and an uncommon association with major malformations, although mild limb anomalies may be present. We have evaluated 43 subjects with de Lange syndrome, 30 with classical features, aged from birth to 21 years, and 13 with the mild phenotype, aged from 18 months to 30 years. In addition to assessment of gestalt and facial change with time, detailed craniofacial measurements have been obtained on each subject and composite pattern profiles compiled. The characteristic face of classical de Lange syndrome is present at birth and changes little throughout life, although there is some lengthening of the face with age and the jaw becomes squared. In mild de Lange syndrome, the characteristic classical appearance may be present at birth, but in some subjects it may be two or three years before the typical face is obvious. In general, the overall impression is less striking, perhaps because of increased facial expression and greater alertness. With age, the face loses the characteristic appearance, the nasal height increases, the philtrum does not seem as long, and the upper vermilion is full and everted, although the crescent shaped mouth with downturned corners remains. Eyebrows may be full and bushy. Objective comparison of the face in mild and classical de Lange syndrome, through the use of craniofacial pattern profiles, shows marked similarity of patterns at 4 to 9 years; both groups have microbrachycephaly, but the individual dimensions of the mild group are slightly closer to normal than their classical counterparts. The correlation coefficient is high (0.83). In the adult groups, similarity of patterns remains but is less marked. The normalisation of scores in the mild group is more

  10. Directed Dedifferentiation Using Partial Reprogramming Induces Invasive Phenotype in Melanoma Cells.

    PubMed

    Knappe, Nathalie; Novak, Daniel; Weina, Kasia; Bernhardt, Mathias; Reith, Maike; Larribere, Lionel; Hölzel, Michael; Tüting, Thomas; Gebhardt, Christoffer; Umansky, Viktor; Utikal, Jochen

    2016-04-01

    The combination of cancer-focused studies and research related to nuclear reprogramming has gained increasing importance since both processes-reprogramming towards pluripotency and malignant transformation-share essential features. Studies have revealed that incomplete reprogramming of somatic cells leads to malignant transformation indicating that epigenetic regulation associated with iPSC generation can drive cancer development [J Mol Cell Biol 2011;341-350; Cell 2012;151:1617-1632; Cell 2014;156:663-677]. However, so far it is unclear whether incomplete reprogramming also affects cancer cells and their function. In the context of melanoma, dedifferentiation correlates to therapy resistance in mouse studies and has been documented in melanoma patients [Nature 2012;490:412-416; Clin Cancer Res 2014;20:2498-2499]. Therefore, we sought to investigate directed dedifferentiation using incomplete reprogramming of melanoma cells. Using a murine model we investigated the effects of partial reprogramming on the cellular plasticity of melanoma cells. We demonstrate for the first time that induced partial reprogramming results in a reversible phenotype switch in melanoma cells. Partially reprogrammed cells at day 12 after transgene induction display elevated invasive potential in vitro and increased lung colonization in vivo. Additionally, using global gene expression analysis of partially reprogrammed cells, we identified SNAI3 as a novel invasion-related marker in human melanoma. SNAI3 expression correlates with tumor thickness in primary melanomas and thus, may be of prognostic value. In summary, we show that investigating intermediate states during the process of reprogramming melanoma cells can reveal novel insights into the pathogenesis of melanoma progression. We propose that deeper analysis of partially reprogrammed melanoma cells may contribute to identification of yet unknown signaling pathways that can drive melanoma progression.

  11. Tracing the sources of human salmonellosis: a multi-model comparison of phenotyping and genotyping methods.

    PubMed

    Mughini-Gras, Lapo; Smid, Joost; Enserink, Remko; Franz, Eelco; Schouls, Leo; Heck, Max; van Pelt, Wilfrid

    2014-12-01

    Salmonella source attribution is usually performed using frequency-matched models, such as the (modified) Dutch and Hald models, based on phenotyping data, i.e. serotyping, phage typing, and antimicrobial resistance profiling. However, for practical and economic reasons, genotyping methods such as Multi-locus Variable Number of Tandem Repeats Analysis (MLVA) are gradually replacing traditional phenotyping of salmonellas beyond the serovar level. As MLVA-based source attribution of human salmonellosis using frequency-matched models is problematic due to the high variability of the genetic targets investigated, other models need to be explored. Using a comprehensive data set from the Netherlands in 2005-2013, this study aimed at attributing sporadic and domestic cases of Salmonella Typhimurium/4,[5],12:i:- and Salmonella Enteritidis to four putative food-producing animal sources (pigs, cattle, broilers, and layers/eggs) using the modified Dutch and Hald models (based on sero/phage typing data) in comparison with a widely applied population genetics model - the asymmetric island model (AIM) - supplied with MLVA data. This allowed us to compare model outcomes and to corroborate whether MLVA-based Salmonella source attribution using the AIM is able to provide sound, comparable results. All three models provided very similar results, confirming once more that most S. Typhimurium/4,[5],12:i:- and S. Enteritidis cases are attributable to pigs and layers/eggs, respectively. We concluded that MLVA-based source attribution using the AIM is a feasible option, at least for S. Typhimurium/4,[5],12:i:- and S. Enteritidis. Enough information seems to be contained in the MLVA profiles to trace the sources of human salmonellosis even in presence of imperfect temporal overlap between human and source isolates. Besides Salmonella, the AIM might also be applicable to other pathogens that do not always comply to clonal models. This would add further value to current surveillance

  12. The variety of photorespiratory phenotypes - employing the current status for future research directions on photorespiration.

    PubMed

    Timm, S; Bauwe, H

    2013-07-01

    Mutations of genes encoding for proteins within the photorespiratory core cycle and associated processes are characterised by lethality under normal air but viability under elevated CO2 conditions. This feature has been described as 'the photorespiratory phenotype' and assumed to be distinctly equal for all of these mutants. In recent years a broad collection of photorespiratory mutants has been isolated, which has allowed a comparative analysis. Distinct phenotypic features were observed when Arabidopsis thaliana mutants defective in photorespiratory enzymes were compared, and during shifts from elevated to ambient CO2 conditions. The exact reasons for the mutant-specific photorespiratory phenotypes are mostly unknown, but they indicate even more plasticity of photorespiratory metabolism. Moreover, a growing body of evidence was obtained that mutant features could be modulated by alterations of several factors, such as CO2 :O2 ratios, photoperiod, light intensity, organic carbon supply and pathogens. Hence, systematic analyses of the responses to these factors appear to be crucial to unravel mechanisms how photorespiration adapts and interacts with the whole cellular metabolism. Here we review current knowledge regarding photorespiratory mutants and propose a new level of phenotypic sub-classification. Finally, we present further questions that should be addressed in the field of photorespiration.

  13. Standard terminology for phenotypic variations: the elements of morphology project, its current progress, and future directions.

    PubMed

    Carey, John C; Allanson, Judith E; Hennekam, Raoul C M; Biesecker, Leslie G

    2012-05-01

    In 2005, the authors of this article formed an international working group to develop standardized definitions and terms to describe the physical variations used in human phenotypic analyses. This project, which came to be known as the Elements of Morphology, resulted in six articles proposing consensus definitions for almost 400 phenotypic variations of the head and face; periorbital region; ear, nose, and philtrum; mouth and lips; and hands and feet. Every variation was accompanied by a representative figure depicting the feature. The articles were published in the January 2009 issue of the American Journal of Medical Genetics Part A and are available for free access on both the Journal's Web page and a National Institutes of Health-based site. The publication of the Elements' definitions has spawned an ongoing dialogue about the proposed terms to describe the phenotype. The working group considered the six articles as only the first step in the process, and four more articles on proposed terminology for the trunk, genital region, skin, and remainder of the limb terms are in preparation. The secondary outcome of the Elements project is the provision of a working methodology for the establishment of standardized terminology and definitions for phenotype analysis in general.

  14. X-chromosomal inactivation directly influences the phenotypic manifestation of X-linked protoporphyria

    PubMed Central

    Brancaleoni, V.; Balwani, M.; Granata, F.; Graziadei, G.; Missineo, P.; Fiorentino, V.; Fustinoni, S.; Cappellini, M.D.; Naik, H.; Desnick, R.J.; Di Pierro, E.

    2015-01-01

    X-linked protoporphyria (XLP), a rare erythropoietic porphyria, results from terminal exon gain-of-function mutations in the ALAS2 gene causing increased ALAS2 activity and markedly increased erythrocyte protoporphyrin levels. Patients present with severe cutaneous photosensitivity and may develop liver dysfunction. XLP was originally reported as X-linked dominant with 100% penetrance in males and females. We characterized 11 heterozygous females from six unrelated XLP families and show markedly varying phenotypic and biochemical heterogeneity, reflecting the degree of X-chromsomal inactivation of the mutant gene. ALAS2 sequencing identified the specific mutation and confirmed heterozygosity among the females. Clinical history, plasma and erythrocyte protoporphyrin levels were determined. Methylation assays of the androgen receptor and zinc-finger MYM type 3 short tandem repeat polymorphisms estimated each heterozygotes X-chromosomal inactivation pattern. Heterozygotes with equal or increased skewing, favoring expression of the wild-type allele had no clinical symptoms and only slightly increased erythrocyte protoporphyrin concentrations and/or frequency of protoporphyrin-containing peripheral blood fluorocytes. When the wild-type allele was preferentially inactivated, heterozygous females manifested the disease phenotype and had both higher erythrocyte protoporphyrin levels and circulating fluorocytes. These findings confirm that the previous dominant classification of XLP is inappropriate and genetically misleading, as the disorder is more appropriately designated XLP. PMID:25615817

  15. Genetic predisposition directs breast cancer phenotype by dictating progenitor cell fate

    PubMed Central

    Proia, Theresa A.; Keller, Patricia J.; Gupta, Piyush B.; Klebba, Ina; Jones, Ainsley D.; Sedic, Maja; Gilmore, Hannah; Tung, Nadine; Naber, Stephen P.; Schnitt, Stuart; Lander, Eric S.; Kuperwasser, Charlotte

    2011-01-01

    Women with inherited mutations in the BRCA1 gene have increased risk of developing breast cancer, but also exhibit a predisposition for the development of aggressive basal-like breast tumors. We report here that breast epithelial cells derived from patients harboring deleterious mutations in BRCA1 (BRCA1mut/+) give rise to tumors with increased basal differentiation relative to cells from BRCA1+/+ patients. Molecular analysis of disease-free breast tissues from BRCA1mut/+ patients revealed defects in progenitor cell lineage commitment even before cancer incidence. Moreover, we discovered that the transcriptional repressor Slug is an important functional regulator of human breast progenitor cell lineage commitment and differentiation and that it is aberrantly expressed in BRCA1mut/+ tissues. Slug expression is necessary for increased basal-like phenotypes prior to and following neoplastic transformation. These findings demonstrate that the genetic background of patient populations, in addition to affecting incidence rates, significantly impacts progenitor cell fate commitment and, therefore, tumor phenotype. PMID:21295272

  16. Direct comparison of two NIST PJVS systems at 10 V

    NASA Astrophysics Data System (ADS)

    Solve, S.; Rüfenacht, A.; Burroughs, C. J.; Benz, S. P.

    2013-10-01

    Two NIST programmable Josephson voltage standard (PJVS) systems are directly compared at 10 V using different nanovoltmeters. These PJVS systems use arrays of triple-stacked superconducting niobium Josephson junctions with barriers made of niobium silicide. Compared with the voltages produced by Josephson voltage standards based on hysteretic junctions, PJVS systems using damped junctions produce predictable voltage levels. However, in order to guarantee the quantization of the voltages and to minimize the errors at the room-temperature voltage output, additional precautions are required. We report several experimental results of voltage measurements that contain significant systematic errors. The generated voltages appear reproducible but they are, in fact, inaccurate. When proper measurement procedures are followed, the results of a direct comparison using an analogue detector show that the two independent PJVS systems agree within 2.6 parts in 1011 at 10 V with a relative total combined uncertainty of 3.4 parts in 1011 (k = 1). Investigations show that the largest systematic error and most significant contribution to the uncertainty budget is caused by the leakage resistance of each PJVS to ground. This paper describes a measurement procedure to characterize this leakage resistance and one approach to including the resulting voltage error in the uncertainty budget.

  17. 32 CFR Appendix C to Part 169a - Simplified Cost Comparison and Direct Conversion of CAs

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... cost comparisons. 3. For activities large in total size (including those with a mix of civilian and... 32 National Defense 1 2014-07-01 2014-07-01 false Simplified Cost Comparison and Direct Conversion... 169a—Simplified Cost Comparison and Direct Conversion of CAs A. This appendix provides guidance...

  18. 32 CFR Appendix C to Part 169a - Simplified Cost Comparison and Direct Conversion of CAs

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... cost comparisons. 3. For activities large in total size (including those with a mix of civilian and... 32 National Defense 1 2011-07-01 2011-07-01 false Simplified Cost Comparison and Direct Conversion... 169a—Simplified Cost Comparison and Direct Conversion of CAs A. This appendix provides guidance...

  19. 32 CFR Appendix C to Part 169a - Simplified Cost Comparison and Direct Conversion of CAs

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... cost comparisons. 3. For activities large in total size (including those with a mix of civilian and... 32 National Defense 1 2013-07-01 2013-07-01 false Simplified Cost Comparison and Direct Conversion... 169a—Simplified Cost Comparison and Direct Conversion of CAs A. This appendix provides guidance...

  20. The application of artificial neural networks for phenotypic drug resistance prediction: evaluation and comparison with other interpretation systems.

    PubMed

    Pasomsub, Ekawat; Sukasem, Chonlaphat; Sungkanuparph, Somnuek; Kijsirikul, Boonserm; Chantratita, Wasun

    2010-03-01

    Although phenotypic resistance testing provides more direct measurement of antiretroviral drug resistance than genotypic testing, it is costly and time-consuming. However, genotypic resistance testing has the advantages of being simpler and more accessible, and it might be possible to use the data obtained for predicting quantitative drug susceptibility to interpret complex mutation combinations. This study applied the Artificial Neural Network (ANN) system to predict the HIV-1 resistance phenotype from the genotype. A total of 7,598 pairs of HIV-1 sequences, with their corresponding phenotypic fold change values for 14 antiretroviral drugs, were trained, validated, and tested in ANN modeling. The results were compared with the HIV-SEQ and Geno2pheno interpretation systems. The prediction performance of the ANN models was measured by 10-fold cross-validation. The results indicated that by using the ANN, with an associated set of amino acid positions known to influence drug resistance for individual antiretroviral drugs, drug resistance was accurately predicted and generalized for individual HIV-1 subtypes. Therefore, high correlation with the experimental phenotype may help physicians choose optimal therapeutic regimens that might be an option, or supporting system, of FDA-approved genotypic resistance testing in heavily treatment-experienced patients.

  1. A direct potential fitting RKR method: Semiclassical vs. quantal comparisons

    NASA Astrophysics Data System (ADS)

    Tellinghuisen, Joel

    2016-12-01

    Quantal and semiclassical (SC) eigenvalues are compared for three diatomic molecular potential curves: the X state of CO, the X state of Rb2, and the A state of I2. The comparisons show higher levels of agreement than generally recognized, when the SC calculations incorporate a quantum defect correction to the vibrational quantum number, in keeping with the Kaiser modification. One particular aspect of this is better agreement between quantal and SC estimates of the zero-point vibrational energy, supporting the need for the Y00 correction in this context. The pursuit of a direct-potential-fitting (DPF) RKR method is motivated by the notion that some of the limitations of RKR potentials may be innate, from their generation by an exact inversion of approximate quantities: the vibrational energy Gυ and rotational constant Bυ from least-squares analysis of spectroscopic data. In contrast, the DPF RKR method resembles the quantal DPF methods now increasingly used to analyze diatomic spectral data, but with the eigenvalues obtained from SC phase integrals. Application of this method to the analysis of 9500 assigned lines in the I2A ← X spectrum fails to alter the quantal-SC disparities found for the A-state RKR curve from a previous analysis. On the other hand, the SC method can be much faster than the quantal method in exploratory work with different potential functions, where it is convenient to use finite-difference methods to evaluate the partial derivatives required in nonlinear fitting.

  2. Direct Lineage Reprogramming Reveals Disease-Specific Phenotypes of Motor Neurons from Human ALS Patients.

    PubMed

    Liu, Meng-Lu; Zang, Tong; Zhang, Chun-Li

    2016-01-05

    Subtype-specific neurons obtained from adult humans will be critical to modeling neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS). Here, we show that adult human skin fibroblasts can be directly and efficiently converted into highly pure motor neurons without passing through an induced pluripotent stem cell stage. These adult human induced motor neurons (hiMNs) exhibit the cytological and electrophysiological features of spinal motor neurons and form functional neuromuscular junctions (NMJs) with skeletal muscles. Importantly, hiMNs converted from ALS patient fibroblasts show disease-specific degeneration manifested through poor survival, soma shrinkage, hypoactivity, and an inability to form NMJs. A chemical screen revealed that the degenerative features of ALS hiMNs can be remarkably rescued by the small molecule kenpaullone. Taken together, our results define a direct and efficient strategy to obtain disease-relevant neuronal subtypes from adult human patients and reveal their promising value in disease modeling and drug identification.

  3. Laboratory diagnosis of legionnaires' disease due to Legionella pneumophila serogroup 1: comparison of phenotypic and genotypic methods.

    PubMed

    Lindsay, Diane S J; Abraham, William H; Findlay, William; Christie, Peter; Johnston, Fiona; Edwards, Giles F S

    2004-03-01

    Laboratory results of 67 cases of legionnaires' disease caused by Legionella pneumophila serogroup (Sg) 1 spanning a 6-year period were analysed by both phenotypic and genotypic methods. The methods compared were urinary antigen enzyme immunoassay (EIA), an immunofluorescent antibody (IFA) test, direct fluorescent antibody (DFA), culture and a 5S rRNA PCR with Southern blotting confirmation. Urine was available in 53 cases, of which 35 (66%) were positive, with an antigen peak observed at 5-10 days after onset of disease symptoms. The IFA test was positive in 62 (92.5%) cases, with 56 (90.3%) cases producing a greater than fourfold rise in titre and 6 (9.7%) giving presumptive high titres of > or =1:128. There were two antibody peaks, one at 10-15 days and another at >25 days after onset. In 23 cases where samples were available, DFA and culture were respectively positive in 5 (22%) and 10 (48%) cases. There was a peak in culture-positives 5-10 days after onset of disease. A Legionella-specific 5S rRNA PCR on patient serum was positive in 54 (80.5%) cases, with a peak in PCR positivity at 6-10 days after disease onset. In 22 of the 67 cases, the full panel of diagnostic methods was available for comparison. The relative sensitivity and specificity of the urinary antigen EIA and the serum PCR was 100%. The IFA gave relative sensitivity and specificity values of 93.8 and 95%. DFA and culture, although 100% specific, produced only low sensitivities, of 19 and 42.8%, respectively. This study has shown that urinary antigen and serum PCR are valuable tests in the acute phase of disease, with excellent sensitivity and specificity values. At present, the Legionella species causing infection requires to be verified by IFA serology and/or culture, but this could become unnecessary as new antigen and L. pneumophila Sg 1-specific PCR tests become available.

  4. Comparison of Molecular and Phenotypic Methods for the Detection and Characterization of Carbapenem Resistant Enterobacteriaceae.

    PubMed

    Somily, Ali M; Garaween, Ghada A; Abukhalid, Norah; Absar, Muhammad M; Senok, Abiola C

    2016-03-01

    In recent years, there has been a rapid dissemination of carbapenem resistant Enterobacteriaceae (CRE). This study aimed to compare phenotypic and molecular methods for detection and characterization of CRE isolates at a large tertiary care hospital in Saudi Arabia. This study was carried out between January 2011 and November 2013 at the King Khalid University Hospital (KKUH) in Saudi Arabia. Determination of presence of extended-spectrum beta-lactamases (ESBL) and carbapenem resistance was in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines. Phenotypic classification was done by the MASTDISCS(TM) ID inhibitor combination disk method. Genotypic characterization of ESBL and carbapenemase genes was performed by the Check-MDR CT102. Diversilab rep-PCR was used for the determination of clonal relationship. Of the 883 ESBL-positive Enterobacteriaceae detected during the study period, 14 (1.6%) isolates were carbapenem resistant. Both the molecular genotypic characterization and phenotypic testing were in agreement in the detection of all 8 metalo-beta-lactamases (MBL) producing isolates. Of these 8 MBL-producers, 5 were positive for blaNDM gene and 3 were positive for blaVIM gene. Molecular method identified additional blaOXA gene isolates while MASTDISCS(TM) ID detected one AmpC producer isolate. Both methods agreed in identifying 2 carbapenem resistant isolates which were negative for carbapenemase genes. Diversilab rep-PCR analysis of the 9 Klebsiella pneumoniae isolates revealed polyclonal distribution into eight clusters. MASTDISCS(TM) ID is a reliable simple cheap phenotypic method for detection of majority of carbapenemase genes with the exception of the blaOXA gene. We recommend to use such method in the clinical laboratory.

  5. Comparison of various urine collection intervals for caffeine and dextromethorphan phenotyping in children.

    PubMed

    Kennedy, Mary Jayne; Abdel-Rahman, Susan M; Kashuba, Angela D M; Leeder, J Steven

    2004-07-01

    Caffeine and dextromethorphan have been used successfully both alone and in combination to assess phenotype and enzyme activity in children of various ages. Previous pediatric phenotyping studies with these agents have used varying durations of urine collection. However, the minimum duration required for accurate phenotypic assessment with these compounds in children remains unknown. We calculated the cumulative metabolite recoveries and molar ratios in urine collected from children for 2, 4, 6, and 8 hours after caffeine and dextromethorphan administration to determine when respective urinary molar ratios stabilize and thus likely accurately reflect enzyme activity. Subjects (n = 24, ages 3-8 years) were given 4 oz of Coca-Cola(R) ( approximately 11.5 mg caffeine) and a single oral dose of dextromethorphan (0.5 mg/kg). Urine was collected at discrete intervals (0-2, 2-4, 4-6, and 6-8 h) during an 8-hour period, and the cumulative metabolite recoveries and urinary molar ratios were calculated. CYP2D6 genotyping was also performed in 21 of 24 subjects. In CYP2D6 extensive metabolizers, the extent of recovery for relevant metabolites was equivalent by 4 hours and represented 45% to 60% of the total amount recovered in the 8-hour period. The 2-hour CYP1A2 ratio was significantly different from those of longer collection intervals. Metabolite ratios for all other enzymes (i.e., NAT-2, XO, and CYP2D6) were independent of the duration of urine collection. These data suggest that a 4-hour urine collection is adequate for the concurrent assessment of hepatic CYP1A2, NAT-2, XO, and CYP2D6 activity in children ages 3 to 8 years who are CYP2D6 extensive metabolizers, using standard caffeine and dextromethorphan phenotyping methods. Longer collection periods may be required, however, in younger children or CYP2D6 poor metabolizers.

  6. Comparison of phenotypic and genotypic profiles among caprine and ovine Mycoplasma ovipneumoniae strains.

    PubMed

    Maksimović, Z; De la Fe, C; Amores, J; Gómez-Martín, Á; Rifatbegović, M

    2017-02-18

    Mycoplasma ovipneumoniae (Movp) is considered to be one of the most important mycoplasmas causing respiratory disease in small ruminants. Most epidemiologic and characterisation studies have been conducted on strains collected from sheep. Information on the presence and characteristics of Movp in healthy and pneumonic goats is limited. Phenotypic or genotypic differences between sheep and goat isolates have never been studied. The objective of our study was to characterise and compare the similarities and differences between caprine and ovine Movp strains isolated from affected and asymptomatic animals in order to elucidate phenotypic and genotypic variability. Four different techniques were used on a set of 23 Movp isolates. These included SDS-PAGE, Western blotting, random amplified polymorphic DNA and the heat shock protein 70 gene sequence-based method. A high degree of phenotypic and genotypic heterogeneity among Movp strains was demonstrated in this study. Our results demonstrated differences between goat and sheep strains, revealing not only a link between strains and host ruminant species, but by geographical origin as well. However, the finding of immunodominant antigens of molecular masses 36, 38, 40 and 70 kDa (±3 kDa) in Movp isolates from sheep and goats foretells their potential use in the development of serological diagnostic tests and vaccines.

  7. Optimization and Application of Direct Infusion Nanoelectrospray HRMS Method for Large-Scale Urinary Metabolic Phenotyping in Molecular Epidemiology

    PubMed Central

    2017-01-01

    Large-scale metabolic profiling requires the development of novel economical high-throughput analytical methods to facilitate characterization of systemic metabolic variation in population phenotypes. We report a fit-for-purpose direct infusion nanoelectrospray high-resolution mass spectrometry (DI-nESI-HRMS) method with time-of-flight detection for rapid targeted parallel analysis of over 40 urinary metabolites. The newly developed 2 min infusion method requires <10 μL of urine sample and generates high-resolution MS profiles in both positive and negative polarities, enabling further data mining and relative quantification of hundreds of metabolites. Here we present optimization of the DI-nESI-HRMS method in a detailed step-by-step guide and provide a workflow with rigorous quality assessment for large-scale studies. We demonstrate for the first time the application of the method for urinary metabolic profiling in human epidemiological investigations. Implementation of the presented DI-nESI-HRMS method enabled cost-efficient analysis of >10 000 24 h urine samples from the INTERMAP study in 12 weeks and >2200 spot urine samples from the ARIC study in <3 weeks with the required sensitivity and accuracy. We illustrate the application of the technique by characterizing the differences in metabolic phenotypes of the USA and Japanese population from the INTERMAP study. PMID:28245357

  8. Direct interaction between sensor kinase proteins mediates acute and chronic disease phenotypes in a bacterial pathogen

    PubMed Central

    Goodman, Andrew L.; Merighi, Massimo; Hyodo, Mamoru; Ventre, Isabelle; Filloux, Alain; Lory, Stephen

    2009-01-01

    The genome of the opportunistic pathogen Pseudomonas aeruginosa encodes over 60 two-component sensor kinases and uses several (including RetS and GacS) to reciprocally regulate the production of virulence factors involved in the development of acute or chronic infections. We demonstrate that RetS modulates the phosphorylation state of GacS by a direct and specific interaction between these two membrane-bound sensors. The RetS–GacS interaction can be observed in vitro, in heterologous systems in vivo, and in P. aeruginosa. This function does not require the predicted RetS phosphorelay residues and provides a mechanism for integrating multiple signals without cross-phosphorylation from sensors to noncognate response regulators. These results suggest that multiple two-component systems found in a single bacterium can form multisensor signaling networks while maintaining specific phosphorelay pathways that remain insulated from detrimental cross-talk. PMID:19171785

  9. A nuclear-directed human pancreatic ribonuclease (PE5) targets the metabolic phenotype of cancer cells.

    PubMed

    Vert, Anna; Castro, Jessica; Ribó, Marc; Benito, Antoni; Vilanova, Maria

    2016-04-05

    Ribonucleases represent a new class of antitumor RNA-damaging drugs. However, many wild-type members of the vertebrate secreted ribonuclease family are not cytotoxic because they are not able to evade the cytosolic ribonuclease inhibitor. We previously engineered the human pancreatic ribonuclease to direct it to the cell nucleus where the inhibitor is not present. The best characterized variant is PE5 that kills cancer cells through apoptosis mediated by the p21(WAF1/CIP1) induction and the inactivation of JNK. Here, we have used microarray-derived transcriptional profiling to identify PE5 regulated genes on the NCI/ADR-RES ovarian cancer cell line. RT-qPCR analyses have confirmed the expression microarray findings. The results show that PE5 cause pleiotropic effects. Among them, it is remarkable the down-regulation of multiple genes that code for enzymes involved in deregulated metabolic pathways in cancer cells.

  10. Phenotypic variability in Angelman syndrome: comparison among different deletion classes and between deletion and UPD subjects.

    PubMed

    Varela, Monica Castro; Kok, Fernando; Otto, Paulo Alberto; Koiffmann, Celia Priszkulnik

    2004-12-01

    Angelman syndrome (AS) can result from either a 15q11-q13 deletion (del), paternal uniparental disomy (UPD), imprinting, or UBE3A mutations. Here, we describe the phenotypic and behavioral variability detected in 49 patients with different classes of deletions and nine patients with UPD. Diagnosis was made by methylation pattern analysis of exon 1 of the SNRPN-SNURF gene and by microsatellite profiling of loci within and outside the 15q11-q13 region. There were no major phenotypic differences between the two main classes (BP1-BP3; BP2-BP3) of AS deletion patients, except for the absence of vocalization, more prevalent in patients with BP1-BP3 deletions, and for the age of sitting without support, which was lower in patients with BP2-BP3 deletions. Our data suggest that gene deletions (NIPA1, NIPA2, CYF1P1, GCP5) mapped to the region between breakpoints BP1 and BP2 may be involved in the severity of speech impairment, since all BP1-BP3 deletion patients showed complete absence of vocalization, while 38.1% of the BP2-BP3 deletion patients were able to pronounce syllabic sounds, with doubtful meaning. Compared to UPD patients, deletion patients presented a higher incidence of swallowing disorders (73.9% del x 22.2% UPD) and hypotonia (73.3% del x 28.57% UPD). In addition, children with UPD showed better physical growth, fewer or no seizures, a lower incidence of microcephaly, less ataxia and higher cognitive skills. As a consequence of their milder or less typical phenotype, AS may remain undiagnosed, leading to an overall underdiagnosis of the disease.

  11. Distribution of Acinetobacter species on human skin: comparison of phenotypic and genotypic identification methods.

    PubMed Central

    Seifert, H; Dijkshoorn, L; Gerner-Smidt, P; Pelzer, N; Tjernberg, I; Vaneechoutte, M

    1997-01-01

    At least 19 genomic species are recognized as constituting the genus Acinetobacter. However, little is known about the natural reservoirs of the various members of the genus. An epidemiological study was therefore performed to investigate the colonization with Acinetobacter spp. of the skin and mucous membranes of 40 patients hospitalized in a cardiology ward and 40 healthy controls. Single samples were obtained once from each of nine different body sites, i.e., forehead, ear, nose, throat, axilla, hand, groin, perineum, and toe web. Identification of Acinetobacter isolates was achieved by using phenotypic properties and was compared to identification by amplified ribosomal DNA restriction analysis. Selected isolates were further investigated with sodium dodecyl sulfate-polyacrylamide gel electrophoresis, ribotyping, and DNA-DNA hybridization. Plasmid profile analysis was used for epidemiological typing. Thirty patients (75%) and 17 controls (42.5%) were found to be colonized with Acinetobacter spp., and the colonization rates of patients increased during their hospital stay. The most frequently isolated species were Acinetobacter lwoffii (47%), A. johnsonii (21%), A. radioresistens (12%), and DNA group 3 (11%). In contrast, A. baumannii and DNA group 13TU, the most important nosocomial Acinetobacter spp., were found only rarely on human skin (0.5 and 1%, respectively) and their natural habitat remains to be defined. A good correlation between phenotypic and genotypic methods for identification of Acinetobacter spp. was observed, and only two isolates could not be assigned to any of the known DNA groups. PMID:9350741

  12. Direct Comparison of GPS and VLBI Velocity Estimates

    NASA Technical Reports Server (NTRS)

    Heflin, Michael

    1995-01-01

    Considerable effort has been made to collocate permanent GPS and VLBI sites for comparison. The global GPS solution is derived from daily measurements spanning four years while the VLBI solution is based on monthly measurements spanning more than 10 years. Current WRMS agreement of velocities is 3-5 mm/yr for horizontal rates and 6-10 mm/yr for vertical rates. Comparison of velocities is limited by the time span of GPS data. Positions agree at the level of 1-2 cm and their comparison is limited by the quality of the site ties. Best and worst agreement will be discussed along with possible sources of systematic error.

  13. Morphological, genetic and phenotypic comparison between human articular chondrocytes and cultured chondrocytes.

    PubMed

    Mata-Miranda, Mónica Maribel; Martinez-Martinez, Claudia María; Noriega-Gonzalez, Jesús Emmanuel; Paredes-Gonzalez, Luis Enrique; Vázquez-Zapién, Gustavo Jesús

    2016-08-01

    Articular cartilage is an avascular and aneural tissue with limited capacity for regeneration. On large articular lesions, it is recommended to use regenerative medicine strategies, like autologous chondrocyte implantation. There is a concern about morphological changes that chondrocytes suffer once they have been isolated and cultured. Due to the fact that there is little evidence that compares articular cartilage chondrocytes with cultured chondrocytes, in this research we proposed to obtain chondrocytes from human articular cartilage, compare them with themselves once they have been cultured and characterize them through genetic, phenotypic and morphological analysis. Knee articular cartilage samples of 10 mm were obtained, and each sample was divided into two fragments; a portion was used to determine gene expression, and from the other portion, chondrocytes were obtained by enzymatic disaggregation, in order to be cultured and expanded in vitro. Subsequently, morphological, genetic and phenotypic characteristics were compared between in situ (articular cartilage) and cultured chondrocytes. Obtained cultured chondrocytes were rounded in shape, possessing a large nucleus with condensed chromatin and a clear cytoplasm; histological appearance was quite similar to typical chondrocyte. The expression levels of COL2A1 and COL10A1 genes were higher in cultured chondrocytes than in situ chondrocytes; moreover, the expression of COL1A1 was almost undetectable on cultured chondrocytes; likewise, COL2 and SOX9 proteins were detected by immunofluorescence. We concluded that chondrocytes derived from adult human cartilage cultured for 21 days do not tend to dedifferentiate, maintaining their capacity to produce matrix and also retaining their synthesis capacity and morphology.

  14. Comparison of enterotoxin production and phenotypic characteristics between emetic and enterotoxic Bacillus cereus.

    PubMed

    Kim, Jung-Beom; Kim, Jai-Moung; Kim, So-Yeong; Kim, Jong-Hyun; Park, Yong-Bae; Choi, Na-Jung; Oh, Deog-Hwan

    2010-07-01

    Bacillus cereus was divided into emetic toxin (cereulide)- and enterotoxin-producing strains, but emetic toxin-producing B. cereus is difficult to detect immunochemically. Screening methods for emetic toxin-producing B. cereus are needed. The objectives of this study were to identify and detect emetic toxin-producing B. cereus among 160 B. cereus strains, and to compare enterotoxin production and phenotypic characteristics between the emetic toxin-producing and enterotoxin-producing strains. Forty emetic toxin-producing B. cereus strains were determined with high-pressure liquid chromatography-mass spectrometry analysis. Among the emetic toxin-producing strains (n = 40), 31 (77.5%) and 3 (7.5%) strains produced nonhemolytic enterotoxin (NHE) and hemolysin BL (HBL) enterotoxins, respectively. In addition, 107 (89.2%) and 100 (83.3%) strains produced NHE and HBL enterotoxins among the enterotoxin-producing strains (n = 120). The number of strains positive for starch hydrolysis, salicin fermentation, and hemolysis among the emetic toxin-producing strains were 3 (7.5%), 3 (7.5%), and 26 (65.0%), respectively, and among enterotoxin-producing strains, these numbers were 101 (84.2%), 100 (83.3%), and 111 (92.5%), respectively. In particular, the three emetic toxin-producing B. cereus strains (JNHE 6, JNHE 36, and KNIH 28) produced the HBL and NHE enterotoxins and were capable of starch hydrolysis and salicin fermentation. The absence of HBL enterotoxin and certain phenotypic properties, such as starch hydrolysis and salicin fermentation, indicates that these properties were not critical characteristics of the emetic toxin-producing B. cereus tested in this study.

  15. Comparison of Zebrafish tmem88a mutant and morpholino knockdown phenotypes

    PubMed Central

    Place, Elsie S.; Smith, James C.

    2017-01-01

    Tmem88a is a transmembrane protein that is thought to be a negative regulator of the Wnt signalling pathway. Several groups have used antisense morpholino oligonucleotides in an effort to characterise the role of tmem88a in zebrafish cardiovascular development, but they have not obtained consistent results. Here, we generate an 8 bp deletion in the coding region of the tmem88a locus using TALENs, and we have gone on to establish a viable homozygous tmem88aΔ8 mutant line. Although tmem88aΔ8 mutants have reduced expression of some key haematopoietic genes, differentiation of erythrocytes and neutrophils is unaffected, contradicting our previous study using antisense morpholino oligonucleotides. We find that expression of the tmem88a paralogue tmem88b is not significantly changed in tmem88aΔ8 mutants and injection of the tmem88a splice-blocking morpholino oligonucleotide into tmem88aΔ8 mutants recapitulates the reduction of erythrocytes observed in morphants using o-Dianisidine. This suggests that there is a partial, but inessential, requirement for tmem88a during haematopoiesis and that morpholino injection exacerbates this phenotype in tmem88a morpholino knockdown embryos. PMID:28192479

  16. Comparison of Zebrafish tmem88a mutant and morpholino knockdown phenotypes.

    PubMed

    Eve, Alexander M J; Place, Elsie S; Smith, James C

    2017-01-01

    Tmem88a is a transmembrane protein that is thought to be a negative regulator of the Wnt signalling pathway. Several groups have used antisense morpholino oligonucleotides in an effort to characterise the role of tmem88a in zebrafish cardiovascular development, but they have not obtained consistent results. Here, we generate an 8 bp deletion in the coding region of the tmem88a locus using TALENs, and we have gone on to establish a viable homozygous tmem88aΔ8 mutant line. Although tmem88aΔ8 mutants have reduced expression of some key haematopoietic genes, differentiation of erythrocytes and neutrophils is unaffected, contradicting our previous study using antisense morpholino oligonucleotides. We find that expression of the tmem88a paralogue tmem88b is not significantly changed in tmem88aΔ8 mutants and injection of the tmem88a splice-blocking morpholino oligonucleotide into tmem88aΔ8 mutants recapitulates the reduction of erythrocytes observed in morphants using o-Dianisidine. This suggests that there is a partial, but inessential, requirement for tmem88a during haematopoiesis and that morpholino injection exacerbates this phenotype in tmem88a morpholino knockdown embryos.

  17. Phenotypic comparison of allergic airway responses to house dust mite in three rat strains.

    PubMed

    Singh, Pramila; Daniels, Mary; Winsett, Darrell W; Richards, Judy; Doerfler, Donald; Hatch, Gary; Adler, Kenneth B; Gilmour, M Ian

    2003-04-01

    Brown Norway (BN) rats develop a robust response to antigens in the lung, characterized by a large increase in allergen-specific immune function and pulmonary eosinophilia. The objective of this study was to investigate alternative models by determining whether other rat strains could be sensitized to house dust mite (HDM) antigen and whether the allergic disease process could be worsened with repeated allergen exposure. In general, BN rats sensitized by either subcutaneous or intratracheal routes exhibited increased pulmonary allergy compared with Sprague-Dawley (SD) and Lewis (L) rats. Multiple intratracheal allergen exposures incrementally increased HDM-specific immune function in BN rats but progressively decreased eosinophil recruitment and markers of lung injury. SD rats had more moderate responses, whereas L rats were relatively unresponsive. Because BN rats developed stronger clinical hallmarks of allergic asthma under various immunization regimes compared with SD and L rats, we conclude that the BN is the most appropriate strain for studying allergic asthma-like responses in rats. Phenotypic differences in response to HDM were associated with differences in the Th1/Th2 cytokine balance and antioxidant capacity.

  18. A Comparison of Direct and Indirect Writing Assessment Methods.

    ERIC Educational Resources Information Center

    Stiggins, Richard J.

    An area of current concern is that of the advantages and disadvantages of measuring writing proficiency directly via writing samples, and indirectly via objective tests. Much research has been completed documenting the correlation between direct and indirect measures. However, there had not yet been a systematic and detailed conceptual analysis…

  19. Experimental Comparison of Inquiry and Direct Instruction in Science

    ERIC Educational Resources Information Center

    Cobern, William W.; Schuster, David; Adams, Betty; Applegate, Brooks; Skjold, Brandy; Undreiu, Adriana; Loving, Cathleen C.; Gobert, Janice D.

    2010-01-01

    There are continuing educational and political debates about "inquiry" versus "direct" teaching of science. Traditional science instruction has been largely direct but in the US, recent national and state science education standards advocate inquiry throughout K-12 education. While inquiry-based instruction has the advantage of modelling aspects…

  20. Comparison of Standardization Methods for the Harmonization of Phenotype Data: An Application to Cognitive Measures.

    PubMed

    Griffith, Lauren E; van den Heuvel, Edwin; Raina, Parminder; Fortier, Isabel; Sohel, Nazmul; Hofer, Scott M; Payette, Hélène; Wolfson, Christina; Belleville, Sylvie; Kenny, Meghan; Doiron, Dany

    2016-10-21

    Standardization procedures are commonly used to combine phenotype data that were measured using different instruments, but there is little information on how the choice of standardization method influences pooled estimates and heterogeneity. Heterogeneity is of key importance in meta-analyses of observational studies because it affects the statistical models used and the decision of whether or not it is appropriate to calculate a pooled estimate of effect. Using 2-stage individual participant data analyses, we compared 2 common methods of standardization, T-scores and category-centered scores, to create combinable memory scores using cross-sectional data from 3 Canadian population-based studies (the Canadian Study on Health and Aging (1991-1992), the Canadian Community Health Survey on Healthy Aging (2008-2009), and the Quebec Longitudinal Study on Nutrition and Aging (2004-2005)). A simulation was then conducted to assess the influence of varying the following items across population-based studies: 1) effect size, 2) distribution of confounders, and 3) the relationship between confounders and the outcome. We found that pooled estimates based on the unadjusted category-centered scores tended to be larger than those based on the T-scores, although the differences were negligible when adjusted scores were used, and that most individual participant data meta-analyses identified significant heterogeneity. The results of the simulation suggested that in terms of heterogeneity, the method of standardization played a smaller role than did different effect sizes across populations and differential confounding of the outcome measure across studies. Although there was general consistency between the 2 types of standardization methods, the simulations identified a number of sources of heterogeneity, some of which are not the usual sources considered by researchers.

  1. Evolution of the additive genetic variance–covariance matrix under continuous directional selection on a complex behavioural phenotype

    PubMed Central

    Careau, Vincent; Wolak, Matthew E.; Carter, Patrick A.; Garland, Theodore

    2015-01-01

    Given the pace at which human-induced environmental changes occur, a pressing challenge is to determine the speed with which selection can drive evolutionary change. A key determinant of adaptive response to multivariate phenotypic selection is the additive genetic variance–covariance matrix (G). Yet knowledge of G in a population experiencing new or altered selection is not sufficient to predict selection response because G itself evolves in ways that are poorly understood. We experimentally evaluated changes in G when closely related behavioural traits experience continuous directional selection. We applied the genetic covariance tensor approach to a large dataset (n = 17 328 individuals) from a replicated, 31-generation artificial selection experiment that bred mice for voluntary wheel running on days 5 and 6 of a 6-day test. Selection on this subset of G induced proportional changes across the matrix for all 6 days of running behaviour within the first four generations. The changes in G induced by selection resulted in a fourfold slower-than-predicted rate of response to selection. Thus, selection exacerbated constraints within G and limited future adaptive response, a phenomenon that could have profound consequences for populations facing rapid environmental change. PMID:26582016

  2. Evolution of the additive genetic variance-covariance matrix under continuous directional selection on a complex behavioural phenotype.

    PubMed

    Careau, Vincent; Wolak, Matthew E; Carter, Patrick A; Garland, Theodore

    2015-11-22

    Given the pace at which human-induced environmental changes occur, a pressing challenge is to determine the speed with which selection can drive evolutionary change. A key determinant of adaptive response to multivariate phenotypic selection is the additive genetic variance-covariance matrix ( G: ). Yet knowledge of G: in a population experiencing new or altered selection is not sufficient to predict selection response because G: itself evolves in ways that are poorly understood. We experimentally evaluated changes in G: when closely related behavioural traits experience continuous directional selection. We applied the genetic covariance tensor approach to a large dataset (n = 17 328 individuals) from a replicated, 31-generation artificial selection experiment that bred mice for voluntary wheel running on days 5 and 6 of a 6-day test. Selection on this subset of G: induced proportional changes across the matrix for all 6 days of running behaviour within the first four generations. The changes in G: induced by selection resulted in a fourfold slower-than-predicted rate of response to selection. Thus, selection exacerbated constraints within G: and limited future adaptive response, a phenomenon that could have profound consequences for populations facing rapid environmental change.

  3. Direct Comparisons of Radiances Measured by Independent Contemporary ERB Instruments

    NASA Technical Reports Server (NTRS)

    Haeffelin, Martial; Wielicki, Bruce; Priestley, Kory; Duvel, Jean Philippe; Viollier, Michel

    2001-01-01

    Comparisons of radiance measurements from overlapping independent Earth and cloud radiation budget (ERB) missions are an important contribution to the validation process of the these missions and are essential to the construction of a consistent long-term record of ERB observations. Measurements from the CERES instrument on TRMM are compared to ScaRaB on Resurs (Jan-Mar 1999) and CERES on Terra (Mar-Apr 2000).

  4. The Social Behavioral Phenotype in Boys and Girls with an Extra X Chromosome (Klinefelter Syndrome and Trisomy X): A Comparison with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    van Rijn, Sophie; Stockmann, Lex; Borghgraef, Martine; Bruining, Hilgo; van Ravenswaaij-Arts, Conny; Govaerts, Lutgarde; Hansson, Kerstin; Swaab, Hanna

    2014-01-01

    The present study aimed to gain more insight in the social behavioral phenotype, and related autistic symptomatology, of children with an extra X chromosome in comparison to children with ASD. Participants included 60 children with an extra X chromosome (34 boys with Klinefelter syndrome and 26 girls with Trisomy X), 58 children with ASD and 106…

  5. Comparison of haemoglobin estimates using direct & indirect cyanmethaemoglobin methods

    PubMed Central

    Bansal, Priyanka Gupta; Toteja, Gurudayal Singh; Bhatia, Neena; Gupta, Sanjeev; Kaur, Manpreet; Adhikari, Tulsi; Garg, Ashok Kumar

    2016-01-01

    Background & objectives: Estimation of haemoglobin is the most widely used method to assess anaemia. Although direct cyanmethaemoglobin method is the recommended method for estimation of haemoglobin, but it may not be feasible under field conditions. Hence, the present study was undertaken to compare indirect cyanmethaemoglobin method against the conventional direct method for haemoglobin estimation. Methods: Haemoglobin levels were estimated for 888 adolescent girls aged 11-18 yr residing in an urban slum in Delhi by both direct and indirect cyanmethaemoglobin methods, and the results were compared. Results: The mean haemoglobin levels for 888 whole blood samples estimated by direct and indirect cyanmethaemoglobin method were 116.1 ± 12.7 and 110.5 ± 12.5 g/l, respectively, with a mean difference of 5.67 g/l (95% confidence interval: 5.45 to 5.90, P<0.001); which is equivalent to 0.567 g%. The prevalence of anaemia was reported as 59.6 and 78.2 per cent by direct and indirect methods, respectively. Sensitivity and specificity of indirect cyanmethaemoglobin method were 99.2 and 56.4 per cent, respectively. Using regression analysis, prediction equation was developed for indirect haemoglobin values. Interpretation & conclusions: The present findings revealed that indirect cyanmethaemoglobin method overestimated the prevalence of anaemia as compared to the direct method. However, if a correction factor is applied, indirect method could be successfully used for estimating true haemoglobin level. More studies should be undertaken to establish agreement and correction factor between direct and indirect cyanmethaemoglobin methods. PMID:28256465

  6. Experimental comparison of inquiry and direct instruction in science

    NASA Astrophysics Data System (ADS)

    Cobern, William W.; Schuster, David; Adams, Betty; Applegate, Brooks; Skjold, Brandy; Undreiu, Adriana; Loving, Cathleen C.; Gobert, Janice D.

    2010-04-01

    There are continuing educational and political debates about 'inquiry' versus 'direct' teaching of science. Traditional science instruction has been largely direct but in the US, recent national and state science education standards advocate inquiry throughout K-12 education. While inquiry-based instruction has the advantage of modelling aspects of the nature of real scientific inquiry, there is little unconfounded comparative research into the effectiveness and efficiency of the two instructional modes for developing science conceptual understanding. This research undertook a controlled experimental study comparing the efficacy of carefully designed inquiry instruction and equally carefully designed direct instruction in realistic science classroom situations at the middle school grades. The research design addressed common threats to validity. We report on the nature of the instructional units in each mode, research design, methods, classroom implementations, monitoring, assessments, analysis and project findings.

  7. Comparison of direct and heterodyne detection optical intersatellite communication links

    NASA Technical Reports Server (NTRS)

    Chen, C. C.; Gardner, C. S.

    1987-01-01

    The performance of direct and heterodyne detection optical intersatellite communication links are evaluated and compared. It is shown that the performance of optical links is very sensitive to the pointing and tracking errors at the transmitter and receiver. In the presence of random pointing and tracking errors, optimal antenna gains exist that will minimize the required transmitter power. In addition to limiting the antenna gains, random pointing and tracking errors also impose a power penalty in the link budget. This power penalty is between 1.6 to 3 dB for a direct detection QPPM link, and 3 to 5 dB for a heterodyne QFSK system. For the heterodyne systems, the carrier phase noise presents another major factor of performance degradation that must be considered. In contrast, the loss due to synchronization error is small. The link budgets for direct and heterodyne detection systems are evaluated. It is shown that, for systems with large pointing and tracking errors, the link budget is dominated by the spatial tracking error, and the direct detection system shows a superior performance because it is less sensitive to the spatial tracking error. On the other hand, for systems with small pointing and tracking jitters, the antenna gains are in general limited by the launch cost, and suboptimal antenna gains are often used in practice. In which case, the heterodyne system has a slightly higher power margin because of higher receiver sensitivity.

  8. Assessing Students' Writing Skills: A Comparison of Direct & Indirect Methods.

    ERIC Educational Resources Information Center

    Koffler, Stephen L.

    This research examined the results from direct and indirect writing assessments to determine the most effective method of discrimination. The New Jersey State Department of Education developed a test for ninth-grade students which was designed to measure the ability to apply writing mechanics to written text and to communicate effectively in…

  9. A Comparison of Direct and Indirect Writing Assessment Methods.

    ERIC Educational Resources Information Center

    Stiggins, Richard J.

    1982-01-01

    Compares direct and indirect writing assessment strategies and contrasts them in terms of the relationship each has to specific classroom decision-making situations, the components of writing assessed, practical testing matters, characteristics of test exercises, test scoring procedures, and procedures for determining test quality. (HOD)

  10. Halo-Independent Comparison of Direct Dark Matter Detection Data

    DOE PAGES

    Del Nobile, Eugenio

    2014-01-01

    We review the halo-independent formalism that allows comparing data from different direct dark matter detection experiments without making assumptions on the properties of the dark matter halo. We apply this method to spin-independent WIMP-nuclei interactions, for both isospin-conserving and isospin-violating couplings, and to WIMPs interacting through an anomalous magnetic moment.

  11. A Comparison of Book Text and Child Directed Speech

    ERIC Educational Resources Information Center

    Cameron-Faulkner, Thea; Noble, Claire

    2013-01-01

    This article evaluates the extent to which pre-schoolers' picture books can be viewed as a form of enriched linguistic input. Twenty best-selling picture books were analysed in terms of syntactic constructions and compared with a sample of Child Directed Speech. The findings of the study demonstrate the prevalence of canonical utterances (i.e.…

  12. Experimental Comparison of Inquiry and Direct Instruction in Science

    ERIC Educational Resources Information Center

    Cobern, William; Schuster, David; Adams, Betty

    2010-01-01

    It is evident that "experientially-based" instruction and "active student engagement" are advantageous for effective science learning. However, "hands-on" and "minds-on" aspects can occur in both inquiry and direct science instruction, and convincing comparative evidence for the superiority of either mode…

  13. Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into rice aluminum tolerance mechanisms.

    PubMed

    Famoso, Adam N; Clark, Randy T; Shaff, Jon E; Craft, Eric; McCouch, Susan R; Kochian, Leon V

    2010-08-01

    The genetic and physiological mechanisms of aluminum (Al) tolerance have been well studied in certain cereal crops, and Al tolerance genes have been identified in sorghum (Sorghum bicolor) and wheat (Triticum aestivum). Rice (Oryza sativa) has been reported to be highly Al tolerant; however, a direct comparison of rice and other cereals has not been reported, and the mechanisms of rice Al tolerance are poorly understood. To facilitate Al tolerance phenotyping in rice, a high-throughput imaging system and root quantification computer program was developed, permitting quantification of the entire root system, rather than just the longest root. Additionally, a novel hydroponic solution was developed and optimized for Al tolerance screening in rice and compared with the Yoshida's rice solution commonly used for rice Al tolerance studies. To gain a better understanding of Al tolerance in cereals, comparisons of Al tolerance across cereal species were conducted at four Al concentrations using seven to nine genetically diverse genotypes of wheat, maize (Zea mays), sorghum, and rice. Rice was significantly more tolerant than maize, wheat, and sorghum at all Al concentrations, with the mean Al tolerance level for rice found to be 2- to 6-fold greater than that in maize, wheat, and sorghum. Physiological experiments were conducted on a genetically diverse panel of more than 20 rice genotypes spanning the range of rice Al tolerance and compared with two maize genotypes to determine if rice utilizes the well-described Al tolerance mechanism of root tip Al exclusion mediated by organic acid exudation. These results clearly demonstrate that the extremely high levels of rice Al tolerance are mediated by a novel mechanism, which is independent of root tip Al exclusion.

  14. Comparison of microleakage between direct placement technics and direct inlay technics.

    PubMed

    Yanikoğlu, F; Scherer, W

    1990-09-01

    Laboratory studies have indicated that improvements in the physical properties of composite restorations, especially for posterior teeth, may be obtained if these materials underwent heat treatment prior to insertion. The purpose of this study was to compare the microleakage in Class II restorations ending on cementum/dentine when these preparations were restored by a direct placement composite resin as opposed to a direct inlay composite resin. Thirty-six human posterior mandibular teeth were used in this study and randomly divided into three equal groups; Group I was prepared and restored with the composite Ful-fil in a direct placement technique. Groups II and III were prepared and restored using a direct composite resin inlay technique. The material used in Group II was Brillant D.I.; that of Group III, Ful-ful. All preparations terminated 1.0 mm apical to the CEJ. The composite resin patterns of Groups II and III were oven-tempered before cementing with D.I. Duo Cement. Specimens were thermocycled 125 times between 5-55 C. Microleakage was noted cervically on a scale of 0 to 5. The composite Ful-fil, used as a direct placement material, exhibited less leakage (P less than 0.05) than either the Brillant D.I. composite or Ful-fil composite when these materials were placed as direct composite inlays.

  15. Case study: Comparison of motivation for achieving higher performance between self-directed and manager-directed aerospace engineering teams

    NASA Astrophysics Data System (ADS)

    Erlick, Katherine

    "The stereotype of engineers is that they are not people oriented; the stereotype implies that engineers would not work well in teams---that their task emphasis is a solo venture and does not encourage social aspects of collaboration" (Miner & Beyerlein, 1999, p. 16). The problem is determining the best method of providing a motivating environment where design engineers may contribute within a team in order to achieve higher performance in the organization. Theoretically, self-directed work teams perform at higher levels. But, allowing a design engineer to contribute to the team while still maintaining his or her anonymity is the key to success. Therefore, a motivating environment must be established to encourage greater self-actualization in design engineers. The purpose of this study is to determine the favorable motivational environment for design engineers and describe the comparison between two aerospace design-engineering teams: one self-directed and the other manager directed. Following the comparison, this study identified whether self-direction or manager-direction provides the favorable motivational environment for operating as a team in pursuit of achieving higher performance. The methodology used in this research was the case study focusing on the team's levels of job satisfaction and potential for higher performance. The collection of data came from three sources, (a) surveys, (b) researcher observer journal and (c) collection of artifacts. The surveys provided information regarding personal behavior characteristics, potentiality for higher performance and motivational attributes. The researcher journal provided information regarding team dynamics, individual interaction, conflict and conflict resolution. The milestone for performance was based on the collection of artifacts from the two teams. The findings from this study illustrated that whether the team was manager-directed or self-directed does not appear to influence the needs and wants of the

  16. Molecular typing of Cryptococcus neoformans by PCR fingerprinting, in comparison with serotyping and Fourier transform infrared-spectroscopy-based phenotyping.

    PubMed

    Lemmer, K; Naumann, D; Raddatz, B; Tintelnot, K

    2004-04-01

    Molecular typing by PCR fingerprinting using the single primer (GACA)4 was performed with 110 isolates of Cryptococcus neoformans. Seventy clinical isolates of C. neoformans var. neoformans from Germany (n = 52) and Africa (n = 18) were included. Of these, serotype A (C. neoformans var. grubii) accounted for 47 isolates, serotype D for 12 and serotype AD for 11. Fourier transform infrared (FT-IR) spectroscopy was evaluated for its discriminatory power in phenotyping. Molecular types, defined by different PCR fingerprinting patterns, were compared to serotypes, and both sets of results were compared with the results of analysis by FT-IR spectroscopy. PCR fingerprinting revealed genotypic diversity within each serotype; it showed three different genotypes (designated VNA1-VNA3) within serotype A, two within serotype D (VND1 and VND2), and three within serotype AD (VNAD1-VNAD3). The nomenclature of molecular types within C. n. var. neoformans, as seen in publications to date, is not uniform. In this study, the name assigned to each genotype was based on the 98.6% concordance of genotypes with serotypes, a correspondence that facilitates interlaboratory comparison. This nomenclature is tentatively recommended as a standard. FT-IR spectroscopy combined with hierarchical cluster analysis successfully distinguished C n. var. neoformans from C. n. var. gattii. For C. n. var. neoformans, FT-IR confirmed three distinct genotypes within serotype A and was able to distinguish isolates derived from particular patients as well as isolates differing at the sub-genotype level. Within C. n. var. gattii, the serotypes B and C did not correlate with the four genotypes VGI-VGIV. However, these serotypes could clearly be separated by FT-IR spectroscopy. The molecular profiles were reproducible, and were more stable and more discriminating than serotyping. In connection with a standardized nomenclature, PCR fingerprinting can be a beneficial tool for global epidemiological studies. FT

  17. Comparison of TaqMan® Array Card and MYCOTB™ with conventional phenotypic susceptibility testing in MDR-TB

    PubMed Central

    Foongladda, S.; Banu, S.; Pholwat, S.; Gratz, J.; O-Thong, S.; Nakkerd, N.; Chinli, R.; Ferdous, S. S.; Rahman, S. M. M.; Rahman, A.; Ahmed, S.; Heysell, S.; Sariko, M.; Kibiki, G.

    2016-01-01

    SUMMARY BACKGROUND: Although phenotypic drug susceptibility testing (DST) is endorsed as the standard for second-line drug testing of Mycobacterium tuberculosis, it is slow and laborious. METHODS: We evaluated the accuracy of two faster, easier methodologies that provide results for multiple drugs: a genotypic TaqMan® Array Card (TAC) and the Sensititre® MYCOTB™ plate. Both methods were tested at three central laboratories in Bangladesh, Tanzania, and Thailand with 212 multidrug-resistant tuberculosis (MDR-TB) isolates and compared with the laboratories' phenotypic method in use. RESULTS: The overall accuracy for ethambutol, streptomycin, amikacin, kanamycin, ofloxacin, and moxifloxacin vs. the phenotypic standard was 87% for TAC (range 70–99) and 88% for the MYCOTB plate (range 76–98). To adjudicate discordances, we re-defined the standard as the consensus of the three methods, against which the TAC and MYCOTB plate yielded 94–95% accuracy, while the phenotypic result yielded 93%. Some isolates with genotypic mutations and high minimum inhibitory concentration (MIC) were phenotypically susceptible, and some isolates without mutations and low MIC were phenotypically resistant, questioning the phenotypic standard. CONCLUSIONS: In our view, the TAC, the MYCOTB plate, and the conventional phenotypic method have similar performance for second-line drugs; however, the former methods offer speed, throughput, and quantitative DST information. PMID:27393547

  18. Representation of comparison signals in cortical area MT during a delayed direction discrimination task.

    PubMed

    Lui, Leo L; Pasternak, Tatiana

    2011-09-01

    Visually guided behavior often involves decisions that are based on evaluating stimuli in the context of those observed previously. Such decisions are made by monkeys comparing two consecutive stimuli, sample and test, moving in the same or opposite directions. We examined whether responses in the motion processing area MT during the comparison phase of this task (test) are modulated by the direction of the preceding stimulus (sample). This modulation, termed comparison signal, was measured by comparing responses to identical test stimuli on trials when it was preceded by sample moving in the same direction (S-trials) with trials when it was preceded by sample moving in a different direction (D-trials). The test always appeared in the neuron's receptive field (RF), whereas sample could appear in the RF or in the contralateral visual field (remote sample). With sample in-RF, we found three types of modulation carried by different sets of neurons: early suppression on S-trials and late enhancement, one on S-trials, and the other on D-trials. Under these conditions, many neurons with and without comparison effects exhibited significant, choice-related activity. Response modulation was also present following the remote sample, even though the information about its direction could only reach MT indirectly via top-down influences. However, unlike on trials with in-RF sample, these signals were dominated by response suppression, shedding light on the contribution of top-down influences to the comparison effects. These results demonstrate that during the task requiring monkeys to compare two directions of motion, MT responses during the comparison phase of this task reflect similarities and differences between the two stimuli, suggesting participation in sensory comparisons. The nature of these signals provides insights into the operation of bottom-up and top-down influences involved in this process.

  19. Ensheathing cell-conditioned medium directs the differentiation of human umbilical cord blood cells into aldynoglial phenotype cells.

    PubMed

    Ponce-Regalado, María Dolores; Ortuño-Sahagún, Daniel; Zarate, Carlos Beas; Gudiño-Cabrera, Graciela

    2012-06-01

    Despite their similarities to bone marrow precursor cells (PC), human umbilical cord blood (HUCB) PCs are more immature and, thus, they exhibit greater plasticity. This plasticity is evident by their ability to proliferate and spontaneously differentiate into almost any cell type, depending on their environment. Moreover, HUCB-PCs yield an accessible cell population that can be grown in culture and differentiated into glial, neuronal and other cell phenotypes. HUCB-PCs offer many potential therapeutic benefits, particularly in the area of neural replacement. We sought to induce the differentiation of HUCB-PCs into glial cells, known as aldynoglia. These cells can promote neuronal regeneration after lesion and they can be transplanted into areas affected by several pathologies, which represents an important therapeutic strategy to treat central nervous system damage. To induce differentiation to the aldynoglia phenotype, HUCB-PCs were exposed to different culture media. Mononuclear cells from HUCB were isolated and purified by identification of CD34 and CD133 antigens, and after 12 days in culture, differentiation of CD34+ HUCB-PCs to an aldynoglia phenotypic, but not that of CD133+ cells, was induced in ensheathing cell (EC)-conditioned medium. Thus, we demonstrate that the differentiation of HUCB-PCs into aldynoglia cells in EC-conditioned medium can provide a new source of aldynoglial cells for use in transplants to treat injuries or neurodegenerative diseases.

  20. Comparison of Direct Solar Energy to Resistance Heating for Carbothermal Reduction of Regolith

    NASA Technical Reports Server (NTRS)

    Muscatello, Anthony C.; Gustafson, Robert J.

    2011-01-01

    A comparison of two methods of delivering thermal energy to regolith for the carbo thermal reduction process has been performed. The comparison concludes that electrical resistance heating is superior to direct solar energy via solar concentrators for the following reasons: (1) the resistance heating method can process approximately 12 times as much regolith using the same amount of thermal energy as the direct solar energy method because of superior thermal insulation; (2) the resistance heating method is more adaptable to nearer-term robotic exploration precursor missions because it does not require a solar concentrator system; (3) crucible-based methods are more easily adapted to separation of iron metal and glass by-products than direct solar energy because the melt can be poured directly after processing instead of being remelted; and (4) even with projected improvements in the mass of solar concentrators, projected photovoltaic system masses are expected to be even lower.

  1. The influence of swimming demand on phenotypic plasticity and morphological integration: a comparison of two polymorphic charr species.

    PubMed

    Peres-Neto, Pedro R; Magnan, Pierre

    2004-06-01

    In northern freshwater lakes, several fish species have populations composed of discrete morphs, usually involving a divergence between benthic and limnetic morphs. Although it has been suggested that swimming demand plays an important role in morphological differentiation, thus influencing habitat selection, it is unclear how it affects reaction norms, patterns in character correlation, and levels of morphological integration. We examined whether swimming demand could induce morphological plasticity in the directions expected under divergent habitat selection, and evaluated its influence on the morphological integration in Arctic charr ( Salvelinus alpinus) and brook charr ( S. fontinalis), two congeneric species exhibiting conspicuous and subtle resource polymorphism, respectively. We found that changes in morphology were induced by differential swimming demands in both species. The length of the pectoral fin was the character that responded most strongly according to the predicted morphological expectations under divergent habitat selection. High levels of morphological plasticity, relatively low levels of integration, and differences found in the morphological correlation structure among water velocity treatments suggest that constraints on morphological change are unlikely in either species, thus allowing great potential for phenotypic flexibility in both species. The magnitude of character integration, however, was larger for Arctic charr than for brook charr. This latter result is discussed in the light of the differences in the level of polymorphism between the two species in the wild. The results of the present study indicate that swimming demand alone may not be sufficient to generate the polymorphism encountered in nature. Given that both diet and swimming demands can induce morphological changes, it would be important to conduct experiments targeting the interaction between the morphological modules related to trophic and swimming demands.

  2. The Koolen-de Vries syndrome: a phenotypic comparison of patients with a 17q21.31 microdeletion versus a KANSL1 sequence variant.

    PubMed

    Koolen, David A; Pfundt, Rolph; Linda, Katrin; Beunders, Gea; Veenstra-Knol, Hermine E; Conta, Jessie H; Fortuna, Ana Maria; Gillessen-Kaesbach, Gabriele; Dugan, Sarah; Halbach, Sara; Abdul-Rahman, Omar A; Winesett, Heather M; Chung, Wendy K; Dalton, Marguerite; Dimova, Petia S; Mattina, Teresa; Prescott, Katrina; Zhang, Hui Z; Saal, Howard M; Hehir-Kwa, Jayne Y; Willemsen, Marjolein H; Ockeloen, Charlotte W; Jongmans, Marjolijn C; Van der Aa, Nathalie; Failla, Pinella; Barone, Concetta; Avola, Emanuela; Brooks, Alice S; Kant, Sarina G; Gerkes, Erica H; Firth, Helen V; Õunap, Katrin; Bird, Lynne M; Masser-Frye, Diane; Friedman, Jennifer R; Sokunbi, Modupe A; Dixit, Abhijit; Splitt, Miranda; Kukolich, Mary K; McGaughran, Julie; Coe, Bradley P; Flórez, Jesús; Nadif Kasri, Nael; Brunner, Han G; Thompson, Elizabeth M; Gecz, Jozef; Romano, Corrado; Eichler, Evan E; de Vries, Bert B A

    2016-05-01

    The Koolen-de Vries syndrome (KdVS; OMIM #610443), also known as the 17q21.31 microdeletion syndrome, is a clinically heterogeneous disorder characterised by (neonatal) hypotonia, developmental delay, moderate intellectual disability, and characteristic facial dysmorphism. Expressive language development is particularly impaired compared with receptive language or motor skills. Other frequently reported features include social and friendly behaviour, epilepsy, musculoskeletal anomalies, congenital heart defects, urogenital malformations, and ectodermal anomalies. The syndrome is caused by a truncating variant in the KAT8 regulatory NSL complex unit 1 (KANSL1) gene or by a 17q21.31 microdeletion encompassing KANSL1. Herein we describe a novel cohort of 45 individuals with KdVS of whom 33 have a 17q21.31 microdeletion and 12 a single-nucleotide variant (SNV) in KANSL1 (19 males, 26 females; age range 7 months to 50 years). We provide guidance about the potential pitfalls in the laboratory testing and emphasise the challenges of KANSL1 variant calling and DNA copy number analysis in the complex 17q21.31 region. Moreover, we present detailed phenotypic information, including neuropsychological features, that contribute to the broad phenotypic spectrum of the syndrome. Comparison of the phenotype of both the microdeletion and SNV patients does not show differences of clinical importance, stressing that haploinsufficiency of KANSL1 is sufficient to cause the full KdVS phenotype.

  3. Comparison of phenotypic versus marker-assisted background selection for the SUB1 QTL during backcrossing in rice

    PubMed Central

    Iftekharuddaula, Khandakar M.; Salam, Muhammad A.; Newaz, Muhammad A.; Ahmed, Helal U.; Collard, Bertrand C. Y.; Septiningsih, Endang M.; Sanchez, Darlene L.; Pamplona, Alvaro M.; Mackill, David J.

    2012-01-01

    Marker assisted backcrossing has been used effectively to transfer the submergence tolerance gene SUB1 into popular rice varieties, but the approach can be costly. The selection strategy comprising foreground marker and phenotypic selection was investigated as an alternative. The non-significant correlation coefficients between ranking of phenotypic selection and ranking of background marker selection in BC2F1, BC3F1 and BC3F2 generations indicated inefficiency of phenotypic selection compared to marker-assisted background selection with respect to recovery of the recipient genome. In addition, the introgression size of the chromosome fragment containing SUB1 was approximately 17 Mb, showing the effects of linkage drag. The significant correlation coefficient between rankings of phenotypic selection with the percentage of recipient alleles in the BC1F1 generation suggested that background selection could be avoided in this generation to minimize the genotyping cost. The phenotypically selected best plant of the BC3F1 generation was selfed and backcross recombinant lines were selected in the resulting BC3F4 generation. The selection strategy could be appropriate for the introgression of SUB1 QTL in countries that lack access to high-throughput genotyping facilities. PMID:23226081

  4. Detection of KPC Carbapenemase in Pseudomonas aeruginosa Isolated From Clinical Samples Using Modified Hodge Test and Boronic Acid Phenotypic Methods and Their Comparison With the Polymerase Chain Reaction

    PubMed Central

    Falahat, Saeed; Shojapour, Mana; Sadeghi, Abdorrahim

    2016-01-01

    Background Bacterial resistance to antibiotics has become a major source of concern for public health. Pseudomonas aeruginosa strains are important opportunistic pathogens. These bacteria have a high resistance to a wide range of existing antimicrobials and antibiotics. Objectives The present study was performed to evaluate the frequency of KPC in P. aeruginosa isolated from clinical samples of educational hospitals of Arak University of Medical Sciences, using the mentioned phenotypic and genotypic methods. Materials and Methods One hundred and eight non-duplicate clinical isolates of P. aeruginosa were collected from hospitals of Arak University of Medical Sciences, Arak, Iran. Antibacterial susceptibility was determined by the disk diffusion method. KPC production was confirmed by the Modified Hodge Test (MHT), which is a phenotypic test, and combined-disk test with boronic acid and the Polymerase Chain Reaction (PCR). Results In the present study, 13 isolates (12%) of P. aeruginosa were positive for KPC, using PCR. Comparison of the two phenotypic methods used in this study showed that boronic acid is more sensitive than MHT in identification of KPC-producing strains (84.6% vs. 77%). Conclusions Utilization of reliable methods for identifying carbapenemase-producing strains and determining their antibiotic resistance pattern could have a very important role in treatment of infections caused by these strains. A substantial amount of P. aeruginosa isolated from clinical samples of hospitals in Arak (Iran) produce KPC carbapenemase. Due to their low specificity, MHT and boronic acid phenotypic methods could not completely identify KPC-producing P. aeruginosa. However, the sensitivity of boronic acid phenotypic method in detection of KPC was higher than MHT. PMID:27800140

  5. Comparison of environmental risk factors for esophageal atresia, anorectal malformations, and the combined phenotype in 263 German families.

    PubMed

    Zwink, N; Choinitzki, V; Baudisch, F; Hölscher, A; Boemers, T M; Turial, S; Kurz, R; Heydweiller, A; Keppler, K; Müller, A; Bagci, S; Pauly, M; Brokmeier, U; Leutner, A; Degenhardt, P; Schmiedeke, E; Märzheuser, S; Grasshoff-Derr, S; Holland-Cunz, S; Palta, M; Schäfer, M; Ure, B M; Lacher, M; Nöthen, M M; Schumacher, J; Jenetzky, E; Reutter, H

    2016-11-01

    Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) and anorectal malformations (ARM) represent the severe ends of the fore- and hindgut malformation spectra. Previous research suggests that environmental factors are implicated in their etiology. These risk factors might indicate the influence of specific etiological mechanisms on distinct developmental processes (e.g. fore- vs. hindgut malformation). The present study compared environmental factors in patients with isolated EA/TEF, isolated ARM, and the combined phenotype during the periconceptional period and the first trimester of pregnancy in order to investigate the hypothesis that fore- and hindgut malformations involve differing environmental factors. Patients with isolated EA/TEF (n = 98), isolated ARM (n = 123), and the combined phenotype (n = 42) were included. Families were recruited within the context of two German multicenter studies of the genetic and environmental causes of EA/TEF (great consortium) and ARM (CURE-Net). Exposures of interest were ascertained using an epidemiological questionnaire. Chi-square, Fisher's exact, and Mann-Whitney U-tests were used to assess differences between the three phenotypes. Newborns with isolated EA/TEF and the combined phenotype had significantly lower birth weights than newborns with isolated ARM (P = 0.001 and P < 0.0001, respectively). Mothers of isolated EA/TEF consumed more alcohol periconceptional (80%) than mothers of isolated ARM or the combined phenotype (each 67%). Parental smoking (P = 0.003) and artificial reproductive techniques (P = 0.03) were associated with isolated ARM. Unexpectedly, maternal periconceptional multivitamin supplementation was most frequent among patients with the most severe form of disorder, i.e. the combined phenotype (19%). Significant differences in birth weight were apparent between the three phenotype groups. This might be attributable to the limited ability of EA/TEF fetuses to swallow amniotic fluid, thus

  6. CONFIRMATIONAL IDENTIFICATION OF ESCHERICHIA COLI, A COMPARISON OF GENOTYPIC AND PHENOTYPIC ASSAYS FOR GLUTAMATE DECARBOXYLASE AND B-D-GLUCURONIDASE

    EPA Science Inventory

    Genotypic and phenotypic assays for glutamate decarboxylase (GAD) and B-D-glucuronidase (GUD) were compared for their abilities to detect various strains of Escherichia coli and to discriminate among other bacterial species. Test strains included nonpathogenic E.coli, three major...

  7. Phenotypic & Genotypic Characteristics of Inflammatory Bowel Disease (IBD) in French-Canadians: comparison with a large North American repository

    PubMed Central

    Bhat, Mamatha; Nguyen, Geoffrey C.; Pare, Pierre; Lahaie, Raymond; Deslandres, Colette; Bernard, Edmond-Jean; Aumais, Guy; Jobin, Gilles; Wild, Gary; Cohen, Albert; Langelier, Diane; Brant, Steven; Dassopoulos, Themistocles; McGovern, Dermot; Torres, Esther; Duerr, Richard; Regueiro, Miguel; Silverberg, Mark S; Steinhart, Hillary; Griffiths, Anne M.; Elkadri, Abdul; Cho, Judy; Proctor, Deborah; Goyette, Philippe; Rioux, John; Bitton, Alain

    2009-01-01

    BACKGROUND Phenotype characteristics of inflammatory bowel disease (IBD) may differ significantly among ethnic subpopulations. The aim of this study was to characterize the IBD phenotype in French-Canadians, the most prominent founder population in North America. METHODS Using well-characterized phenotype data in the NIDDK-IBD Genetics Consortium repository on IBD patients, we compared phenotypic characteristics of 202 French-Canadians to those of 1287 other Caucasian patients. These included: diagnosis, anatomical location, disease behaviour, extraintestinal manifestations, surgical history, and family history of IBD. RESULTS French-Canadian CD patients were less likely to have stricturing disease (11 vs 21%, P=0.005; OR 0.45, 95% CI: 0.24– 0.85). Using a stringent definition of ethnicity (3 out of 4 grandparents being French-Canadian, as opposed to self-report, n= 148), French-Canadians had a tendency towards developing fistulizing CD (37% vs 28%, p= 0.07), and there was an increased prevalence of sacroiliitis among French-Canadians with IBD (4% vs 2%, p=0.045). Among French-Canadians, the numbers of current smokers in CD (40 vs 25%, p=0.006) and former smokers in UC (35% vs 20%, p=0.03) were significantly higher. The prevalence of one of the three main variant NOD2 SNPs among French-Canadian CD patients was 43.2%. The 3020insC SNP correlated with small bowel disease in French-Canadians (75% versus 0%, P=0.006). CONCLUSION French-Canadians exhibit an IBD phenotype profile distinct from other Caucasian IBD populations, with an accentuated association between smoking status and IBD. This unique profile may have implications regarding the need for a different approach to management of IBD in this population. PMID:19513023

  8. Variation in phenotypic plasticity and selection patterns in blue tit breeding time: between- and within-population comparisons.

    PubMed

    Porlier, Melody; Charmantier, Anne; Bourgault, Patrice; Perret, Philippe; Blondel, Jacques; Garant, Dany

    2012-09-01

    1. Phenotypic plasticity, the response of individual phenotypes to their environment, can allow organisms to cope with spatio-temporal variation in environmental conditions. Recent studies have shown that variation exists among individuals in their capacity to adjust their traits to environmental changes and that this individual plasticity can be under strong selection. Yet, little is known on the extent and ultimate causes of variation between populations and individuals in plasticity patterns. 2. In passerines, timing of breeding is a key life-history trait strongly related to fitness and is known to vary with the environment, but few studies have investigated the within-species variation in individual plasticity. 3. Here, we studied between- and within-population variation in breeding time, phenotypic plasticity and selection patterns for this trait in four Mediterranean populations of blue tits (Cyanistes caeruleus) breeding in habitats varying in structure and quality. 4. Although there was no significant warming over the course of the study, we found evidence for earlier onset of breeding in warmer years in all populations, with reduced plasticity in the less predictable environment. In two of four populations, there was significant inter-individual variation in plasticity for laying date. Interestingly, selection for earlier laying date was significant only in populations where there was no inter-individual differences in plasticity. 5. Our results show that generalization of plasticity patterns among populations of the same species might be challenging even at a small spatial scale and that the amount of within-individual variation in phenotypic plasticity may be linked to selective pressures acting on these phenotypic traits.

  9. A comparison of four direct geometry time-of-flight spectrometers at the Spallation Neutron Source

    SciTech Connect

    Stone, M. B.; Abernathy, D. L.; Ehlers, G.; Garlea, O.; Podlesnyak, A.; Winn, B.; Niedziela, J. L.; DeBeer-Schmitt, L.; Graves-Brook, M.; Granroth, G. E.; Kolesnikov, A. I.

    2014-04-15

    The Spallation Neutron Source at Oak Ridge National Laboratory now hosts four direct geometry time-of-flight chopper spectrometers. These instruments cover a range of wave-vector and energy transfer space with varying degrees of neutron flux and resolution. The regions of reciprocal and energy space available to measure at these instruments are not exclusive and overlap significantly. We present a direct comparison of the capabilities of this instrumentation, conducted by data mining the instrument usage histories, and specific scanning regimes. In addition, one of the common science missions for these instruments is the study of magnetic excitations in condensed matter systems. We have measured the powder averaged spin wave spectra in one particular sample using each of these instruments, and use these data in our comparisons.

  10. A comparison of four direct geometry time-of-flight spectrometers at the Spallation Neutron Source.

    PubMed

    Stone, M B; Niedziela, J L; Abernathy, D L; DeBeer-Schmitt, L; Ehlers, G; Garlea, O; Granroth, G E; Graves-Brook, M; Kolesnikov, A I; Podlesnyak, A; Winn, B

    2014-04-01

    The Spallation Neutron Source at Oak Ridge National Laboratory now hosts four direct geometry time-of-flight chopper spectrometers. These instruments cover a range of wave-vector and energy transfer space with varying degrees of neutron flux and resolution. The regions of reciprocal and energy space available to measure at these instruments are not exclusive and overlap significantly. We present a direct comparison of the capabilities of this instrumentation, conducted by data mining the instrument usage histories, and specific scanning regimes. In addition, one of the common science missions for these instruments is the study of magnetic excitations in condensed matter systems. We have measured the powder averaged spin wave spectra in one particular sample using each of these instruments, and use these data in our comparisons.

  11. A comparison of four direct geometry time-of-flight spectrometers at the Spallation Neutron Source

    SciTech Connect

    Stone, Matthew B; Niedziela, Jennifer L; Abernathy, Douglas L; Debeer-Schmitt, Lisa M; Garlea, Vasile O; Granroth, Garrett E; Graves-Brook, Melissa K; Ehlers, Georg; Kolesnikov, Alexander I; Podlesnyak, Andrey A; Winn, Barry L

    2014-04-01

    The Spallation Neutron Source at Oak Ridge National Laboratory now hosts four direct geometry time-of-flight chopper spectrometers. These instruments cover a range of wave vector and energy transfer space with varying degrees of neutron flux and resolution. The regions of reciprocal and energy space available to measure at these instruments is not exclusive and overlaps significantly. We present a direct comparison of the capabilities of this instrumentation, conducted by data mining the instrument usage histories, and specific scanning regimes. In addition, one of the common science missions for these instruments is the study of magnetic excitations in condensed matter systems. We have measured the powder averaged spin wave spectra in one particular sample using each of these instruments, and use these data in our comparisons.

  12. A comparison of in situ and airborne radar observations of ocean wave directionality

    NASA Technical Reports Server (NTRS)

    Jackson, F. C.; Walton, W. T.; Peng, C. Y.

    1985-01-01

    The directional spectrum of a fully arisen, about 3 m sea as measured by an experimental airborne radar, the NASA K(u)-band radar ocean wave spectrometer (ROWS), is compared to reference pitch-roll buoy data and to the classical SWOP (stereo wave observations project) spectrum for fully developed conditions. The ROWS spectrum, inferred indirectly from backscattered power measurements at 5-km altitude, is shown to be in excellent agreement with the buoy spectrum. Specifically, excellent agreement is found between the two nondirectional height spectra, and mean wave directions and directional spreads as functions of frequency. A comparison of the ROWS and SWOP spectra shows the two spectra to be very similar, in detailed shape as well as in terms of the gross spreading characteristics. Both spectra are seen to exhibit bimodal structures which accord with the Phillips' (1958) resonance mechanism. This observation is thus seen to support Phillips' contention that the SWOP modes were indeed resonance modes, not statistical artifacts.

  13. INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

    PubMed

    Manda, Prashanti; Mungall, Christopher J; Balhoff, James P; Lapp, Hilmar; Vision, Todd J

    2016-01-01

    There is growing use of ontologies for the measurement of cross-species phenotype similarity. Such similarity measurements contribute to diverse applications, such as identifying genetic models for human diseases, transferring knowledge among model organisms, and studying the genetic basis of evolutionary innovations. Two organismal features, whether genes, anatomical parts, or any other inherited feature, are considered to be homologous when they are evolutionarily derived from a single feature in a common ancestor. A classic example is the homology between the paired fins of fishes and vertebrate limbs. Anatomical ontologies that model the structural relations among parts may fail to include some known anatomical homologies unless they are deliberately added as separate axioms. The consequences of neglecting known homologies for applications that rely on such ontologies has not been well studied. Here, we examine how semantic similarity is affected when external homology knowledge is included. We measure phenotypic similarity between orthologous and non-orthologous gene pairs between humans and either mouse or zebrafish, and compare the inclusion of real with faux homology axioms. Semantic similarity was preferentially increased for orthologs when using real homology axioms, but only in the more divergent of the two species comparisons (human to zebrafish, not human to mouse), and the relative increase was less than 1% to non-orthologs. By contrast, inclusion of both real and faux random homology axioms preferentially increased similarities between genes that were initially more dissimilar in the other comparisons. Biologically meaningful increases in semantic similarity were seen for a select subset of gene pairs. Overall, the effect of including homology axioms on cross-species semantic similarity was modest at the levels of divergence examined here, but our results hint that it may be greater for more distant species comparisons.

  14. Comparison of Phenotypic and Genotypic Approaches to Capsule Typing of Neisseria meningitidis by Use of Invasive and Carriage Isolate Collections

    PubMed Central

    Mohamed, Naglaa; Rojas, Eduardo; Andrew, Lubomira; Hoyos, Johanna; Hawkins, Julio C.; McNeil, Lisa K.; Jiang, Qin; Mayer, Leonard W.; Wang, Xin; Gilca, Rodica; De Wals, Philippe; Pedneault, Louise; Eiden, Joseph; Jansen, Kathrin U.; Anderson, Annaliesa S.

    2015-01-01

    Neisseria meningitidis serogroup B (MnB) is a leading cause of bacterial meningitis; however, MnB is most commonly associated with asymptomatic carriage in the nasopharyngeal cavity, as opposed to the disease state. Two vaccines are now licensed for the prevention of MnB disease; a possible additional benefit of these vaccines could be to protect against disease indirectly by disrupting nasopharyngeal carriage (e.g., herd protection). To investigate this possibility, accurate diagnostic approaches to characterize MnB carriage isolates are required. In contrast to invasive meningococcal disease (IMD) isolates, which can be readily serogrouped, carriage isolates often lack capsule expression, making standard phenotypic assays unsuitable for strain characterization. Several antibody-based methods were evaluated for their abilities to serogroup isolates and were compared with two genotyping methods (real-time PCR [rt-PCR] and whole-genome sequencing [WGS]) to identify which approach would most accurately ascertain the polysaccharide groups associated with carriage isolates. WGS and rt-PCR were in agreement for 99% of IMD isolates, including those with coding sequences for MnB, MnC, MnW, and MnY, and the phenotypic methods correctly identified serogroups for 69 to 98% of IMD isolates. In contrast, only 47% of carriage isolates were groupable by genotypic methods, due to mutations within the capsule operon; of the isolates identified by genotypic methods, ≤43% were serogroupable with any of the phenotypic methods tested. These observations highlight the difficulties in the serogrouping and capsular genogrouping of meningococcal carriage isolates. Based on our findings, WGS is the most suitable approach for the characterization of meningococcal carriage isolates. PMID:26311858

  15. Genotype/phenotype correlations in the fragile X syndrome: Comparison of FMR1 DNA patterns in lymphocytes, lymphoblasts and fibroblasts

    SciTech Connect

    Brown, C.A.; Chitayat, D.; Ray, P.N.

    1994-09-01

    The predominant mutation in the fragile X syndrome is an amplification of a CGG repeat in the 5{prime} untranslated region of the FMR 1 gene. An amplification of > 200 repeats (full mutation) usually results in the methylation of an adjacent CpG island resulting in the loss of FMR1 gene expression. The highly variable phenotype of fragile X individuals has been proposed to be a result of DNA mosaicism resulting in only partial absence of FMR1 expression. We have utilized Southern blot analysis and PCR to analyze the CGG repeat expansion and degree of methylation of the FMR1 gene in genomic DNA isolated from lymphocytes, lymphoblasts and fibroblasts from fragile X individuals to determine the best available tissue to evaluate genotype/phenotype correlations. While in many kindreds the degree of expansion and methylation observed were similar, two exceptions are described. Individual 1A was initially identified as a non-penetrant male but demonstrated 3% fragile X expression on chromosome studies. Molecular studies on lymphocyte, lymphoblast, fibroblast and sperm samples revealed that the FMR1 region was unmethylated in all tissues with significant size (from pre- to full mutation) variation observed between tissues. In family 2, individual 2A is more severely affected than his brother 2B. Analysis of lymphocyte DNA revealed that while both individuals carried full mutations in the FMR1 gene and were methylation mosaics, 2B had a much greater extent of methylation. These DNA findings do not appear to correlate with the degree of cognitive functioning. Analysis of fibroblast DNA revealed no methylation mosaicism for either brother and a larger expansion in the more severely affected brother 2A, more closely correlating with phenotype. Our results show that there is variability between tissues with respect to FMR1 size and methylation status and suggest that fibroblast DNA patterns may more accurately reflect the level of cognitive functioning in fragile X individuals.

  16. Comparison of the phenotypes and genotypes of biofilm and solitary epiphytic bacterial populations on broad-leaved endive.

    PubMed

    Boureau, T; Jacques, M A; Berruyer, R; Dessaux, Y; Dominguez, H; Morris, C E

    2004-01-01

    The discovery that biofilms are ubiquitous among the epiphytic microflora of leaves has prompted research about the impact of biofilms on the ecology of epiphytic microorganisms and on the efficiency of strategies to manage these populations for disease control and to ensure food safety. Biofilms are likely to influence the microenvironment and phenotype of the microorganisms they harbor. However, it is also important to determine whether there are differences in the types of bacteria within biofilms compared to those outside of biofilms so as to better target microorganisms via disease control strategies. Broad-leaved endive (Cichorium endivia var. latifolia) harbors biofilms containing fluorescent pseudomonads. These bacteria can cause considerable post-harvest losses when this plant is used for manufacturing minimally processed salads. To determine whether the population structure of the fluorescent pseudomonads in biofilms is different from that outside of biofilms on the same leaves, bacteria were isolated quantitatively from the biofilm and solitary components of the epiphytic population on leaves of field-grown broad-leaved endive. Population structure was determined in terms of taxonomic identities of the bacteria isolated, in terms of genotypic profiles, and in terms of phenotypic traits related to surface colonization and biofilm formation. The results illustrate that there are no systematic differences in the composition and structure of biofilm and solitary populations of fluorescent pseudomonads, in terms of either genotypic profiles or phenotypic profiles of the strains. However, Gram-positive bacteria tended to occur more frequently within biofilms than outside of biofilms. We suggest that leaf colonization by fluorescent pseudomonads involves a flux of cells between biofilm and solitary states. This would allow bacteria to exploit the advantages of these two types of existence; biofilms would favor resistance to stressful conditions, whereas

  17. DIRECT COMPARISON OF KINETIC AND LOCAL EQUILIBRIUM FORMULATIONS FOR SOLUTE TRANSPORT AFFECTED BY SURFACE REACTIONS.

    USGS Publications Warehouse

    Bahr, Jean M.; Rubin, Jacob

    1987-01-01

    Modeling transport of reacting solutes in porous media often requires a choice between models based on the local equilibrium assumption (LEA) and models involving reaction kinetics. Direct comparison of the mathematical formulations for these two types of transport models can aid in this choice. For cases of transport affected by surface reaction, such a comparison is made possible by a new derivation procedure. This procedure yields a kinetics-based formulation that is the sum of the LEA formulation and one or more kinetically influenced terms. The dimensionless form of the new kinetics-based formulation facilitates identification of critical parameter groupings which control the approach to transport behavior consistent with LEA model predictions. Results of numerical experiments demonstrate that criteria for LEA applicability can be expressed conveniently in terms of these parameter groupings. The derivation procedure is demonstrated for examples of surface reactions including first-order reversible sorption, Langmuir-type kinetics and binary, homovalent ion exchange.

  18. Comparison of phenotypic methods in predicting methicillin resistance in coagulase-negative Staphylococcus (CoNS) from animals.

    PubMed

    Zhang, Yifan; Wang, Xiaogang; LeJeune, Jeffrey T; Zervos, Marcus; Bhargava, Kanika

    2011-02-01

    Phenotypic detection of methicillin resistance in coagulase-negative Staphylococcus (CoNS) of animal origin has been challenging due to the heterogeneous expression of mecA. To compare different phenotypic methods in predicting the mecA presence in CoNS, a total of 87 CoNS isolates from agricultural animals were analyzed in this study by agar dilution, disk diffusion, and broth microdilution. mecA was present in 81 CoNS isolates. Broth microdilution demonstrated the highest sensitivity of 100% in predicting the mecA presence, followed by 72.8% by agar dilution and 70.4% by disk diffusion. The results indicate that broth microdilution may be more suitable for predicting the presence of mecA in CoNS from animals than the other two methods, although staphylococcal species may also be a factor affecting the sensitivities of the methods as the top three staphylococcal species in this study were Staphylococcus lentus, Staphylococcus sciuri, and Staphylococcus xylosus (a total of 75 of 87).

  19. Uncertainty in direction estimation: a comparison of small arrays and three-component stations

    SciTech Connect

    Harris, D.B.

    1982-10-08

    This report presents a comparison of the relative capabilities of isolated three-component seismometers and small arrays for ascertaining the back-azimuth of regional events. The Cramer-Rao bound, a method well-known in estimation theory, is used to obtain quantitative predictions of the errors to be expected in estimating direction in the presence of noise. These quantitative error estimates form the basis for comparison. The theoretical approach taken assumes spatially coherent signals and incoherent noise. There are ranges of inter-station separation for which these models are reasonable approximations. Within the limitations on array aperture and element density imposed by the spatial correlation lengths of real signals and noise, the theory demonstrates that arrays have a definite advantage over isolated triaxial seismometers in estimating the direction of P waves. The gain in performance is proportional to the product of the aperture and the square root of the number of array elements. The performance of arrays of three-component elements in estimating P wave direction is examined also. Although such arrays have an advantage over arrays of vertical sensors for this purpose, the advantage is slight compared to the increased data bandwidth required. Consequently, the usefulness of horizontal sensors appears to depend on the importance of horizontally polarized phases for monitoring purposes or on the degree of noise polarization. Conditions of highly polarized noise favor the use of triaxial elements, since such noise can be reduced by polarization filtering.

  20. Coral calcification under environmental change: a direct comparison of the alkalinity anomaly and buoyant weight techniques

    NASA Astrophysics Data System (ADS)

    Schoepf, Verena; Hu, Xinping; Holcomb, Michael; Cai, Wei-Jun; Li, Qian; Wang, Yongchen; Xu, Hui; Warner, Mark E.; Melman, Todd F.; Hoadley, Kenneth D.; Pettay, D. Tye; Matsui, Yohei; Baumann, Justin H.; Grottoli, Andréa G.

    2017-03-01

    Two primary methods—the buoyant weight (BW) and alkalinity anomaly (AA) techniques—are currently used to quantify net calcification rates ( G) in scleractinian corals. However, it remains unclear whether they are directly comparable since the few method comparisons conducted to date have produced inconsistent results. Further, such a comparison has not been made for tropical corals. We directly compared G BW and G AA in four tropical and one temperate coral species cultured under various pCO2, temperature, and nutrient conditions. A range of protocols for conducting alkalinity depletion incubations was assessed. For the tropical corals, open-top incubations with manual stirring produced G AA that were highly correlated with and not significantly different from G BW. Similarly, G AA of the temperate coral was not significantly different from G BW when incubations provided water motion using a pump, but were significantly lower than G BW by 16% when water motion was primarily created by aeration. This shows that the two techniques can produce comparable calcification rates in corals but only when alkalinity depletion incubations are conducted under specific conditions. General recommendations for incubation protocols are made, especially regarding adequate water motion and incubation times. Further, the re-analysis of published data highlights the importance of using appropriate regression statistics when both variables are random and measured with error. Overall, we recommend the AA technique for investigations of community and short-term day versus night calcification, and the BW technique to measure organism calcification rates integrated over longer timescales due to practical limitations of both methods. Our findings will facilitate the direct comparison of studies measuring coral calcification using either method and thus have important implications for the fields of ocean acidification research and coral biology in general.

  1. Direct Comparison of a Solar Moreton Wave, EUV Wave and CME (Preprint)

    DTIC Science & Technology

    2013-10-30

    Patsourakos, S. & Vourlidas , A. 2009, Astrophys. J. Letters, 700, L182 —. 2012, Solar Phys., 281, 187 Patsourakos, S., Vourlidas , A., Wang, Y. M., Stenborg...Physics of Approved for public release; distribution is unlimited. 12 the Solar Corona , ed. C. J. Macris, 156 Temmer, M., Veronig, A. M., Gopalswamy...AFRL-RV-PS- AFRL-RV-PS- TP-2014-0004 TP-2014-0004 DIRECT COMPARISON OF A SOLAR MORETON WAVE, EUV WAVE AND CME (PREPRINT) S. M. White, et al. 30

  2. Direct comparison of defect ensembles extracted from damage probability and raster scan measurements

    NASA Astrophysics Data System (ADS)

    BatavičiÅ«tÄ--, G.; Ščiuka, M.; Melninkaitis, A.

    2015-09-01

    The presented study addresses the characterization of nanometer sized defects acting as damage precursors in nanosecond laser pulse duration regime. Two approaches are used to extract distributions of localized damage precursors, namely, damage probability and damage density measurements. Testing is performed on uncoated and SiO2 monolayer film deposited fused silica substrate exposed with pulsed UV irradiation (355 nm, 4.8 ns). Then, a direct comparison of damage precursor ensembles obtained from both methods is carried out. Our analysis indicates apparent differences between both methods that are discussed in detail. Contamination by ablation products is identified as one of the key factors that influence damage density measurements.

  3. A Simplified Direct Lipid Mixing Lipoplex Preparation: Comparison of Liposomal-, Dimethylsulfoxide-, and Ethanol-Based Methods

    PubMed Central

    Meisel, Joseph W.; Gokel, George W.

    2016-01-01

    Established transfection methodology often uses commercial reagents, which must be formed into liposomes in a sequence of about half a dozen steps. The simplified method reported here is a direct lipid mixing approach that requires fewer steps, less manipulation, and is less time-consuming. Results are comparable to those obtained with more commonly used methods, as judged by a variety of analytical techniques and by comparisons of transfection results. The method reported here may be applied to non-liposome-forming compounds, thereby greatly expanding the range of structures that can be tested for transfection ability. PMID:27323668

  4. A comparison of three self-report measures of the broader autism phenotype in a non-clinical sample.

    PubMed

    Ingersoll, Brooke; Hopwood, Christopher J; Wainer, Allison; Brent Donnellan, M

    2011-12-01

    Three self-report measures of the broader autism phenotype (BAP) were evaluated in terms of their internal consistency, distribution of scores, factor structure, and criterion-related validity in a non-clinical sample. All measures showed a continuous distribution. The SRS-A and BAPQ showed expected sex differences and were superior to the AQ in terms of internal consistency. The proposed factor structure of the BAPQ replicated better than the proposed structures of the other measures. All measures showed evidence of criterion validity via correlations with related constructs and each measure incremented the others in predicting related constructs. However, the SRS-A and BAPQ were generally stronger in this domain. Recommendations for the use of these instruments for measuring the BAP in non-clinical populations are discussed.

  5. Comparison of phenotypically indistinguishable but geographically distinct Neisseria meningitidis Group B isolates in a serum bactericidal antibody assay.

    PubMed

    Findlow, Jamie; Holland, Ann; Andrews, Nick; Weynants, Vincent; Sotolongo, Franklin; Balmer, Paul; Poolman, Jan; Borrow, Ray

    2007-11-01

    The "gold standard" assay for measuring serologic protection against Neisseria meningitidis group B (MenB) is the serum bactericidal antibody (SBA) assay. Of vital importance to the outcome of the SBA assay is the choice of the target strain(s), which is often chosen on the basis of phenotype or genotype. We therefore investigated the effect on the results produced by the SBA assay of using phenotypically indistinguishable but geographically distinct MenB isolates. Nine PorA P1.19,15 and 11 PorA P1.7-2,4 MenB isolates were incorporated into the SBA assay using human complement and were assayed against sera obtained either before or after outer membrane vesicle vaccination. Large differences in the results produced by the isolates in the SBA assay were demonstrated. These included differences as great as 5.8-fold in SBA geometric mean titers and in the proportions of subjects with SBA titers of >/=4. Ranges of as many as 9 SBA titers were achieved by individual sera across the panels of isolates. To determine the reasons for the differences observed, investigations into the expression of capsular polysaccharide, PorA, PorB, Opc, and lipooligosaccharide (LOS) and into LOS sialylation were completed. However, minor differences were found between strains, indicating similar expression and no antigen masking. These results have implications for the choice of MenB target strains for inclusion in future studies of MenB vaccines and highlight the requirement for standardization of target strains between laboratories.

  6. Hypercholesterolemia and neurodegeneration. Comparison of hippocampal phenotypes in LDLr knockout and APPswe/PS1dE9 mice.

    PubMed

    Ettcheto, Miren; Petrov, Dmitry; Pedrós, Ignacio; de Lemos, Luisa; Pallàs, Mercè; Alegret, Marta; Laguna, Juan Carlos; Folch, Jaume; Camins, Antoni

    2015-05-01

    Previous studies suggest that Alzheimer's disease (AD) neurobiology could not be explained solely by an increase in β-amyloid levels. Recently, it has been proposed that alterations in brain cholesterol metabolism may contribute to the pathogenesis of AD. In the present work, we focus on early changes in the hippocampal phenotypes of two mouse models in which cognitive impairments were previously described: a) the hypercholesterolemic LDL receptor knockout (LDLr -/-) and b) the APPswe/PS1dE9 (APP/PS1) transgenic model of familial AD. Our initial analysis, subsequent validation and additional experiments at the mRNA and protein levels demonstrate some parallels between the hippocampal phenotypes of these 2 mouse models, however our data suggest that the molecular mechanisms leading to cognitive decline are distinct in LDLr -/- and APP/PS1 animals. Genes related to cytokine signaling were significantly down-regulated in LDLr -/- mice when compared to both the wild-type and APP/PS1 mice, and these include prostaglandin-endoperoxide synthases 1 and 2 (ptgs1 and 2) and nerve grow factor (ngf). We have also detected reduced expression of genes related to lipid metabolism in LDLr -/- mice: peroxisome proliferator activated receptor gamma (pparg), pro-opiomelanocortin-alpha (pomc) and of protein kinase, AMP-activated, alpha 1 catalytic subunit of AMPK (prkaa1). Our array data also indicate that transcriptional activity of early genes involved in memory process, such as FBJ osteosarcoma oncogene (Fos) and the activity regulated cytoskeletal-associated protein (Arc) gene, are increased in the hippocampus of LDLr -/- mice. Several proteins like insulin degrading enzyme (IDE), PGC-1α, OXPHOS 1, NMDAR1 and cyclic AMP response element binding protein (CREB) are up-regulated in the LDLr -/- mice, while in the APP/PS1 mouse model only OXPHOS complexes 2, 3 and 5 are slightly downregulated. Further studies are necessary to understand the molecular pathways involved in memory loss

  7. Anthropometric indices to identify metabolic syndrome and hypertriglyceridemic waist phenotype: a comparison between the three stages of adolescence

    PubMed Central

    Pereira, Patrícia Feliciano; de Faria, Franciane Rocha; de Faria, Eliane Rodrigues; Hermsdorff, Helen Hermana Miranda; Peluzio, Maria do Carmo Gouveia; Franceschini, Sylvia do Carmo Castro; Priore, Silvia Eloiza

    2015-01-01

    OBJECTIVE: To determine the prevalence of metabolic syndrome (MS) and the hypertriglyceridemic waist phenotype (HW) in a representative adolescent sample; as well as to establish which anthropometric indicator better identifies MS and HW, according to gender and adolescent age. METHODS: This cross sectional study had the participation of 800 adolescents (414 girls) from 10-19 years old. Anthropometric indicators (body mass index, waist perimeter, waist/stature ratio, waist/hip ratio, and central/peripheral skinfolds) were determined by standard protocols. For diagnosis of MS, the criteria proposed by de Ferranti et al. (2004) were used. HW was defined by the simultaneous presence of increased waist perimeter (>75th percentile for age and sex) and high triglycerides (>100 mg/dL). The ability of anthropometric indicators was evaluated by Receiver Operating Characteristic curve. RESULTS: The prevalence of MS was identical to HW (6.4%), without differences between genders and the adolescence phases. The waist perimeter showed higher area under the curve for the diagnosis of MS, except for boys with 17-19 years old, for whom the waist/stature ratio exhibited better performance. For diagnosing HW, waist perimeter also showed higher area under the curve, except for boys in initial and final phases, in which the waist/stature ratio obtained larger area under the curve. The central/peripheral skinfolds had the lowest area under the curve for the presence of both MS and HW phenotype. CONCLUSIONS: The waist perimeter and the waist/stature showed a better performance to identify MS and HW in both genders and in all three phases of adolescence. PMID:25913494

  8. Comparison of Direct Normal Irradiance Derived from Silicon and Thermopile Global Hemispherical Radiation Detectors: Preprint

    SciTech Connect

    Myers, D. R.

    2010-01-01

    Concentrating solar applications utilize direct normal irradiance (DNI) radiation, a measurement rarely available. The solar concentrator industry has begun to deploy numerous measurement stations to prospect for suitable system deployment sites. Rotating shadowband radiometers (RSR) using silicon photodiodes as detectors are typically deployed. This paper compares direct beam estimates from RSR to a total hemispherical measuring radiometer (SPN1) multiple fast thermopiles. These detectors simultaneously measure total and diffuse radiation from which DNI can be computed. Both the SPN1 and RSR-derived DNI are compared to DNI measured with thermopile pyrheliometers. Our comparison shows that the SPN1 radiometer DNI estimated uncertainty is somewhat greater than, and on the same order as, the RSR DNI estimates for DNI magnitudes useful to concentrator technologies.

  9. A quantitative comparison of human HT-1080 fibrosarcoma cells and primary human dermal fibroblasts identifies a 3D migration mechanism with properties unique to the transformed phenotype.

    PubMed

    Schwartz, Michael P; Rogers, Robert E; Singh, Samir P; Lee, Justin Y; Loveland, Samuel G; Koepsel, Justin T; Witze, Eric S; Montanez-Sauri, Sara I; Sung, Kyung E; Tokuda, Emi Y; Sharma, Yasha; Everhart, Lydia M; Nguyen, Eric H; Zaman, Muhammad H; Beebe, David J; Ahn, Natalie G; Murphy, William L; Anseth, Kristi S

    2013-01-01

    Here, we describe an engineering approach to quantitatively compare migration, morphologies, and adhesion for tumorigenic human fibrosarcoma cells (HT-1080s) and primary human dermal fibroblasts (hDFs) with the aim of identifying distinguishing properties of the transformed phenotype. Relative adhesiveness was quantified using self-assembled monolayer (SAM) arrays and proteolytic 3-dimensional (3D) migration was investigated using matrix metalloproteinase (MMP)-degradable poly(ethylene glycol) (PEG) hydrogels ("synthetic extracellular matrix" or "synthetic ECM"). In synthetic ECM, hDFs were characterized by vinculin-containing features on the tips of protrusions, multipolar morphologies, and organized actomyosin filaments. In contrast, HT-1080s were characterized by diffuse vinculin expression, pronounced β1-integrin on the tips of protrusions, a cortically-organized F-actin cytoskeleton, and quantitatively more rounded morphologies, decreased adhesiveness, and increased directional motility compared to hDFs. Further, HT-1080s were characterized by contractility-dependent motility, pronounced blebbing, and cortical contraction waves or constriction rings, while quantified 3D motility was similar in matrices with a wide range of biochemical and biophysical properties (including collagen) despite substantial morphological changes. While HT-1080s were distinct from hDFs for each of the 2D and 3D properties investigated, several features were similar to WM239a melanoma cells, including rounded, proteolytic migration modes, cortical F-actin organization, and prominent uropod-like structures enriched with β1-integrin, F-actin, and melanoma cell adhesion molecule (MCAM/CD146/MUC18). Importantly, many of the features observed for HT-1080s were analogous to cellular changes induced by transformation, including cell rounding, a disorganized F-actin cytoskeleton, altered organization of focal adhesion proteins, and a weakly adherent phenotype. Based on our results, we

  10. Event history calendars and question list surveys: a direct comparison of interviewing methods.

    PubMed

    Belli, R F; Shay, W L; Stafford, F P

    2001-01-01

    The research reported in this article provides the first direct experimental comparison between Event History Calendar (EHC; N=309; 84.4 percent response rate) and standardized state-of-the-art question list (Q-list; N=307; 84.1 percent response rate) interviewing methodologies. Respondents and 20 interviewers were randomly assigned to EHC and Q-list interviews that were conducted via telephone in the spring of 1998. All interviews asked for retrospective reports on social and economic behaviors that occurred during the calendar years of 1996 and 1997. Using data from the same respondents collected 1 year earlier on events reported during 1996 as a standard of comparison, the quality of retrospective reports on 1996 events from the 1998 administration of EHC and Q-list interviews was assessed. In comparison to the Q-list, the EHC condition led to better-quality retrospective reports on moves, income, weeks unemployed, and weeks missing work resulting from self illness, the illness of another, or missing work for these reasons in combination with other ones. For reports of household members entering the residence, and number of jobs, the EHC led to significantly more overreporting than the Q-list. Contingent on additional research that examines a wider range of reference periods and different modes of interviewing, the EHC may become a viable and potentially superior method to the Q-list in the collection of self-reported retrospective information.

  11. Direct Comparison of Møller and Compton Polarimeters in Hall C at Jefferson Lab

    NASA Astrophysics Data System (ADS)

    Gaskell, Dave

    2017-01-01

    Knowledge of the electron beam polarization is one of the most important systematic uncertainties in precision, parity-violating electron scattering experiments with next generation experiments aiming to measure the electron beam polarization to better than 0.5%. At high energies, the most typical polarimetry techniques are Møller (polarized electron-electron) and Compton (polarized electron-photon) scattering. The use of two techniques with different systematic uncertainties provides confidence in the extracted beam polarization. Direct comparisons of the two polarimetry techniques are challenging in that Compton polarimeters typically desire maximum beam flux (high beam currents) while Møller polarimeters need to limit the beam current to avoid depolarization effects in the target. We have performed a direct comparison of the Møller and Compton polarimeters in experimental Hall C at Jefferson Lab. This test is unique in that the data were taken sequentially under identical beam conditions at 4.5 μA. We found excellent agreement between the Hall C Møller and Compton polarimeters. Combined with high-current Compton data, we were also able to limit the beam current dependence of the beam polarization to 1% or less up to a beam current of 180 μA. Supported in part by the U.S. Deparment of Energy, contract number AC05-06OR23177, under which Jefferson Science Associates, LLC operates Thomas Jefferson National Accelerator Facility.

  12. A Direct Comparison of HI and Lyα Morphologies in Two LARS Galaxies

    NASA Astrophysics Data System (ADS)

    Fitzgibbon, Kathleen; Cannon, John M.; Freeland, Emily; Hayes, Matthew; Östlin, Göran; LARS Team

    2016-01-01

    The Lyman-Alpha Reference Sample (LARS) and its extension (eLARS) represent an exhaustive campaign to reverse-engineer galaxies. The main goal is to understand how Lyα is transported within galaxies: what fraction of it escapes, and what physical properties affect Lyα morphology and radiative transport (e.g. dust and gas content, metallicity, kinematics, properties of the stellar population). Neutral hydrogen emission, which can be used to determine a galaxy's structure and kinematics, was observed using the B and C configurations of the Very Large Array in two galaxies from the sample: LARS02 and LARS09. Images of the HI mass surface density and of the intensity weighted HI velocity field were created at angular scales of ~8 arcseconds. Extended HI gas is detected at high significance up to ˜30 kpc from the optical body of LARS02. LARS09 has a severely disturbed optical morphology; our new HI observations reveal that LARS09 is interacting with the nearby field galaxy SDSS J082353.65+280622.2. In combination with direct imaging of the Lyα morphology from the Hubble Space Telescope, this program has produced the first direct comparison of Lyα and HI morphologies. These observations demonstrate concept for a significant observational campaign that will produce similar comparisons in the remaining 40 LARS+eLARS galaxies.KF was partially supported by a Science Education Award from the Howard Hughes Medical Institute (HHMI) to Macalester College.

  13. HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles.

    PubMed

    Saccone, Valentina; Consalvi, Silvia; Giordani, Lorenzo; Mozzetta, Chiara; Barozzi, Iros; Sandoná, Martina; Ryan, Tammy; Rojas-Muñoz, Agustin; Madaro, Luca; Fasanaro, Pasquale; Borsellino, Giovanna; De Bardi, Marco; Frigè, Gianmaria; Termanini, Alberto; Sun, Xin; Rossant, Janet; Bruneau, Benoit G; Mercola, Mark; Minucci, Saverio; Puri, Pier Lorenzo

    2014-04-15

    Fibro-adipogenic progenitors (FAPs) are important components of the skeletal muscle regenerative environment. Whether FAPs support muscle regeneration or promote fibro-adipogenic degeneration is emerging as a key determinant in the pathogenesis of muscular diseases, including Duchenne muscular dystrophy (DMD). However, the molecular mechanism that controls FAP lineage commitment and activity is currently unknown. We show here that an HDAC-myomiR-BAF60 variant network regulates the fate of FAPs in dystrophic muscles of mdx mice. Combinatorial analysis of gene expression microarray, genome-wide chromatin remodeling by nuclease accessibility (NA) combined with next-generation sequencing (NA-seq), small RNA sequencing (RNA-seq), and microRNA (miR) high-throughput screening (HTS) against SWI/SNF BAF60 variants revealed that HDAC inhibitors (HDACis) derepress a "latent" myogenic program in FAPs from dystrophic muscles at early stages of disease. Specifically, HDAC inhibition induces two core components of the myogenic transcriptional machinery, MYOD and BAF60C, and up-regulates the myogenic miRs (myomiRs) (miR-1.2, miR-133, and miR-206), which target the alternative BAF60 variants BAF60A and BAF60B, ultimately directing promyogenic differentiation while suppressing the fibro-adipogenic phenotype. In contrast, FAPs from late stage dystrophic muscles are resistant to HDACi-induced chromatin remodeling at myogenic loci and fail to activate the promyogenic phenotype. These results reveal a previously unappreciated disease stage-specific bipotency of mesenchimal cells within the regenerative environment of dystrophic muscles. Resolution of such bipotency by epigenetic intervention with HDACis provides a molecular rationale for the in situ reprogramming of target cells to promote therapeutic regeneration of dystrophic muscles.

  14. Multiple number and letter comparison: directionality and accessibility in numeric and alphabetic memories.

    PubMed

    Jou, Jerwen

    2003-01-01

    In 3 experiments, subjects made comparativejudgments on a set of 2 numbers or letters, 3 numbers or letters, or 5 numbers or letters. Numeric and alphabetic serial order memories were contrasted. Three aspects of serial order memory processes were identified: computational complexity, directionality, and accessibility. Computational complexity is the number of algorithmic steps involved in identifying a target. Directional bias is measured as the speed differences in identifying serial targets of equal computational complexity in a stimulus array. Memory accessibility is measured as the numeric and alphabetic serial position effects. Subjects had a slight directional bias favoring backward ordering for single digits but no bias in 2-digit number ordering, in contrast to a strong forward directional advantage in letter ordering. The speed of number access was found to steadily and evenly decrease along the numeric scale, in contrast to a systematic pattern of variations in alphabet access along the alphabetic scale. Finally, the middle item effect (the middle item in a multi-item array is identified most slowly) found in Jou's (1997) multiple-letter comparison study was generalized to numbers.

  15. Beware how you compare: comparison direction dictates stimulus-valence-modulated presentation-order effects in preference judgment.

    PubMed

    Englund, Mats P; Hellström, Åke

    2013-07-01

    Englund and Hellström (Journal of Behavioral Decision Making 25:82-94, 2012a) found a tendency to prefer the left (first-read) of two attractive alternatives but the right (second-read) of two unattractive alternatives-a valence-dependent word-order effect (WOE). They used stimulus pairs spaced horizontally, and preference was indicated by choosing one of several written statements (e.g., "apple I like more than pear"). The results were interpreted as being due to stimulus position, with the magnitude of the left stimulus having a greater impact on the comparison outcome than the magnitude of the right. Here we investigated the effects of the positioning of the stimuli versus the semantics of the response alternatives (i.e., comparison direction) on the relative impacts of the stimuli. Participants rated preferences for stimuli spaced horizontally with the response alternatives not dictating a comparison direction (Exp. 1), and stimuli spaced vertically using Englund and Hellström's (Journal of Behavioral Decision Making 25:82-94, 2012a) response alternatives, which dictate a comparison direction semantically (Exp. 2). The results showed that the valence-dependent WOE found by Englund and Hellström (Journal of Behavioral Decision Making 25:82-94, 2012a) was not due to the horizontal stimulus positioning per se, but to the induced comparison direction, with the effect probably being mediated by attention directed at the subject of the comparison. We concluded that a set comparison direction is required for the valence-dependent WOE to appear, and that using Hellström's sensation-weighting model to determine stimulus weights is a way to verify the comparison direction.

  16. A comparison of direct and iterative finite element inversion techniques in dynamic elastography.

    PubMed

    Honarvar, M; Rohling, R; Salcudean, S E

    2016-04-21

    As part of tissue elasticity imaging or elastography, an inverse problem needs to be solved to find the elasticity distribution from the measured displacements. The finite element method (FEM) is a common method for solving the inverse problem in dynamic elastography. This problem has been solved with both direct and iterative FEM schemes. Each of these methods has its own advantages and disadvantages which are examined in this paper. Choosing the data resolution and the excitation frequency are critical for achieving the best estimation of the tissue elasticity in FEM methods. In this paper we investigate the performance of both direct and iterative FEMs for different ranges of excitation frequency. A new form of iterative method is suggested here which requires a lower mesh density compared to the original form. Also two forms of the direct method are compared in this paper: one using the exact fit for derivatives calculation and the other using the least squares fit. We also perform a study on the spatial resolution of these methods using simulations. The comparison is also validated using a phantom experiment. The results suggest that the direct method with least squares fit is more robust to noise compared to other methods but has slightly lower resolution results. For example, for the homogenous region with 20 dB noise added to the data, the RMS error for the direct method with least squares fit is approximately half of the iterative method. It was observed that the ratio of voxel size to the wavelength should be within a specific range for the results to be reliable. For example for the direct method with least squares fit, for the case of 20 dB noise level, this ratio should be between 0.1 to 0.2. On balance, considering the much higher computational cost of the iterative method, the dependency of the iterative method on the initial guess, and the greater robustness of the direct method to noise, we suggest using the direct method with least squares fit for

  17. A comparison of direct and iterative finite element inversion techniques in dynamic elastography

    NASA Astrophysics Data System (ADS)

    Honarvar, M.; Rohling, R.; Salcudean, S. E.

    2016-04-01

    As part of tissue elasticity imaging or elastography, an inverse problem needs to be solved to find the elasticity distribution from the measured displacements. The finite element method (FEM) is a common method for solving the inverse problem in dynamic elastography. This problem has been solved with both direct and iterative FEM schemes. Each of these methods has its own advantages and disadvantages which are examined in this paper. Choosing the data resolution and the excitation frequency are critical for achieving the best estimation of the tissue elasticity in FEM methods. In this paper we investigate the performance of both direct and iterative FEMs for different ranges of excitation frequency. A new form of iterative method is suggested here which requires a lower mesh density compared to the original form. Also two forms of the direct method are compared in this paper: one using the exact fit for derivatives calculation and the other using the least squares fit. We also perform a study on the spatial resolution of these methods using simulations. The comparison is also validated using a phantom experiment. The results suggest that the direct method with least squares fit is more robust to noise compared to other methods but has slightly lower resolution results. For example, for the homogenous region with 20 dB noise added to the data, the RMS error for the direct method with least squares fit is approximately half of the iterative method. It was observed that the ratio of voxel size to the wavelength should be within a specific range for the results to be reliable. For example for the direct method with least squares fit, for the case of 20 dB noise level, this ratio should be between 0.1 to 0.2. On balance, considering the much higher computational cost of the iterative method, the dependency of the iterative method on the initial guess, and the greater robustness of the direct method to noise, we suggest using the direct method with least squares fit for

  18. Million-body star cluster simulations: comparisons between Monte Carlo and direct N-body

    NASA Astrophysics Data System (ADS)

    Rodriguez, Carl L.; Morscher, Meagan; Wang, Long; Chatterjee, Sourav; Rasio, Frederic A.; Spurzem, Rainer

    2016-12-01

    We present the first detailed comparison between million-body globular cluster simulations computed with a Hénon-type Monte Carlo code, CMC, and a direct N-body code, NBODY6++GPU. Both simulations start from an identical cluster model with 106 particles, and include all of the relevant physics needed to treat the system in a highly realistic way. With the two codes `frozen' (no fine-tuning of any free parameters or internal algorithms of the codes) we find good agreement in the overall evolution of the two models. Furthermore, we find that in both models, large numbers of stellar-mass black holes (>1000) are retained for 12 Gyr. Thus, the very accurate direct N-body approach confirms recent predictions that black holes can be retained in present-day, old globular clusters. We find only minor disagreements between the two models and attribute these to the small-N dynamics driving the evolution of the cluster core for which the Monte Carlo assumptions are less ideal. Based on the overwhelming general agreement between the two models computed using these vastly different techniques, we conclude that our Monte Carlo approach, which is more approximate, but dramatically faster compared to the direct N-body, is capable of producing an accurate description of the long-term evolution of massive globular clusters even when the clusters contain large populations of stellar-mass black holes.

  19. Using Consensus Building Procedures with Expert Raters to Establish Comparison Scores of Behavior for Direct Behavior Rating

    ERIC Educational Resources Information Center

    Jaffery, Rose; Johnson, Austin H.; Bowler, Mark C.; Riley-Tillman, T. Chris; Chafouleas, Sandra M.; Harrison, Sayward E.

    2015-01-01

    To date, rater accuracy when using Direct Behavior Rating (DBR) has been evaluated by comparing DBR-derived data to scores yielded through systematic direct observation. The purpose of this study was to evaluate an alternative method for establishing comparison scores using expert-completed DBR alongside best practices in consensus building…

  20. Comparison of the viscoelastic properties of cells from different kidney cancer phenotypes measured with atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Rebelo, L. M.; de Sousa, J. S.; Mendes Filho, J.; Radmacher, M.

    2013-02-01

    The viscoelastic properties of human kidney cell lines from different tumor types (carcinoma (A-498) and adenocarcinoma (ACHN)) are compared to a non-tumorigenic cell line (RC-124). Our methodology is based on the mapping of viscoelastic properties (elasticity modulus E and apparent viscosity η) over the surface of tens of individual cells with atomic force microscopy (AFM). The viscoelastic properties are averaged over datasets as large as 15000 data points per cell line. We also propose a model to estimate the apparent viscosity of soft materials using the hysteresis observed in conventional AFM deflection-displacement curves, without any modification to the standard AFM apparatus. The comparison of the three cell lines show that the non-tumorigenic cells are less deformable and more viscous than cancerous cells, and that cancer cell lines have distinctive viscoelastic properties. In particular, we obtained that ERC-124 > EA-498 > EACHN and ηRC-124 > ηA-498 > ηACHN.

  1. A Direct Comparison of Two High Precision Relative Gravity Meters at Optimal Performance

    NASA Astrophysics Data System (ADS)

    van Westrum, D.

    2015-12-01

    NGS has maintained and operated GWR Superconducting Gravimeter #024 since 1995. It has been widely considered one of the most quiet instruments from that era. It was recently upgraded with state of the art electronics and its operating parameters reoptimzied. A Micro-g LaCoste gPhoneX, installed on a high precision tilt table, was collocated with the SG at the Table Mountain Geophysical Observatory near Boulder, CO and the two instruments operated side by side for approximately two months. Results in both the frequency domain and selected time series from large seismic signals (e.g. earthquakes) will be presented, allowing for a direct comparison between the instruments in identical, ideal conditions.

  2. Comparison of five directed graph measures for identification of leading interictal epileptic regions

    PubMed Central

    Amini, Ladan; Jutten, Christian; Achard, Sophie; David, Olivier; Kahane, Philippe; Vercueil, Laurent; Minotti, Lorella; Hossein-Zadeh, Gh. Ali; Soltanian-Zadeh, Hamid

    2010-01-01

    Directed graphs (digraphs) derived from interictal periods of intracerebral EEG (iEEG) recordings can be used to estimate the leading interictal epileptic regions for presurgery evaluations. For this purpose, quantification of the emittance contribution of each node to the rest of digraph is important. However, the usual digraph measures are not very well suited for this quantification. Here we compare the efficiency of recently introduced local information measure LI and a new measure called total global efficiency with classical measures like global efficiency, local efficiency and node degree. For evaluation, the estimated leading interictal epileptic regions based on five measures are compared with seizure onset zones obtained by visual inspection of epileptologists for five patients. The comparison revealed the superior performance of LI measure. We showed efficiency of different digraph measures for the purpose of source and sink node identification. PMID:20952817

  3. When is a metric not a metric? Remarks on direct curve comparison in bioequivalence studies.

    PubMed

    Jawień, Wojciech

    2009-06-01

    The majority of measures proposed to date for direct curve comparison in bioequivalence studies were investigated. These measures have often been called metrics, but in most cases this was incorrect in the mathematical sense. It was demonstrated, with a set of counter-examples, that the axioms of a metric are fulfilled only for the integral p-metric and some of its transforms. The Rescigno index and two other measures devised by Polli and McLean are the semi-metrics, lacking the triangle inequality, while others also lack symmetry. The use of the p-metric is therefore recommended, and statistical analysis is suggested as a point at which the scaling of differences might be carried out.

  4. Comparison of China's Environmental Impact Assessment (EIA) law with the European Union (EU) EIA Directive.

    PubMed

    Chen, Qiaoling; Zhang, Yuanzhi; Ekroos, Ari

    2007-09-01

    In this paper, we first review the development of China's Environmental Impact Assessment (EIA) system in the past 30 years. Then we compare the framework and operational procedures of China's new EIA law with those of the EU EIA Directive. We also compare public participation, as well as sanctions and control in the two EIA systems. In addition, we identify where the processes in both EIA systems are similar or different from one another. By comparison, we noted that there are at least three obvious weaknesses in China's EIA system: (1) the application of new models for EIA legislation; (2) the improvement of EIA guidance and education; and (3) the enhancement of public participation in EIA process. Our study indicates that these three major shortcomings should be overcome and improved in China's EIA system, when compared with the EU EIA system.

  5. Direct comparison of graphene devices before and after transfer to different substrates

    SciTech Connect

    Sachs, Raymond; Lin, Zhisheng; Odenthal, Patrick; Kawakami, Roland; Shi, Jing

    2014-01-20

    The entire graphene field-effect-transistor devices first fabricated on SiO{sub 2}/Si are peeled from the surface and placed on a different wafer. Both longitudinal and transverse resistivity measurements of the devices before and after the transfer are measured to calculate the mobility for a direct comparison. After transferred to different SiO{sub 2}/Si wafers, the mobility, generally, is comparable, and the defect density does not show any significant increase, which indicates the degradation due to the transfer process itself is minimal. The same method can be applied to transfer graphene devices to any arbitrary substrates (e.g., SrTiO{sub 3} or STO). The transfer method developed here not only eliminates the need to locate single-layer graphene on non-SiO{sub 2}/Si substrates for patterning but also provides a convenient way to study the effects of various substrates on graphene electronic properties.

  6. Direct comparison of defect ensembles extracted from damage probability and raster scan measurements

    SciTech Connect

    Batavičiūtė, G. Ščiuka, M.; Melninkaitis, A.

    2015-09-14

    The presented study addresses the characterization of nanometer sized defects acting as damage precursors in nanosecond laser pulse duration regime. Two approaches are used to extract distributions of localized damage precursors, namely, damage probability and damage density measurements. Testing is performed on uncoated and SiO{sub 2} monolayer film deposited fused silica substrate exposed with pulsed UV irradiation (355 nm, 4.8 ns). Then, a direct comparison of damage precursor ensembles obtained from both methods is carried out. Our analysis indicates apparent differences between both methods that are discussed in detail. Contamination by ablation products is identified as one of the key factors that influence damage density measurements.

  7. Direct comparison of linear and macrocyclic compound libraries as a source of protein ligands.

    PubMed

    Gao, Yu; Kodadek, Thomas

    2015-03-09

    There has been much discussion of the potential desirability of macrocyclic molecules for the development of tool compounds and drug leads. But there is little experimental data comparing otherwise equivalent macrocyclic and linear compound libraries as a source of protein ligands. In this Letter, we probe this point in the context of peptoid libraries. Bead-displayed libraries of macrocyclic and linear peptoids containing four variable positions and 0-2 fixed residues, to vary the ring size, were screened against streptavidin and the affinity of every hit for the target was measured. The data show that macrocyclization is advantageous, but only when the ring contains 17 atoms, not 20 or 23 atoms. This technology will be useful for conducting direct comparisons between many different types of chemical libraries to determine their relative utility as a source of protein ligands.

  8. Direct Comparison of Phosphate Uptake by Adnate and Loosely Attached Microalgae within an Intact Biofilm Matrix

    PubMed Central

    Burkholder, JoAnn M.; Wetzel, Robert G.; Klomparens, Karen L.

    1990-01-01

    We report a direct comparison of phosphate uptake by adnate and loosely attached microalgae in an intact biofilm matrix, with resolution at the level of individual cells. Track scanning electron microscope autoradiography enabled assay of [33P]phosphate uptake from the overlying water by adnate algae left undisturbed on mature leaves of the macrophyte Potamogeton illinoensis or on artificial plant mimics. The epiphyte communities developed in either phosphate-poor or moderately phosphate-enriched water, and they were assayed on both natural and artificial plants. All adnate taxa examined from both natural and artificial plants in both habitats took up significantly less radiolabel when assayed beneath the overlying matrix than when they were exposed to the water upon removal of the overstory material. Track scanning electron microscope autoradiography and track light microscope autoradiography were intercalibrated to enable comparison of [33P]phosphate uptake by adnate and loosely attached components of the epiphyte matrix. Loosely attached cells on substrata from both habitats took up significantly more radiolabel than did underlying adnate cells, indicating that access to phosphate supplies from the water depended on the position of microbial cells in the matrix. In this short-term assay, the adnate microalgae were relatively isolated from the water column nutrient source. Images PMID:16348296

  9. Phenotypic analysis of pulmonary perivascular mononuclear infiltrates that occur as a direct result of acute lethal graft-versus-host disease describes the onset of interstitial pneumonitis.

    PubMed Central

    Workman, D. L.; Clancy, J.

    1995-01-01

    We recently determined that the sequential development of interstitial pneumonitis and lymphocytic bronchiolitis/bronchitis occurs as a direct result of acute lethal graft-versus-host disease. Interstitial pneumonitis develops before lymphocytic bronchiolitis/bronchitis primarily from the dissemination of perivascular mononuclear infiltrates. We have used the adult, nonirradiated (DA x LEW) F1 hybrid rat in the absence of chemotherapy, immunosuppression, or overt infection to determine the phenotype of infiltrating perivascular mononuclear cells throughout acute lethal graft-versus-host disease. F1 animals were intravenously injected with 1 x 10(6) DA parental lymphoid cells/g body weight, which produced 100% morbidity and mortality by day 21. Graft-versus-host disease animals were killed on days 3, 7, 10, 14, and 15 to 21 after injection. Whole left lung lobes were frozen, serially sectioned (4 microns), and incubated with a panel of mouse anti-rat monoclonal antibodies. Labeled antibody density was determined by computerized image analysis. Perivascular infiltration was observed first for ED1+, OX8+, and W3/25+ cells, and then OX41+, W3/13+ and OX19/25+ populations. OX6 was expressed in control tissues and at all time points tested. OX12+, OX39+ and MOM/3F12/F2+ cells were not quantifiable. The present study has determined that the process of perivascular infiltration was produced through a biphasic influx of OX6+, T-cell, and macrophage populations. Images Figure 1 Figure 4 PMID:7485398

  10. Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.

    PubMed

    Latouche, G N; Daniel, H M; Lee, O C; Mitchell, T G; Sorrell, T C; Meyer, W

    1997-12-01

    A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers.

  11. Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.

    PubMed Central

    Latouche, G N; Daniel, H M; Lee, O C; Mitchell, T G; Sorrell, T C; Meyer, W

    1997-01-01

    A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers. PMID:9399515

  12. Initial Comparison of Direct and Legacy Modeling Approaches for Radial Core Expansion Analysis

    SciTech Connect

    Shemon, Emily R.

    2016-10-10

    not conservative and could be overestimating reactivity feedback effects that are closely tied to reactor safety. We conclude that there is indeed value in performing direct simulation of deformed meshes despite the increased computational expense. PROTEUS-SN is already part of the SHARP multi-physics toolkit where both thermal hydraulics and structural mechanical feedback modeling can be applied but this is the first comparison of direct simulation to legacy techniques for radial core expansion.

  13. Direct burial and vault emplacement data quality comparison at Dotson Ranch, New Mexico

    NASA Astrophysics Data System (ADS)

    Beaudoin, B. C.; Aderhold, K.; Anderson, K.; Pfeifer, M.; Parker, T.; Miller, P. E.; Slad, G. W.; Reusch, A.

    2013-12-01

    We compare the data quality of two emplacement methods for portable broadband seismic stations, traditional vault and direct burial, using power spectral density analysis to examine temporal trends in noise, the ratio of signal-to-noise for local, regional and teleseismic earthquakes, coherence of both noise and earthquake signal recordings as well as overall data return. Sensor emplacement in the past has been overwhelmingly dominated by traditional vaults requiring more materials, manpower and time. A new technique of directly burying sensors drastically reduces the expense, personnel and time required to install a seismic station. Comparisons between the data quality of vault and direct buried sensors are needed to show that the time and money saved in emplacement does not downgrade the quality of the data collected. Two identical shallow vaults were installed adjacent to two identical direct burial sites at Dotson Ranch in San Antonio, New Mexico, in a deliberately-chosen noisy, wet and generally inhospitable location. These four sites each used a Guralp 3T sensor retrofitted with a waterproof lid and connector. Eight months of data recorded during 2012 from these four sensors are compared in order to determine if the emplacement method has a profound and systematic effect on data quality using several different metrics that mimic the actual use of seismic data in research. A posthole installation with a Nanometrics Trillium 120PH sensor was also installed at the site for a portion of the study and six months of data are included in the analysis. Overall the variability in data quality metrics used in this study is comparable between sites with differing emplacement method as it is between sites with the same emplacement method. Noise in the vaults is higher in amplitude during the transition from spring to summer as compared to the direct burials and is especially evident on the horizontal components at long periods between 20-170 seconds. Diurnal changes in

  14. 3D flame topography obtained by tomographic chemiluminescence with direct comparison to planar Mie scattering measurements.

    PubMed

    Xu, Wenjiang; Wickersham, A J; Wu, Yue; He, Fan; Ma, Lin

    2015-03-20

    This work reports the measurements of 3D flame topography using tomographic chemiluminescence and its validation by direct comparison against planar Mie scattering measurements. Tomographic measurements of the 3D topography of various well-controlled laboratory flames were performed using projections measured by seven cameras, and a simultaneous Mie scattering measurement was performed to measure a 2D cross section of the 3D flame topography. The tomographic measurements were based on chemiluminescence emissions from the flame, and the Mie scattering measurements were based on micrometer-size oil droplets seeded into the flow. The flame topography derived from the 3D tomographic and the Mie scattering measurement was then directly compared. The results show that the flame topography obtained from tomographic chemiluminescence and the Mie measurement agreed qualitatively (i.e., both methods yielded the same profile of the flame fronts), but a quantitative difference on the order of millimeters was observed between these two methods. These results are expected to be useful for understanding the capabilities and limitations of the 3D tomographic and Mie scattering techniques in combustion diagnostics.

  15. Coronary angioplasty: a comparison of direct measurement and subjective assessment of angiographic narrowing.

    PubMed

    Silverton, N P

    1986-03-01

    Systematic differences in the assessment by two methods of the severity of coronary artery stenosis were evaluated in 38 patients having coronary angioplasty. The cine angiograms obtained before and after 45 angioplasty procedures and, in 23 of the patients, at the time of a further investigation several months later, were assessed by direct manual measurement of the dilated stenoses and by simple reading of the radiographs. Comparison was made of the most severe estimates of vessel narrowing obtained from any of the projections recorded. No significant difference was found between the estimates of the severity of narrowing in 45 vessels examined immediately before angioplasty and in 23 vessels studied again several months after an initially successful dilatation. However, in the 45 vessels examined immediately following angioplasty there was a tendency for the results of direct measurement of stenosis severity to be greater than those of subjective assessment. These results suggest that in patients having coronary angioplasty the manual measurement of stenosis severity from coronary angiograms is unlikely to add clinically useful information to that obtained from the reading of the radiographs by experienced and informed observers.

  16. Comparison of direct and geodetic mass balances on an annual time scale

    NASA Astrophysics Data System (ADS)

    Fischer, A.; Schneider, H.; Merkel, G.; Sailer, R.

    2011-02-01

    Very accurate airborne laserscanning (ALS) elevation data was used to calculate the annual volume changes for Hintereisferner and Kesselwandferner in the Ötztal Alps, Austria for 2001/2002-2008/2009. The comparison of the altitude of 51 recently GPS surveyed ground control points showed that the accuracy of the ALS DEMs is better than 0.3 m. The geodetic mass balance was calculated from the volume change using detailed maps of the firn cover and applying corrections for the seasonal snow cover. The maximum snow height at the time of the elevation data flight was 0.5 m averaged over the glacier surface. The volume change data was compared to in situ mass balance data for the total area and at the stakes. For the total period of 8 yr, the difference between the geodetic and the direct mass balance is 2.398 m w.e. on Hintereisferner and 1.380 m w.e. on Kesselwandferner, corresponding to about two times the mean annual mass balance. The vertical ice flow velocity was measured and found to be on the same order of magnitude as the mass balance at KWF. This is an indicator that volume change data does not allow the calculation of ablation or accumulation rates without detailed measurements or models of the vertical ice flow velocity. Therefore, only direct mass balance data allow process studies or investigation of the climatic controls of the resulting mass changes.

  17. A direct comparison between single-fliud and Hall-MHD turbulence

    NASA Astrophysics Data System (ADS)

    Miura, Hideaki; Araki, Keisuke

    2013-10-01

    Effects of the Hall term on energy transfer in MHD turbulence and on intermittency are studied numerically through a direct comparison of the single-fluid MHD turbulence and Hall MHD turbulence, aiming at clarifying and modeling the small-scales so that we can carry out macroscopic simulations of torus plasma and solar wind plasmas with the appropriate contributions by the small scales. Direct numerical simulations of freely decaying incompressible turbulence are carried out. In the single-fluid MHD turbulence, both the enstrophy density and the current density show a typical sheet-like structure. On the other hand, the enstrophy density in Hall MHD turbulence shows a tubular structure which is similar to that in hydrodynamic turbulence. Such a transition can cause a qualitative change of the micro-transport by the fluid flow. We can show that the JxB force is superior to the advection term in the momentum equation. It is conjectured that the magnetic pressure, a part of the JxB force, can play a significant role to form the tubular structure of the enstrophy density once the Hall term is introduced. We will examine the conjecture through detailed analysis of the local field structures as well as through the energy transfer function analysis. This research is partially supported by the NIFS Collaborative Research Program (NIFS13KNSS039, NIFS13KNTS023) and Grant-in-Aid for Scientific Research, KAKENHI(22540509,23340182,23540583).

  18. Direct noise simulation of a canonical high lift device and comparison with an analytical model.

    PubMed

    Salas, Pablo; Fauquembergue, Guillaume; Moreau, Stéphane

    2016-09-01

    The noise of a canonical main-element/flap high-lift device (HLD) is computed directly using compressible wall-resolved Large Eddy Simulation. An experimental database for the chosen configuration allows us to successfully validate the chosen numerical approach. Both the noise sources and the far-field acoustic pressure are shown to be well predicted. Although the two elements trailing-edge noise can be observed in the near field, the flap remains as the dominant source in the far-field. The simplicity of the studied configuration enables the comparison of the validated numerical results with a recently developed analytical model that takes into account the diffraction of the flap noise by the main-element. A two-dimensional (2D) (with and without Kutta condition) and a three-dimensional (without Kutta correction) analytical formulations are compared with the numerical results. All formulations compare favorably with the numerical reference in terms of noise levels and directivities. However, the 2D formulation with a Kutta correction provides the best quantitative agreement as expected from the narrow span of the numerical domain. The recently developed analytical model is therefore a good predictive tool for HLD, showing that it can properly account for the diffraction effect of the main element on the flap main noise source.

  19. Predicting manual arm strength: A direct comparison between artificial neural network and multiple regression approaches.

    PubMed

    La Delfa, Nicholas J; Potvin, Jim R

    2016-02-29

    In ergonomics, strength prediction has typically been accomplished using linked-segment biomechanical models, and independent estimates of strength about each axis of the wrist, elbow and shoulder joints. It has recently been shown that multiple regression approaches, using the simple task-relevant inputs of hand location and force direction, may be a better method for predicting manual arm strength (MAS) capabilities. Artificial neural networks (ANNs) also serve as a powerful data fitting approach, but their application to occupational biomechanics and ergonomics is limited. Therefore, the purpose of this study was to perform a direct comparison between ANN and regression models, by evaluating their ability to predict MAS with identical sets of development and validation MAS data. Multi-directional MAS data were obtained from 95 healthy female participants at 36 hand locations within the reach envelope. ANN and regression models were developed using a random, but identical, sample of 85% of the MAS data (n=456). The remaining 15% of the data (n=80) were used to validate the two approaches. When compared to the development data, the ANN predictions had a much higher explained variance (90.2% vs. 66.5%) and much lower RMSD (9.3N vs. 17.2N), vs. the regression model. The ANN also performed better with the independent validation data (r(2)=78.6%, RMSD=15.1) compared to the regression approach (r(2)=65.3%, RMSD=18.6N). These results suggest that ANNs provide a more accurate and robust alternative to regression approaches, and should be considered more often in biomechanics and ergonomics evaluations.

  20. Comparison of Plasma Activation of Thin Water Layers by Direct and Remote Plasma Sources

    NASA Astrophysics Data System (ADS)

    Kushner, Mark

    2014-10-01

    Plasma activation of liquids is now being investigated for a variety of biomedical applications. The plasma sources used for this activation can be generally classified as direct (the plasma is in contact with the surface of the liquid) or remote (the plasma does not directly touch the liquid). The direct plasma source may be a dielectric barrier discharge (DBD) where the surface of the liquid is a floating electrode or a plasma jet in which the ionization wave forming the plasma plume reaches the liquid. The remote plasma source may be a DBD with electrodes electrically isolated from the liquid or a plasma jet in which the ionization wave in the plume does not reach the liquid. In this paper, a comparison of activation of thin water layers on top of tissue, as might be encountered in wound healing, will be discussed using results from numerical investigations. We used the modeling platform nonPDPSIM to simulate direct plasma activation of thin water layers using DBDs and remote activation using plasma jets using up to hundreds of pulses. The DBDs are sustained in humid air while the plasma jets consist of He/O2 mixtures flowed into humid air. For similar number of pulses and energy deposition, the direct DBD plasma sources produce more acidification and higher production of nitrates/nitrites in the liquid. This is due to the accumulation of NxOy plasma jets, the convective flow removes many of these species prior to their diffusing into the water or reacting to form higher nitrogen oxides. This latter effect is sensitive to the repetition rate which determines whether reactive species formed during prior pulses overlap with newly produced reactive species. in the gas phase. In the plasma jets, the convective flow removes many of these species prior to their diffusing into the water or reacting to form higher nitrogen oxides. This latter effect is sensitive to the repetition rate which determines whether reactive species formed during prior pulses overlap with

  1. A comparison of phenotypic plasticity in the native dandelion Taraxacum ceratophorum and its invasive congener T. officinale.

    PubMed

    Brock, Marcus T; Weinig, Cynthia; Galen, Candace

    2005-04-01

    We compared plastic responses to variation in the light environment for sympatric populations of native and exotic dandelion species, Taraxacum ceratophorum and Taraxacum officinale. Plasticity in leaf size, inflorescence height, reproductive phenology and dispersal-related traits were measured under experimentally altered light quality (red : far-red light ratio, R : FR) and light intensity (photosynthetically active radiation, PAR). To test whether differences in means and reaction norms of dispersal-related traits between species affected colonization potential, we created seed-dispersal models based on seed-fall rate and release height. Differences in plasticity between species were not systematic, but varied in direction and magnitude among traits. Taraxacum officinale produced larger leaves that exhibited greater plasticity in size under variable light intensity than T. ceratophorum. Plasticity in scape length at flowering occurred in relation to R : FR ratio in both species, but tended to be greater in T. ceratophorum. Seed-bearing scapes of T. officinale were taller and more canalized in height across light regimes than scapes of T. ceratophorum. Seeds of T. officinale were smaller than seeds of T. ceratophorum. Models predict greater dispersal in T. officinale within open and vegetated habitats. In contrast to the idea that plasticity promotes invasiveness, results suggest that the lack of plasticity in dispersal-related traits enhances the colonization potential of T. officinale.

  2. Social parasitism and the molecular basis of phenotypic evolution

    PubMed Central

    Cini, Alessandro; Patalano, Solenn; Segonds-Pichon, Anne; Busby, George B. J.; Cervo, Rita; Sumner, Seirian

    2015-01-01

    Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer—Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization. PMID:25741361

  3. Social parasitism and the molecular basis of phenotypic evolution.

    PubMed

    Cini, Alessandro; Patalano, Solenn; Segonds-Pichon, Anne; Busby, George B J; Cervo, Rita; Sumner, Seirian

    2015-01-01

    Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer-Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization.

  4. HF radar comparisons with moored estimates of current speed and direction: Expected differences and implications

    NASA Astrophysics Data System (ADS)

    Graber, Hans C.; Haus, Brian K.; Chapman, Rickey D.; Shay, Lynn K.

    1997-08-01

    The validation of estimates of ocean surface current speed and direction from high-frequency (HF) Doppler radars can be obtained through comparisons with measurements from moored near-surface current meters, acoustic Doppler current profilers, or drifters. Expected differences between current meter (CM) and HF radar estimates of ocean surface vector currents depend on numerous sources of errors and differences such as instrument and sensor limitations, sampling characteristics, mooring response, and geophysical variability. We classify these sources of errors and differences as being associated exclusively with the current meter, as being associated exclusively with the HF radar, or as a result of differing methodologies in which current meters and HF radars sample the spatially and temporally varying ocean surface current vector field. In this latter context we consider three geophysical processes, namely, the Stokes drift, Ekman drift, and baroclinicity, which contribute to the differences between surface and near-surface vector current measurements. The performance of the HF radar is evaluated on the basis of these expected differences. Vector currents were collected during the High Resolution Remote Sensing Experiment II off the coast of Cape Hatteras, North Carolina, in June 1993. The results of this analysis suggest that 40%-60% of the observed differences between near-surface CM and HF radar velocity measurements can be explained in terms of contributions from instrument noise, collocation and concurrence differences, and geophysical processes. The rms magnitude difference ranged from 11 to 20 cm s-1 at the four mooring sites. The average angular difference ranged between 15° and 25° of which about 10° is attributed to the directional error of the radar current vector estimates due to the alignment of the radial beams.

  5. Direct comparison between confocal and multiphoton microscopy for rapid histopathological evaluation of unfixed human breast tissue

    NASA Astrophysics Data System (ADS)

    Yoshitake, Tadayuki; Giacomelli, Michael G.; Cahill, Lucas C.; Schmolze, Daniel B.; Vardeh, Hilde; Faulkner-Jones, Beverly E.; Connolly, James L.; Fujimoto, James G.

    2016-12-01

    Rapid histopathological examination of surgical specimen margins using fluorescence microscopy during breast conservation therapy has the potential to reduce the rate of positive margins on postoperative histopathology and the need for repeat surgeries. To assess the suitability of imaging modalities, we perform a direct comparison between confocal fluorescence microscopy and multiphoton microscopy for imaging unfixed tissue and compare to paraffin-embedded histology. An imaging protocol including dual channel detection of two contrast agents to implement virtual hematoxylin and eosin images is introduced that provides high quality imaging under both one and two photon excitation. Corresponding images of unfixed human breast tissue show that both confocal and multiphoton microscopy can reproduce the appearance of conventional histology without the need for physical sectioning. We further compare normal breast tissue and invasive cancer specimens imaged at multiple magnifications, and assess the effects of photobleaching for both modalities using the staining protocol. The results demonstrate that confocal fluorescence microscopy is a promising and cost-effective alternative to multiphoton microscopy for rapid histopathological evaluation of ex vivo breast tissue.

  6. Comparisons of spectral characteristics of wind noise between omnidirectional and directional microphones.

    PubMed

    Chung, King

    2012-06-01

    Wind noise reduction is a topic of ongoing research and development for hearing aids and cochlear implants. The purposes of this study were to examine spectral characteristics of wind noise generated by directional (DIR) and omnidirectional (OMNI) microphones on different styles of hearing aids and to derive wind noise reduction strategies. Three digital hearing aids (BTE, ITE, and ITC) were fitted to Knowles Electronic Manikin for Acoustic Research. They were programmed to have linear amplification and matching frequency responses between the DIR and OMNI modes. Flow noise recordings were made from 0° to 360° azimuths at flow velocities of 4.5, 9.0, and 13.5 m/s in a quiet wind tunnel. Noise levels were analyzed in one-third octave bands from 100 to 8000 Hz. Comparison of wind noise revealed that DIR generally produced higher noise levels than OMNI for all hearing aids, but it could result in lower levels than OMNI at some frequencies and head angles. Wind noise reduction algorithms can be designed to detect noise levels of DIR and OMNI outputs in each frequency channel, remove the constraint to switch to OMNI in low-frequency channel(s) only, and adopt the microphone mode with lower noise levels to take advantage of the microphone differences.

  7. Direct and quantitative comparison of pixelated density profiles to high resolution X-ray reflectivity data.

    SciTech Connect

    Fenter, Paul; Lee, S. S.; Skelton, A A; Cummings, Peter T

    2011-01-01

    A method for comparing pixelated density profiles (e.g. obtained from molecular dynamics or other computational techniques) with experimental X-ray reflectivity data both directly and quantitatively is described. The conditions under which such a comparison can be made quantitatively (e.g. with errors <1%) are determined theoretically by comparing calculated structure factors for an intrinsic continuous density profile with those obtained from density profiles that have been binned into regular spatial increments. The accuracy of the X-ray reflectivity calculations for binned density profiles is defined in terms of the inter-relationships between resolution of the X-ray reflectivity data (i.e. its range in momentum transfer), the chosen bin size and the width of the intrinsic density profile. These factors play a similar role in the application of any structure-factor calculations that involve the use of pixelated density profiles, such as those obtained from iterative phasing algorithms for inverting structures from X-ray reflectivity and coherent diffraction imaging data. Finally, it is shown how simulations of a quartz water interface can be embedded into an exact description of the bulk phases (including the substrate crystal and the fluid water, below and above the actual interface) to quantitatively reproduce the experimental reflectivity data of a solid liquid interface.

  8. Spectroscopic investigation and direct comparison of the reactivities of iron pyridyl oxidation catalysts

    NASA Astrophysics Data System (ADS)

    Song, Yang; Mayes, Howard G.; Queensen, Matthew J.; Bauer, Eike B.; Dupureur, Cynthia M.

    2017-03-01

    The growing interest in green chemistry has fueled attention to the development and characterization of effective iron complex oxidation catalysts. A number of iron complexes are known to catalyze the oxidation of organic substrates utilizing peroxides as the oxidant. Their development is complicated by a lack of direct comparison of the reactivities of the iron complexes. To begin to correlate reactivity with structural elements, we compare the reactivities of a series of iron pyridyl complexes toward a single dye substrate, malachite green (MG), for which colorless oxidation products are established. Complexes with tetradentate, nitrogen-based ligands with cis open coordination sites were found to be the most reactive. While some complexes reflect sensitivity to different peroxides, others are similarly reactive with either H2O2 or tBuOOH, which suggests some mechanistic distinctions. [Fe(S,S-PDP)(CH3CN)2](SbF6)2 and [Fe(OTf)2(tpa)] transition under the oxidative reaction conditions to a single intermediate at a rate that exceeds dye degradation (PDP = bis(pyridin-2-ylmethyl) bipyrrolidine; tpa = tris(2-pyridylmethyl)amine). For the less reactive [Fe(OTf)2(dpa)] (dpa = dipicolylamine), this reaction occurs on a timescale similar to that of MG oxidation. Thus, the spectroscopic method presented herein provides information about the efficiency and mechanism of iron catalyzed oxidation reactions as well as about potential oxidative catalyst decomposition and chemical changes of the catalyst before or during the oxidation reaction.

  9. Spectroscopic investigation and direct comparison of the reactivities of iron pyridyl oxidation catalysts.

    PubMed

    Song, Yang; Mayes, Howard G; Queensen, Matthew J; Bauer, Eike B; Dupureur, Cynthia M

    2017-03-05

    The growing interest in green chemistry has fueled attention to the development and characterization of effective iron complex oxidation catalysts. A number of iron complexes are known to catalyze the oxidation of organic substrates utilizing peroxides as the oxidant. Their development is complicated by a lack of direct comparison of the reactivities of the iron complexes. To begin to correlate reactivity with structural elements, we compare the reactivities of a series of iron pyridyl complexes toward a single dye substrate, malachite green (MG), for which colorless oxidation products are established. Complexes with tetradentate, nitrogen-based ligands with cis open coordination sites were found to be the most reactive. While some complexes reflect sensitivity to different peroxides, others are similarly reactive with either H2O2 or tBuOOH, which suggests some mechanistic distinctions. [Fe(S,S-PDP)(CH3CN)2](SbF6)2 and [Fe(OTf)2(tpa)] transition under the oxidative reaction conditions to a single intermediate at a rate that exceeds dye degradation (PDP=bis(pyridin-2-ylmethyl) bipyrrolidine; tpa=tris(2-pyridylmethyl)amine). For the less reactive [Fe(OTf)2(dpa)] (dpa=dipicolylamine), this reaction occurs on a timescale similar to that of MG oxidation. Thus, the spectroscopic method presented herein provides information about the efficiency and mechanism of iron catalyzed oxidation reactions as well as about potential oxidative catalyst decomposition and chemical changes of the catalyst before or during the oxidation reaction.

  10. Direct comparison of XAFS spectroscopy and sequential extraction for arsenic speciation in coal

    USGS Publications Warehouse

    Huggins, Frank E.; Huffman, G.P.; Kolker, A.; Mroczkowski, S.; Palmer, C.A.; Finkelman, R.B.

    2000-01-01

    The speciation of arsenic in an Ohio bituminous coal and a North Dakota lignite has been examined by the complementary methods of arsenic XAFS spectroscopy and sequential extraction by aqueous solutions of ammonium acetate, HCl, HF, and HNO3. In order to facilitate a more direct comparison of the two methods, the arsenic XAFS spectra were obtained from aliquots of the coal prepared after each stage of the leaching procedure. For the aliquots, approximately linear correlations (r2 > 0.98 for the Ohio coal, > 0.90 for the ND lignite) were observed between the height of the edge-step in the XAFS analysis and the concentration of arsenic measured by instrumental neutron activation analysis. Results from the leaching sequence indicate that there are two major arsenic forms present in both coals; one is removed by leaching with HCl and the other by HNO3. Whereas the XAFS spectral signatures of the arsenic leached by HCl are compatible with arsenate for both coals, the arsenic leached by HNO3 is identified as arsenic associated with pyrite for the Ohio coal and as an As3+ species for the North Dakota lignite. Minor arsenate forms persist in both coals after the final leaching with nitric acid. The arsenate forms extracted in HCl are believed to be oxidation products derived from the other major arsenic forms upon exposure of the pulverized coals to air.

  11. Comparison of intraductal ultrasonography-directed and cholangiography-directed endoscopic retrograde biliary drainage in patients with a biliary obstruction

    PubMed Central

    Rew, Soo-Jung; Lee, Du-Hyeon; Park, Chang-Hwan; Jeon, Jin; Kim, Hyun-Soo; Choi, Sung-Kyu; Rew, Jong-Sun

    2016-01-01

    Background/Aims: Endoscopic retrograde biliary drainage (ERBD) has become a standard procedure in patients with a biliary obstruction. Intraductal ultrasonography (IDUS) has emerged as a new tool for managing extrahepatic biliary diseases. IDUS-directed ERBD can be performed without conventional cholangiography (CC). The goal of this study was to assess the effectiveness and safety of IDUS-directed ERBD compared to CC-directed ERBD in patients with an extrahepatic biliary obstruction. Methods: A total of 210 patients who had undergone IDUS-directed ERBD (IDUS-ERBD, n = 105) and CC-directed ERBD (CC-ERBD, n = 105) between October 2013 and April 2014 were analyzed retrospectively. The primary outcome measure was the procedural success rate. Secondary outcome measures included clinical outcomes, total procedure time, radiation exposure time, and overall complication rates. Results: The total technical success rate of ERBD was 100% (105/105) in the IDUS-ERBD and CC-ERBD groups. Mean procedure time was slightly prolonged in the IDUS-ERBD group than that in the CC-ERBD group (32.1 ± 9.9 minutes vs. 28.4 ± 11.6 minutes, p = 0.023). Mean radiation exposure time was one-third less in the IDUS-ERBD group than that in the CC-ERBD group (28.0 ± 49.3 seconds vs. 94.2 ± 57.3 seconds, p < 0.001). No significant differences in complication rates were detected between the groups. Conclusions: IDUS-ERBD was equally effective and safe as CC-ERBD in patients with an extrahepatic biliary obstruction. Although IDUS-ERBD increased total procedure time, it significantly decreased radiation exposure. PMID:27097771

  12. Direct comparison of highly efficient solution- and vacuum-processed organic solar cells based on merocyanine dyes.

    PubMed

    Kronenberg, Nils M; Steinmann, Vera; Bürckstümmer, Hannah; Hwang, Jaehyung; Hertel, Dirk; Würthner, Frank; Meerholz, Klaus

    2010-10-01

    Identically configured bulk heterojunction organic solar cells based on merocyanine dye donor and fullerene acceptor compounds (see figure) are manufactured either from solution or by vacuum deposition, to enable a direct comparison. Whereas the former approach is more suitable for screening purposes, the latter approach affords higher short-circuit current density and power conversion efficiency.

  13. Direct demonstration of transsynaptic degeneration in the human visual system: a comparison of retrograde and anterograde changes

    PubMed Central

    Beatty, RM; Sadun, AA; Smith, LEH; Vonsattel, JP; Richardson, EP

    1982-01-01

    Transneuronal degeneration of retinal ganglion cells was directly demonstrated in a patient who had unilateral removal of the striate cortex forty years prior to necropsy. For comparison, another case is presented showing anterograde transneuronal atrophy forty years after enucleation of one eye. Images PMID:7069426

  14. Comparison of Self-Scoring Error Rate for SDS (Self Directed Search) (1970) and the Revised SDS (1977).

    ERIC Educational Resources Information Center

    Price, Gary E.; And Others

    A comparison of Self-Scoring Error Rate for Self Directed Search (SDS) and the revised SDS is presented. The subjects were college freshmen and sophomores who participated in career planning as a part of their orientation program, and a career workshop. Subjects, N=190 on first study and N=84 on second study, were then randomly assigned to the SDS…

  15. A Comparison of 2pi and 4pi Photometric Testing of Directional and Omnidirectional Sources in an Integrating Sphere

    SciTech Connect

    Richman, Eric E.; Merzouk, Massine B.

    2014-06-12

    A Comparison of 2pi and 4pi Photometric Testing of Directional and Omnidirectional Sources in an Integrating Sphere. These data will help determine if differences in methods should be addresed in test methods specifically for LED products but applicable to other technologies as well

  16. Field Comparisons of Direct and Component Measurements of Net Radiation under Clear Skies.

    NASA Astrophysics Data System (ADS)

    Duchon, Claude E.; Wilk, Gregory E.

    1994-02-01

    Accurate measurements of net radiation are basic to all studies of the surface energy budget. In preparation for an energy budget experiment significant differences were found between direct and component measurement of net radiation, which prompted this investigation of their cause. The instruments involved were an all-black single-dome Fritschen-type net pyrradiometer, two Eppley model 8 48 pyranometers, and an Eppley model PIR pyrgeometer. Each had recently been calibrated. The accuracy of the component instruments was considered first. Comparisons of about one hour on each of three nights between the pyrgeometer and five empirical formulas showed that the average departure over all formulas from the pyrgeometer average was 1%. Other comparisons between the pyrgeometer and an infrared thermometer viewing the surface yielded similar results. Alternate shading and unshading of the pyrgeometer looking upward during daytime resulted in a formula that was used to correct the downward longwave radiation under clear skies. The correction is dependent on wind speed, in contrast to a recent paper showing negligible dependence, but is in accord with earlier findings. Based on the manufacturer's specifications, the pyranometer calibrations were considered to be within 2% of the World Radiation Reference.Thus a series of experiments was carried out using what were believed to be reasonably accurate component measurements of net radiation and measurements from the net pyrradiometer. The results showed that the sensitivity of the latter was less in the longwave band than in the shortwave band in agreement with findings of others. Speculating on possible further dependence of sensitivity to the upward and downward streams of radiation, a method was developed to determine the magnitude of the individual net pyrmdiometer components. A reflective double-shell hemispherical cup was affixed to the upward or downward face of the net pyrradiometer such that linear regression could be

  17. A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds

    PubMed Central

    Berthier, David; Peylhard, Moana; Dayo, Guiguigbaza-Kossigan; Flori, Laurence; Sylla, Souleymane; Bolly, Seydou; Sakande, Hassane; Chantal, Isabelle; Thevenon, Sophie

    2015-01-01

    Background Animal African Trypanosomosis particularly affects cattle and dramatically impairs livestock development in sub-Saharan Africa. African Zebu (AFZ) or European taurine breeds usually die of the disease in the absence of treatment, whereas West African taurine breeds (AFT), considered trypanotolerant, are able to control the pathogenic effects of trypanosomosis. Up to now, only one AFT breed, the longhorn N’Dama (NDA), has been largely studied and is considered as the reference trypanotolerant breed. Shorthorn taurine trypanotolerance has never been properly assessed and compared to NDA and AFZ breeds. Methodology/Principal Findings This study compared the trypanotolerant/susceptible phenotype of five West African local breeds that differ in their demographic history. Thirty-six individuals belonging to the longhorn taurine NDA breed, two shorthorn taurine Lagune (LAG) and Baoulé (BAO) breeds, the Zebu Fulani (ZFU) and the Borgou (BOR), an admixed breed between AFT and AFZ, were infected by Trypanosoma congolense IL1180. All the cattle were genetically characterized using dense SNP markers, and parameters linked to parasitaemia, anaemia and leukocytes were analysed using synthetic variables and mixed models. We showed that LAG, followed by NDA and BAO, displayed the best control of anaemia. ZFU showed the greatest anaemia and the BOR breed had an intermediate value, as expected from its admixed origin. Large differences in leukocyte counts were also observed, with higher leukocytosis for AFT. Nevertheless, no differences in parasitaemia were found, except a tendency to take longer to display detectable parasites in ZFU. Conclusions We demonstrated that LAG and BAO are as trypanotolerant as NDA. This study highlights the value of shorthorn taurine breeds, which display strong local adaptation to trypanosomosis. Thanks to further analyses based on comparisons of the genome or transcriptome of the breeds, these results open up the way for better knowledge

  18. Comparison between different direct search optimization algorithms in the calibration of a distributed hydrological model

    NASA Astrophysics Data System (ADS)

    Campo, Lorenzo; Castelli, Fabio; Caparrini, Francesca

    2010-05-01

    The modern distributed hydrological models allow the representation of the different surface and subsurface phenomena with great accuracy and high spatial and temporal resolution. Such complexity requires, in general, an equally accurate parametrization. A number of approaches have been followed in this respect, from simple local search method (like Nelder-Mead algorithm), that minimize a cost function representing some distance between model's output and available measures, to more complex approaches like dynamic filters (such as the Ensemble Kalman Filter) that carry on an assimilation of the observations. In this work the first approach was followed in order to compare the performances of three different direct search algorithms on the calibration of a distributed hydrological balance model. The direct search family can be defined as that category of algorithms that make no use of derivatives of the cost function (that is, in general, a black box) and comprehend a large number of possible approaches. The main benefit of this class of methods is that they don't require changes in the implementation of the numerical codes to be calibrated. The first algorithm is the classical Nelder-Mead, often used in many applications and utilized as reference. The second algorithm is a GSS (Generating Set Search) algorithm, built in order to guarantee the conditions of global convergence and suitable for a parallel and multi-start implementation, here presented. The third one is the EGO algorithm (Efficient Global Optimization), that is particularly suitable to calibrate black box cost functions that require expensive computational resource (like an hydrological simulation). EGO minimizes the number of evaluations of the cost function balancing the need to minimize a response surface that approximates the problem and the need to improve the approximation sampling where prediction error may be high. The hydrological model to be calibrated was MOBIDIC, a complete balance

  19. Power comparison of admixture mapping and direct association analysis in genome-wide association studies.

    PubMed

    Qin, Huaizhen; Zhu, Xiaofeng

    2012-04-01

    When dense markers are available, one can interrogate almost every common variant across the genome via imputation and single nucleotide polymorphism (SNP) test, which has become a routine in current genome-wide association studies (GWASs). As a complement, admixture mapping exploits the long-range linkage disequilibrium (LD) generated by admixture between genetically distinct ancestral populations. It is then questionable whether admixture mapping analysis is still necessary in detecting the disease associated variants in admixed populations. We argue that admixture mapping is able to reduce the burden of massive comparisons in GWASs; it therefore can be a powerful tool to locate the disease variants with substantial allele frequency differences between ancestral populations. In this report we studied a two-stage approach, where candidate regions are defined by conducting admixture mapping at stage 1, and single SNP association tests are followed at stage 2 within the candidate regions defined at stage 1. We first established the genome-wide significance levels corresponding to the criteria to define the candidate regions at stage 1 by simulations. We next compared the power of the two-stage approach with direct association analysis. Our simulations suggest that the two-stage approach can be more powerful than the standard genome-wide association analysis when the allele frequency difference of a causal variant in ancestral populations, is larger than 0.4. Our conclusion is consistent with a theoretical prediction by Risch and Tang ([2006] Am J Hum Genet 79:S254). Surprisingly, our study also suggests that power can be improved when we use less strict criteria to define the candidate regions at stage 1.

  20. Southeast Atlantic Ocean aerosol direct radiative effects over clouds: Comparison of observations and simulations

    NASA Astrophysics Data System (ADS)

    de Graaf, M.; Haywood, J.; Bellouin, N.; Tilstra, L. G.; Stammes, P.

    2017-02-01

    Absorbing aerosols exert a warming or a cooling effect on the Earth's system, depending on the circumstances. The direct radiative effect (DRE) of absorbing aerosols is negative (cooling) at the top-of-the-atmosphere (TOA) over a dark surface like the ocean, as the aerosols increase the planetary albedo, but it is positive (warming) over bright backgrounds like clouds. Furthermore, radiation absorption by aerosols heat the atmosphere locally, and, through rapid adjustments of the atmospheric column and cloud dynamics, the net effect can be amplified considerably. We developed a technique to study the absorption of radiation of smoke over low lying clouds using satellite spectrometry. The TOA DRE of smoke over clouds is large and positive over the southeast Atlantic Ocean off the west coast of Africa, which can be explained by the large decrease of reflected radiation by a polluted cloud, especially in the UV. However, general circulation models (GCMs) fail to reproduce these strong positive DRE, and in general GCMs disagree on the magnitude and even sign of the aerosol DRE in the southeast Atlantic region. Our satellite-derived DRE measurements show clear seasonal and inter-annual variations, consistent with other satellite measurements, which are not reproduced by GCMs. A comparison with model results showed discrepancies with the Ångström exponent of the smoke aerosols, which is larger than assumed in simulations, and a sensitivity to emission scenarios. However, this was not enough to explain the discrepancies, and we suspect that the modeling of cloud distributions and microphysics will have the necessary larger impact on DRE that will explain the differences between observations and modeling.

  1. Direct comparison of two statistical methods for determination of evoked-potential thresholds

    NASA Astrophysics Data System (ADS)

    Langford, Ted L.; Patterson, James H., Jr.

    1994-07-01

    Several statistical procedures have been proposed as objective methods for determining evoked-potential thresholds. Data have been presented to support each of the methods, but there have not been direct comparisons using the same data. The goal of the present study was to evaluate correlation and variance ratio statistics using common data. A secondary goal was to evaluate the utility of a derived potential for determining thresholds. Chronic, bipolar electrodes were stereotaxically implanted in the inferior colliculi of six chinchillas. Evoked potentials were obtained at 0.25, 0.5, 1.0, 2.0, 4.0 and 8.0 kHz using 12-ms tone bursts and 12-ms tone bursts superimposed on 120-ms pedestal tones which were of the same frequency as the bursts, but lower in amplitude by 15 dB. Alternate responses were averaged in blocks of 200 to 4000 depending on the size of the response. Correlations were calculated for the pairs of averages. A response was deemed present if the correlation coefficient reached the 0.05 level of significance in 4000 or fewer averages. Threshold was defined as the mean of the level at which the correlation was significant and a level 5 dB below that at which it was not. Variance ratios were calculated as described by Elberling and Don (1984) using the same data. Averaged tone burst and tone burst-plus pedestal data were differenced and the resulting waveforms subjected to the same statistical analyses described above. All analyses yielded thresholds which were essentially the same as those obtained using behavioral methods. When the difference between stimulus durations is taken into account, however, evoked-potential methods produced lower thresholds than behavioral methods.

  2. Estimates of oceanic surface wind speed and direction using orthogonal beam scatterometer measurements and comparison of recent sea scattering theories

    NASA Technical Reports Server (NTRS)

    Moore, R. K.; Fung, A. K.; Dome, G. J.; Birrer, I. J.

    1978-01-01

    The wind direction properties of radar backscatter from the sea were empirically modelled using a cosine Fourier series through the 4th harmonic in wind direction (referenced to upwind). A comparison with 1975 JONSWAP (Joint North Sea Wave Project) scatterometer data, at incidence angles of 40 and 65, indicates that effects to third and fourth harmonics are negligible. Another important result is that the Fourier coefficients through the second harmonic are related to wind speed by a power law expression. A technique is also proposed to estimate the wind speed and direction over the ocean from two orthogonal scattering measurements. A comparison between two different types of sea scatter theories, one type presented by the work of Wright and the other by that of Chan and Fung, was made with recent scatterometer measurements. It demonstrates that a complete scattering model must include some provisions for the anisotropic characteristics of the sea scatter, and use a sea spectrum which depends upon wind speed.

  3. Influence of Additive and Multiplicative Structure and Direction of Comparison on the Reversal Error

    ERIC Educational Resources Information Center

    González-Calero, José Antonio; Arnau, David; Laserna-Belenguer, Belén

    2015-01-01

    An empirical study has been carried out to evaluate the potential of word order matching and static comparison as explanatory models of reversal error. Data was collected from 214 undergraduate students who translated a set of additive and multiplicative comparisons expressed in Spanish into algebraic language. In these multiplicative comparisons…

  4. Comparison of Direct Medical Costs Between Automated and Continuous Ambulatory Peritoneal Dialysis

    PubMed Central

    Cortés-Sanabria, Laura; Rodríguez-Arreola, Brenda E.; Ortiz-Juárez, Victor R.; Soto-Molina, Herman; Pazarín-Villaseñor, Leonardo; Martínez-Ramírez, Héctor R.; Cueto-Manzano, Alfonso M.

    2013-01-01

    ♦ Objective: We set out to estimate the direct medical costs (DMCs) of peritoneal dialysis (PD) and to compare the DMCs for continuous ambulatory PD (CAPD) and automated PD (APD). In addition, DMCs according to age, sex, and the presence of peritonitis were evaluated. ♦ Methods: Our retrospective cohort analysis considered patients initiating PD, calculating 2008 costs and, for comparison, updating the results for 2010. The analysis took the perspective of the Mexican Institute of Social Security, including outpatient clinic and emergency room visits, dialysis procedures, medications, laboratory tests, hospitalizations, and surgeries. ♦ Results: No baseline differences were observed for the 41 patients evaluated (22 on CAPD, 19 on APD). Median annual DMCs per patient on PD were US$15 072 in 2008 and US$16 452 in 2010. When analyzing percentage distribution, no differences were found in the DMCs for the modality groups. In both APD and CAPD, the main costs pertained to the dialysis procedure (CAPD 41%, APD 47%) and hospitalizations (CAPD 37%, APD 32%). Dialysis procedures cost significantly more (p = 0.001) in APD (US$7 084) than in CAPD (US$6 071), but total costs (APD US$15 389 vs CAPD US$14 798) and other resources were not different. The presence of peritonitis increased the total costs (US$16 075 vs US$14 705 for patients without peritonitis, p = 0.05), but in the generalized linear model analysis, DMCs were not predicted by age, sex, dialysis modality, or peritonitis. A similar picture was observed for costs extrapolated to 2010, with a 10% - 20% increase for each component—except for laboratory tests, which increased 52%, and dialysis procedures, which decreased 3%, from 2008. ♦ Conclusions: The annual DMCs per patient on PD in this study were US$15 072 in 2008 and US$16 452 in 2010. Total DMCs for dialysis procedures were higher in APD than in CAPD, but the difference was not statistically significant. In both APD and CAPD, 90% of costs were

  5. Comparison of the validity of direct pediatric developmental evaluation versus developmental screening by parent report

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To compare the validity of direct pediatric developmental evaluation with developmental screening by parent report, parents completed a developmental screen (the Child Development Review), a pediatrician performed a direct developmental evaluation (Capute Scales), and a psychologist administered the...

  6. Intentional Forgetting of Actions: Comparison of List-Method and Item-Method Directed Forgetting

    ERIC Educational Resources Information Center

    Sahakyan, Lili; Foster, Nathaniel L.

    2009-01-01

    Performing action phrases (subject-performed tasks, SPTs) leads to better memory than verbal learning instructions (verbal tasks, VTs). In Experiments 1-3, the list-method directed forgetting design produced equivalent directed forgetting impairment for VTs and SPTs; however, directed forgetting enhancement emerged only for VTs, but not SPTs.…

  7. Comparison of Synchronization Techniques for the AFIT Direct Sequence Spread Spectrum System

    DTIC Science & Technology

    1992-04-21

    13 Sklar , Bernard . Digital Communications - Fundamentals and Applications. Englewood Cliffs, N.J.: Prentice Hall, 1988. 14. Stephens, James P. Direct...Transmitted Reference Synchronization Diagram ..... ... 17 3. Baseband Digital Matched Filter ...... ............ .. 22 4. Delay Line Matched Filter...direct sequence technique uses a pseudo-noise (PN) digital code to directly modulate a conventional frequency modulated (FM) carrier in the AFIT system

  8. Laser-induced stimulated Raman scattering in the forward direction of a droplet - Comparison of Mie theory with geometrical optics

    NASA Technical Reports Server (NTRS)

    Srivastava, Vandana; Jarzembski, Maurice A.

    1991-01-01

    This paper uses Mie theory to treat electromagnetic scattering and to evaluate field enhancement in the forward direction of a small droplet irradiated by a high-energy beam and compares the results of calculations with the field-enhancement evaluation obtained via geometrical optics treatment. Results of this comparison suggest that the field enhancement located at the critical ring region encircling the axis in the forward direction of the droplet can support laser-induced Raman scattering. The results are supported by experimental observations of the interaction of a 120-micron-diam water droplet with a high-energy Nd:YAG laser beam.

  9. A Comparison of Direction Finding Results From an FFT Peak Identification Technique With Those From the Music Algorithm

    DTIC Science & Technology

    1991-07-01

    MUSIC ALGORITHM (U) by L.E. Montbrland go I July 1991 CRC REPORT NO. 1438 Ottawa I* Government of Canada Gouvsrnweient du Canada I o DParunnt of...FINDING RESULTS FROM AN FFT PEAK IDENTIFICATION TECHNIQUE WITH THOSE FROM THE MUSIC ALGORITHM (U) by L.E. Montbhrand CRC REPORT NO. 1438 July 1991...Ottawa A Comparison of Direction Finding Results From an FFT Peak Identification Technique With Those From the Music Algorithm L.E. Montbriand Abstract A

  10. Achievement Goal Orientations and Adolescents’ Subjective Well-Being in School: The Mediating Roles of Academic Social Comparison Directions

    PubMed Central

    Tian, Lili; Yu, Tingting; Huebner, E. Scott

    2017-01-01

    The purpose of this study was to examine the multiple mediational roles of academic social comparison directions (upward academic social comparison and downward academic social comparison) on the relationships between achievement goal orientations (i.e., mastery goals, performance-approach goals, and performance-avoidance goals) and subjective well-being (SWB) in school (school satisfaction, school affect) in adolescent students in China. A total of 883 Chinese adolescent students (430 males; Mean age = 12.99) completed a multi-measure questionnaire. Structural equation modeling was used to examine the hypotheses. Results indicated that (1) mastery goal orientations and performance-approach goal orientations both showed a statistically significant, positive correlation with SWB in school whereas performance-avoidance goal orientations showed a statistically significant, negative correlation with SWB in school among adolescents; (2) upward academic social comparisons mediated the relation between the three types of achievement goal orientations (i.e., mastery goals, performance-approach goals, and performance-avoidance goals) and SWB in school; (3) downward academic social comparisons mediated the relation between mastery goal orientations and SWB in school as well as the relation between performance-avoidance goal orientations and SWB in school. The findings suggest possible important cultural differences in the antecedents of SWB in school in adolescent students in China compared to adolescent students in Western nations. PMID:28197109

  11. Achievement Goal Orientations and Adolescents' Subjective Well-Being in School: The Mediating Roles of Academic Social Comparison Directions.

    PubMed

    Tian, Lili; Yu, Tingting; Huebner, E Scott

    2017-01-01

    The purpose of this study was to examine the multiple mediational roles of academic social comparison directions (upward academic social comparison and downward academic social comparison) on the relationships between achievement goal orientations (i.e., mastery goals, performance-approach goals, and performance-avoidance goals) and subjective well-being (SWB) in school (school satisfaction, school affect) in adolescent students in China. A total of 883 Chinese adolescent students (430 males; Mean age = 12.99) completed a multi-measure questionnaire. Structural equation modeling was used to examine the hypotheses. Results indicated that (1) mastery goal orientations and performance-approach goal orientations both showed a statistically significant, positive correlation with SWB in school whereas performance-avoidance goal orientations showed a statistically significant, negative correlation with SWB in school among adolescents; (2) upward academic social comparisons mediated the relation between the three types of achievement goal orientations (i.e., mastery goals, performance-approach goals, and performance-avoidance goals) and SWB in school; (3) downward academic social comparisons mediated the relation between mastery goal orientations and SWB in school as well as the relation between performance-avoidance goal orientations and SWB in school. The findings suggest possible important cultural differences in the antecedents of SWB in school in adolescent students in China compared to adolescent students in Western nations.

  12. 32 CFR Appendix C to Part 169a - Simplified Cost Comparison and Direct Conversion of CAs

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... available. The type of employee appointment (e.g., career, career-conditional, etc., or change from... for CA simplified cost comparison decisions are required for Agencies without their own Legislative Affairs (LA) and Public Affairs (PA) offices. Those Agencies shall submit their draft decision brief...

  13. A Comparison of Two Methods of Direct Instruction of Preservice Teachers.

    ERIC Educational Resources Information Center

    Klesius, Janell P.; And Others

    1990-01-01

    Two methods of delivering direct instruction to preservice teachers were compared. Students (n=37) in a reading course learned the Directed Reading Activity (DRA) via lecture and discussion; 37 others learned with videotape and related practice. The latter group retained and used DRA knowledge better over a longer period. (Author/SM)

  14. Comparison of the One- and Bi-Direction Chained Equipercentile Equating

    ERIC Educational Resources Information Center

    Oh, Hyeonjoo; Moses, Tim

    2012-01-01

    This study investigated differences between two approaches to chained equipercentile (CE) equating (one- and bi-direction CE equating) in nearly equal groups and relatively unequal groups. In one-direction CE equating, the new form is linked to the anchor in one sample of examinees and the anchor is linked to the reference form in the other…

  15. Comparison of "direct" and "indirect" nuclear cystography in the diagnosis of vesicoureteric reflux.

    PubMed

    Khriesat, I; Khriesat, S; Hazza, I

    2001-01-01

    This study was undertaken to compare "direct" and "indirect" nuclear cystography for the detection of vesicoureteral reflux (VUR). Forty-five children (15 males and 30 females), ranging in age from 5 months to 10 years, were studied at the King Hussein Medical Center, Amman, Jordan between January 1998 and December 1999, using both direct (catheter) and indirect techniques of nuclear cystography (NC). Of the 82 ureters that could be compared, 32 ureters were positive for VUR on the direct technique while only 20 ureters showed VUR on the indirect technique (sensitivity 62%). Nine ureters, which did not show VUR on the direct cystogram, were read as positive on the indirect cystogram (specificity 82%). The false positive results of indirect nuclear cystogram make it invalid for VUR screening program, while the ease of assessment and low radiation dose from the direct NC has made this the recommended test for screening and follow-up of VUR.

  16. A comparison of direct versus self-report measures for assessing physical activity in adults: a systematic review

    PubMed Central

    Prince, Stéphanie A; Adamo, Kristi B; Hamel, Meghan E; Hardt, Jill; Gorber, Sarah Connor; Tremblay, Mark

    2008-01-01

    Background Accurate assessment is required to assess current and changing physical activity levels, and to evaluate the effectiveness of interventions designed to increase activity levels. This study systematically reviewed the literature to determine the extent of agreement between subjectively (self-report e.g. questionnaire, diary) and objectively (directly measured; e.g. accelerometry, doubly labeled water) assessed physical activity in adults. Methods Eight electronic databases were searched to identify observational and experimental studies of adult populations. Searching identified 4,463 potential articles. Initial screening found that 293 examined the relationship between self-reported and directly measured physical activity and met the eligibility criteria. Data abstraction was completed for 187 articles, which described comparable data and/or comparisons, while 76 articles lacked comparable data or comparisons, and a further 30 did not meet the review's eligibility requirements. A risk of bias assessment was conducted for all articles from which data was abstracted. Results Correlations between self-report and direct measures were generally low-to-moderate and ranged from -0.71 to 0.96. No clear pattern emerged for the mean differences between self-report and direct measures of physical activity. Trends differed by measure of physical activity employed, level of physical activity measured, and the gender of participants. Results of the risk of bias assessment indicated that 38% of the studies had lower quality scores. Conclusion The findings suggest that the measurement method may have a significant impact on the observed levels of physical activity. Self-report measures of physical activity were both higher and lower than directly measured levels of physical activity, which poses a problem for both reliance on self-report measures and for attempts to correct for self-report – direct measure differences. This review reveals the need for valid, accurate

  17. Is the Calcite-Water Interface Understood? Direct Comparisons of Molecular Dynamics Simulations with Specular X-ray Reflectivity Data

    SciTech Connect

    Fenter, Paul; Kerisit, Sebastien N.; Raiteri, Paolo; Gale, Julian D.

    2013-04-01

    New insights into the structure of the calcite-water interface are obtained through direct model-independent comparison of multiple classical molecular dynamics (MD) simulations with high-resolution specular X-ray reflectivity (XR) data. This set of comparisons, with four different state-of-the-art force fields (including two non-polarizable, one polarizable, and one reactive force field), reveal new insights into the absolute accuracy of the simulated structures and the uniqueness of the XR-derived structural results. These four simulations, while qualitatively similar, have visibly distinct interfacial structure, and are distinguished through a quantitative comparison of the XR signals calculated from these simulations with experimental XR data. The results demonstrate that the simulated calcite-water interface structures, as a whole, are not consistent with the XR data (i.e., within their precision and accuracy). This disagreement is largely due to the simulation of the calcite lattice. The simulated interfacial water profiles show substantially different levels of agreement with the XR data. Of these, the rigid-ion model (RIM) simulations show the best consistency with the experimental XR data. Further model-dependent comparisons of the structural parameters that describe the interfacial structure (derived from both the MD simulations and the XR data) provide further insight into the sources of differences between these two approaches. Using the new insights from the RIM simulations, new structures of the calcite-water interface consistent with both the experimental data and the simulation are identified and compared to recent results.

  18. Consumers' willingness to pay for beef direct sales. A regional comparison across the Pyrenees.

    PubMed

    Sanjuán, Ana I; Resano, Helena; Zeballos, Gabriela; Sans, Pierre; Panella-Riera, Nuria; Campo, M Mar; Khliji, Saoussan; Guerrero, Ana; Oliver, M Angels; Sañudo, Carlos; Santolaria, Pilar

    2012-06-01

    Willingness to pay (WTP) for direct market of beef is investigated in two Spanish and two French regions located on both sides of the Pyrenees. Given the novelty of this distribution system, especially in Spain, a contingent valuation approach is undertaken, and a double-bounded model is estimated. Different patterns of awareness, use and WTP are found across regions. Likewise, the profile of current and potential users of direct sale chains is investigated. Experience in the different stages involved from choice to final consumption of beef, intensity of varied beef consumption, familiarity with direct market of food in general, and beef in particular, are some of the relevant factors to explain WTP and the probability of getting engaged into a direct distribution system of beef.

  19. Comparison of Hydraulic Conductivity Determinations in Co-located Conventional and Direct-Push Monitoring Wells

    DTIC Science & Technology

    2011-03-08

    province of the Appalachian Mountains (Hunt 1967) (Figure A-1). Underlying bands of metamorphic and igneous bedrock in this province have produced N-NE...metasedimentary and rock (Lyons 1955). Availa- ble borehole and geophysical data indicate that the majority of the site is located on top of a buried...transmissive zone is in direct con- tact with the bedrock. It generally includes a sandy glacial till lying directly on the rock surface and a coarser

  20. Comparison Of Direct Simple Shear Confinement Methods On Clay And Silt Specimens

    DTIC Science & Technology

    2011-12-20

    Shape of a Rubber Specimen Under Constant Height Direct Simple Shear Condition: (a) strain < 10%, (b) strain >10% (DeGroot et al, 1992...wire-reinforced rubber membrane constructed at the Norwegian Geotechnical Institute (NGI) (Figure 1-3). Figure 1-3 – Direct Simple Shear Confinement...confined specimens using a rubber membrane and aluminum rings. The rings were packed tightly together and the sample was consolidated using lead weights

  1. A Comparison of GPS and Scatterometer Sensing of Ocean Wind Speed and Direction

    NASA Technical Reports Server (NTRS)

    Armatys, Michael; Komjathy, Attila; Axelrad, Penina; Katzberg, Stephen J.

    2000-01-01

    Initial estimates of ocean surface wind speed and direction based on observations of reflected Global Positioning System (GPS) signals are presented and compared to QuikSCAT wind fields. The two wind speed estimates are generally in agreement to within 2-3 m/s, and under favorable conditions of well developed seas and stable winds, direction estimates agree to within 10 deg. An overview of the GPS technique is presented as well as a presentation and discussion of these first results.

  2. Comparison of Two Methods of Obtaining Digital Orthodontic Models: Direct vs. Indirect

    DTIC Science & Technology

    2013-05-17

    either a traditional impression or a digital impression taken directly from the dentition . Various manufacturers developed model scanning devices...main advantage to direct intraoral scanning of the dentition is the obvious elimination of potential error that is inherent in creating an impression...of the maxillary and mandibular dentition and associated bite registration. We attempted to reduce the amount of potential error in several ways

  3. Phenotypic comparisons between wild relatives and cultivars of kiwifruit, persimmon, mulberry, and olive at the National Clonal Germplasm Repository, Davis, CA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotypic traits were characterized for 23 wild species and 4 cultivars of 4 clonal fruit crops including, Kiwifruit (Actinidia), Persimmon (Diospyros), Mulberry (Morus) and Olive (Olea). Across all four crops, the wild species varied distinctly, especially when compared with the cultivars. The wil...

  4. Direct Contra Naïve-Indirect Comparison of Clinical Failure Rates between High-Viscosity GIC and Conventional Amalgam Restorations: An Empirical Study

    PubMed Central

    Mickenautsch, Steffen; Yengopal, Veerasamy

    2013-01-01

    Background Naïve-indirect comparisons are comparisons between competing clinical interventions’ evidence from separate (uncontrolled) trials. Direct comparisons are comparisons within randomised control trials (RCTs). The objective of this empirical study is to test the null-hypothesis that trends and performance differences inferred from naïve-indirect comparisons and from direct comparisons/RCTs regarding the failure rates of amalgam and direct high-viscosity glass-ionomer cement (HVGIC) restorations in permanent posterior teeth have similar direction and magnitude. Methods A total of 896 citations were identified through systematic literature search. From these, ten and two uncontrolled clinical longitudinal studies for HVGIC and amalgam, respectively, were included for naïve-indirect comparison and could be matched with three out twenty RCTs. Summary effects sizes were computed as Odds ratios (OR; 95% Confidence intervals) and compared with those from RCTs. Trend directions were inferred from 95% Confidence interval overlaps and direction of point estimates; magnitudes of performance differences were inferred from the median point estimates (OR) with 25% and 75% percentile range, for both types of comparison. Mann-Whitney U test was applied to test for statistically significant differences between point estimates of both comparison types. Results Trends and performance differences inferred from naïve-indirect comparison based on evidence from uncontrolled clinical longitudinal studies and from direct comparisons based on RCT evidence are not the same. The distributions of the point estimates differed significantly for both comparison types (Mann–Whitney U  =  25, nindirect  =  26; ndirect  =  8; p  =  0.0013, two-tailed). Conclusion The null-hypothesis was rejected. Trends and performance differences inferred from either comparison between HVGIC and amalgam restorations failure rates in permanent posterior teeth are not the same. It is

  5. Comparison of direct and geodetic mass balances on a multi-annual time scale

    NASA Astrophysics Data System (ADS)

    Fischer, A.

    2010-07-01

    Glacier mass balance is measured with the direct or the geodetic method. In this study, the geodetic mass balances of six Austrian glaciers in 19 periods between 1953 and 2006 are compared to the direct mass balances in the same periods. The mean annual geodetic mass balance for all periods is -0.5 m w.e./year. The mean difference between the geodetic and the direct data is -0.7 m w.e., the minimum -7.3 m w.e. and the maximum 5.6 m w.e. The accuracy of geodetic mass balance resulting from the accuracy of the DEMs ranges from 2 m w.e. for photogrammetric data to 0.002 m w.e. for LIDAR data. Basal melt, seasonal snow cover and density changes of the surface layer contribute up to 0.7 m w.e. for the period of 10 years to the difference to the direct method. The characteristics of published data of Griesgletscher, Gulkana Glacier, Lemon Creek glacier, South Cascade, Storbreen, Storglaciären, and Zongo Glacier is similar to these Austrian glaciers. For 26 analyzed periods with an average length of 18 years the mean difference between the geodetic and the direct data is -0.4 m w.e., the minimum -7.2 m w.e. and the maximum 3.6 m w.e. Longer periods between the acquisition of the DEMs do not necessarily result in a higher accuracy of the geodetic mass balance. Specific glaciers show specific trends of the difference between the direct and the geodetic data according to their type and state. In conclusion, geodetic and direct mass balance data are complementary, but differ systematically.

  6. Probing the Reproducibility of Leaf Growth and Molecular Phenotypes: A Comparison of Three Arabidopsis Accessions Cultivated in Ten Laboratories1[W

    PubMed Central

    Massonnet, Catherine; Vile, Denis; Fabre, Juliette; Hannah, Matthew A.; Caldana, Camila; Lisec, Jan; Beemster, Gerrit T.S.; Meyer, Rhonda C.; Messerli, Gaëlle; Gronlund, Jesper T.; Perkovic, Josip; Wigmore, Emma; May, Sean; Bevan, Michael W.; Meyer, Christian; Rubio-Díaz, Silvia; Weigel, Detlef; Micol, José Luis; Buchanan-Wollaston, Vicky; Fiorani, Fabio; Walsh, Sean; Rinn, Bernd; Gruissem, Wilhelm; Hilson, Pierre; Hennig, Lars; Willmitzer, Lothar; Granier, Christine

    2010-01-01

    A major goal of the life sciences is to understand how molecular processes control phenotypes. Because understanding biological systems relies on the work of multiple laboratories, biologists implicitly assume that organisms with the same genotype will display similar phenotypes when grown in comparable conditions. We investigated to what extent this holds true for leaf growth variables and metabolite and transcriptome profiles of three Arabidopsis (Arabidopsis thaliana) genotypes grown in 10 laboratories using a standardized and detailed protocol. A core group of four laboratories generated similar leaf growth phenotypes, demonstrating that standardization is possible. But some laboratories presented significant differences in some leaf growth variables, sometimes changing the genotype ranking. Metabolite profiles derived from the same leaf displayed a strong genotype × environment (laboratory) component. Genotypes could be separated on the basis of their metabolic signature, but only when the analysis was limited to samples derived from one laboratory. Transcriptome data revealed considerable plant-to-plant variation, but the standardization ensured that interlaboratory variation was not considerably larger than intralaboratory variation. The different impacts of the standardization on phenotypes and molecular profiles could result from differences of temporal scale between processes involved at these organizational levels. Our findings underscore the challenge of describing, monitoring, and precisely controlling environmental conditions but also demonstrate that dedicated efforts can result in reproducible data across multiple laboratories. Finally, our comparative analysis revealed that small variations in growing conditions (light quality principally) and handling of plants can account for significant differences in phenotypes and molecular profiles obtained in independent laboratories. PMID:20200072

  7. Comparison between NuGEN's WT-Ovation Pico and one-direct amplification systems.

    PubMed

    Morse, Alison M; Carballo, Valentina; Baldwin, Donald A; Taylor, Christopher G; McIntyre, Lauren M

    2010-09-01

    Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser-capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser-capture microdissection. Arabidopsis root cells undergoing giant cell formation as a result of nematode infestation and uninfested control root cells were laser-captured and used to evaluate two amplification systems. One, NuGEN's WT-Ovation Pico (Pico) amplification system, uses total RNA as starting material, and the other, NuGEN's WT-One-Direct (One-Direct) amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The One-Direct system was less reproducible and more variable than the Pico system. The Pico amplification kit resulted in the detection of thousands of differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the One-Direct amplification kit.

  8. Comparison between NuGEN's WT-Ovation Pico and One-Direct Amplification Systems

    PubMed Central

    Morse, Alison M.; Carballo, Valentina; Baldwin, Donald A.; Taylor, Christopher G.; McIntyre, Lauren M.

    2010-01-01

    Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser-capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser-capture microdissection. Arabidopsis root cells undergoing giant cell formation as a result of nematode infestation and uninfested control root cells were laser-captured and used to evaluate two amplification systems. One, NuGEN's WT-Ovation Pico (Pico) amplification system, uses total RNA as starting material, and the other, NuGEN's WT-One-Direct (One-Direct) amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The One-Direct system was less reproducible and more variable than the Pico system. The Pico amplification kit resulted in the detection of thousands of differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the One-Direct amplification kit. PMID:20808643

  9. Comparison of patients' and health care professionals' attitudes towards advance directives.

    PubMed Central

    Blondeau, D; Valois, P; Keyserlingk, E W; Hébert, M; Lavoie, M

    1998-01-01

    OBJECTIVES: This study was designed to identify and compare the attitudes of patients and health care professionals towards advance directives. Advance directives promote recognition of the patient's autonomy, letting the individual exercise a certain measure of control over life-sustaining care and treatment in the eventuality of becoming incompetent. DESIGN: Attitudes to advance directives were evaluated using a 44-item self-reported questionnaire. It yields an overall score as well as five factor scores: autonomy, beneficence, justice, external norms, and the affective dimension. SETTING: Health care institutions in the province of Québec, Canada. Survey sample: The sampling consisted of 921 subjects: 123 patients, 167 physicians, 340 nurses and 291 administrators of health care institutions. RESULTS: Although the general attitude of each population was favourable to the expression of autonomy, multivariate analysis of variance (MANOVA) indicated that physicians attached less importance to this subscale than did other populations (p < .001). Above all, they favoured legal external norms and beneficence. Physicians and administrators also attached less importance to the affective dimension than did patients and nurses. Specifically, physicians' attitudes towards advance directives were shown to be less positive than patients' attitudes. CONCLUSION: More attention should be given to the importance of adequately informing patients about advance directives because they may not represent an adequate means for patients to assert their autonomy. PMID:9800589

  10. Numerical Simulation and Comparison of Powder Jet Profiles for Different Types of Coaxial Nozzles in Direct Material Deposition

    NASA Astrophysics Data System (ADS)

    Kovaleva, I.; Kovalev, O.; Zaitsev, A.; Smurov, I.

    Laser direct metal deposition has become an established processing technique for the repair and manufacture of products and the functionalization of surfaces in a variety of industrial applications. The properties of surfaces and parts, depends on the characteristics of the gas-powder flow between the nozzle and the deposition point. A detailed research of the gas- powder stream parameters is conducted. Three-dimensional physical and mathematical model of gas-jet transportation of metal powder particles for different coaxial nozzles has been developed. 3D mass and quantitative powder flows on the substrate are obtained numerically. The comparison of obtained parameters of powder stream is performed.

  11. Comparison of direct and indirect measurement of the elastocaloric effect in natural rubber

    NASA Astrophysics Data System (ADS)

    Xie, Zhongjian; Sebald, Gael; Guyomar, Daniel

    2016-01-01

    The directly measured temperature change Δ T upon deformation (elastocaloric effect) of natural rubber was compared with indirect method, which is deduced from the Clausius-Clapeyron factor ( ∂ σ / ∂ T ) ɛ , where σ is the stress and ɛ is the strain. The factor ( ∂ σ / ∂ T ) ɛ can be measured by two different methods. One is to measure the stress vs. strain behavior at different static temperatures. It is found that the Δ T deduction is underestimated or even of opposite sign compared with the directly measured one. These behaviors are different from elastocaloric effect of shape memory alloys. An interpretation based on strain-induced crystallite is proposed. The other characterization is to measure the stress vs. temperature at constant strain. It results in a prediction, which is in good quantitative agreement with the directly measured one. The stress appears then to be a non-state variable, thus questioning the ergodicity of the material.

  12. Comparison of the marginal adaptation of direct and indirect composite inlay restorations with optical coherence tomography

    PubMed Central

    TÜRK, Ayşe Gözde; SABUNCU, Metin; ÜNAL, Sena; ÖNAL, Banu; ULUSOY, Mübin

    2016-01-01

    ABSTRACT Objective The purpose of the study was to use the photonic imaging modality of optical coherence tomography (OCT) to compare the marginal adaptation of composite inlays fabricated by direct and indirect techniques. Material and Methods Class II cavities were prepared on 34 extracted human molar teeth. The cavities were randomly divided into two groups according to the inlay fabrication technique. The first group was directly restored on cavities with a composite (Esthet X HD, Dentsply, Germany) after isolating. The second group was indirectly restored with the same composite material. Marginal adaptations were scanned before cementation with an invisible infrared light beam of OCT (Thorlabs), allowing measurement in 200 µm intervals. Restorations were cemented with a self-adhesive cement resin (SmartCem2, Dentsply), and then marginal adaptations were again measured with OCT. Mean values were statistically compared by using independent-samples t-test and paired samples t-test (p<0.05), before and after cementation. Results Direct inlays presented statistically smaller marginal discrepancy values than indirect inlays, before (p=0.00001442) and after (p=0.00001466) cementation. Marginal discrepancy values were increased for all restorations after cementation (p=0.00008839, p=0.000000952 for direct and indirect inlays, respectively). The mean marginal discrepancy value of the direct group increased from 56.88±20.04 µm to 91.88±31.7 µm, whereas the indirect group increased from 107.54±35.63 µm to 170.29±54.83 µm. Different techniques are available to detect marginal adaptation of restorations, but the OCT system can give quantitative information about resin cement thickness and its interaction between tooth and restoration in a nondestructive manner. Conclusions Direct inlays presented smaller marginal discrepancy than indirect inlays. The marginal discrepancy values were increased for all restorations that refer to cement thickness after cementation

  13. Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database.

    PubMed

    Hill, Janet E; Paccagnella, Ana; Law, Kee; Melito, Pasquale L; Woodward, David L; Price, Lawrence; Leung, Amy H; Ng, Lai-King; Hemmingsen, Sean M; Goh, Swee Han

    2006-04-01

    A robust method for the identification of Campylobacter spp. based on direct sequencing of PCR-amplified partial cpn60 sequences and comparison of these to a reference database of cpn60 sequences is reported. A total of 53 Campylobacter isolates, representing 15 species, were identified and distinguished from phenotypically similar Helicobacter and Arcobacter strains. Pairwise cpn60 sequence identities between Campylobacter spp. ranged from 71 to 92 %, with most between 71 and 79 %, making discrimination of these species obvious. The method described overcomes limitations of existing PCR-based methods, which require time-consuming and complex post-amplification steps such as the cloning of amplification products. The results of this study demonstrate the potential for use of the reference chaperonin sequence database, cpnDB, as a tool for identification of bacterial isolates based on cpn60 sequences amplified with universal primers.

  14. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

    PubMed Central

    Ragonnet-Cronin, Manon L.; Shilaih, Mohaned; Günthard, Huldrych F.; Hodcroft, Emma B.; Böni, Jürg; Fearnhill, Esther; Dunn, David; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Yang, Wan-Lin; Brown, Alison E.; Lycett, Samantha J.; Kouyos, Roger; Brown, Andrew J. Leigh

    2016-01-01

    Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes. PMID:27642070

  15. Direct comparison between two {gamma}-alumina structural models by DFT calculations

    SciTech Connect

    Ferreira, Ary R.; Martins, Mateus J.F.; Konstantinova, Elena; Capaz, Rodrigo B.; Souza, Wladmir F.; Chiaro, Sandra Shirley X.; Leitao, Alexandre A.

    2011-05-15

    We selected two important {gamma}-alumina models proposed in literature, a spinel-like one and a nonspinel one, to perform a theoretical comparison. Using ab initio calculations, the models were compared regarding their thermodynamic stability, lattice vibrational modes, and bulk electronic properties. The spinel-like model is thermodynamically more stable by 4.55 kcal/mol per formula unit on average from 0 to 1000 K. The main difference between the models is in their simulated infrared spectra, with the spinel-like model showing the best agreement with experimental data. Analysis of the electronic density of states and charge transfer between atoms reveal the similarity on the electronic structure of the two models, despite some minor differences. -- Graphical abstract: Two {gamma}-Alumina bulk models selected in this work for a comparison focusing in the electronic structure and thermodynamics of the systems. (a) The nonspinel model and (b) the spinel-like model. Display Omitted Highlights: {yields} There is still a debate about the {gamma}-Alumina structure in the literature. {yields} Models of surfaces are constructed from different bulk structural models. {yields} Two models commonly used in the literate were selected and compared. {yields} One model reproduce better the experimental data. {yields} Both presented a similar electronic structure.

  16. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

    NASA Astrophysics Data System (ADS)

    Ragonnet-Cronin, Manon L.; Shilaih, Mohaned; Günthard, Huldrych F.; Hodcroft, Emma B.; Böni, Jürg; Fearnhill, Esther; Dunn, David; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Yang, Wan-Lin; Brown, Alison E.; Lycett, Samantha J.; Kouyos, Roger; Brown, Andrew J. Leigh

    2016-09-01

    Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes.

  17. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland.

    PubMed

    Ragonnet-Cronin, Manon L; Shilaih, Mohaned; Günthard, Huldrych F; Hodcroft, Emma B; Böni, Jürg; Fearnhill, Esther; Dunn, David; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Yang, Wan-Lin; Brown, Alison E; Lycett, Samantha J; Kouyos, Roger; Brown, Andrew J Leigh

    2016-09-19

    Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes.

  18. Retrieval comparison of EndNote to search MEDLINE (Ovid and PubMed) versus searching them directly.

    PubMed

    Gall, Carole; Brahmi, Frances A

    2004-01-01

    Using EndNote version 7.0, the authors tested the search capabilities of the EndNote search engine for retrieving citations from MEDLINE for importation into EndNote, a citation management software package. Ovid MEDLINE and PubMed were selected for the comparison. Several searches were performed on Ovid MEDLINE and PubMed using EndNote as the search engine, and the same searches were run on both Ovid and PubMed directly. Findings indicate that it is preferable to search MEDLINE directly rather than using EndNote. The publishers of EndNote do warn its users about the limitations of their product as a search engine when searching external databases. In this article, the limitations of EndNote as a search engine for searching MEDLINE were explored as related to MeSH, non-MeSH, citation verification, and author searching.

  19. Are Horses Like Zebras, or Vice Versa? Children's Sensitivity to the Asymmetries of Directional Comparisons

    ERIC Educational Resources Information Center

    Chestnut, Eleanor K.; Markman, Ellen M.

    2016-01-01

    Adults exhibit strong preferences when framing symmetrical relations. Adults prefer, for example, "A zebra is like a horse" to "A horse is like a zebra," and "The bicycle is near the building" to "The building is near the bicycle." This is because directional syntax requires more typical or prominent items…

  20. Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background Several studies have examined the accuracy of genomic selection both within and across purebred beef or dairy populations. However, the accuracy of direct genomic breeding values (DGVs) has been less well studied in crossbred or admixed cattle populations. We used a population of 3,240 cr...

  1. Evidence-Based Youth Psychotherapies Versus Usual Clinical Care: A Meta-Analysis of Direct Comparisons

    ERIC Educational Resources Information Center

    Weisz, John R.; Jensen-Doss, Amanda; Hawley, Kristin M.

    2006-01-01

    In the debate over evidence-based treatments (EBTs) for youth, one question is central: Do EBTs produce better outcomes than the usual interventions employed in clinical care? The authors addressed this question through a meta-analysis of 32 randomized trials that directly compared EBTs with usual care. EBTs outperformed usual care. Effects fell…

  2. A Comparison of Pyramidal Staff Training and Direct Staff Training in Community-Based Day Programs

    ERIC Educational Resources Information Center

    Haberlin, Alayna T.; Beauchamp, Ken; Agnew, Judy; O'Brien, Floyd

    2012-01-01

    This study evaluated two methods of training staff who were working with individuals with developmental disabilities: pyramidal training and consultant-led training. In the pyramidal training, supervisors were trained in the principles of applied behavior analysis (ABA) and in delivering feedback. The supervisors then trained their direct-care…

  3. Comparison of Self- and Faculty-Directed Learning of Psychomotor Skills.

    PubMed

    Majumdar, Basanti; Roberts, Jacqueline; Knechtel, Rosemary; Noesgaard, Charlotte; Campbell, Karen; Tkachuk, Susan

    1998-01-01

    This randomized controlled trial compared the effectiveness of self-directed learning (SDL) and faculty directed, demonstration-return-demonstration learning (DRD) for psychomotor clinical nursing skills and level of knowledge of second year baccalaureate nursing students. The self-directed learning approach of a university was compared to a community college's approach of tutor demonstration-student return demonstration for students from the University. Data were collected using questionnaires measuring academic outcomes after the students were exposed to the different learning approaches. The data were compared for differences in grades in an objective structured clinical examination (OSCE). Findings indicated that students perceived there were differences in the learning process, however there were no differences of interest in most of the academic outcomes. While students did not differ on the total OSCE grade, students using the SDL method received higher grades in only one of the marker stations and students using the DRD method received higher grades in only one marker and one observer station. The group of students receiving the DRD method indicated that they were given enough help from faculty, were allowed sufficient practice time and expected that the SDL method would be more stressful. 30.8% of the students in the SDL group recommended their learning method to future second year students, while 100% of the DRD group recommended the DRD method. Although the outcome appeared not to differ, more students indicated satisfaction with the faculty-directed (DRD) approach.

  4. Estimating Familial Loading in SLI: A Comparison of Direct Assessment versus Parental Interview

    ERIC Educational Resources Information Center

    Conti-Ramsden, Gina; Simkin, Zoe; Pickles, Andrew

    2006-01-01

    Purpose: Two approaches commonly used for estimating prevalence of language disorders in families were compared. The 1st involved examining a subset of language items from an investigator-based interview used to record parental information on the language and literacy difficulties in relatives. The 2nd was the direct assessment of ability in…

  5. Comparison of Direct and Indirect Measures of E-cigarette Risk Perceptions

    PubMed Central

    Wackowski, Olivia A.; Bover Manderski, Michelle T.; Delnevo, Cristine D.

    2015-01-01

    Objectives Risk perception measures of tobacco products relative to cigarettes are commonly used and important to tobacco research given that they may be associated with and predict tobacco use. However, results may differ based on measures used. This study compares direct and indirect approaches to measuring e-cigarette/cigarette risk perceptions. Methods We compared the responses of 519 current smokers on a nationally representative 2014 survey that gauged perceptions of e-cigarettes’ harm relative to cigarettes in two ways: 1) a single-item direct measure of comparative harm and a two-item indirect measure (which measured perceived levels of harm from e-cigarettes and cigarettes independently in two parallel questions). Results We found that 60% of smokers rated e-cigarettes “less harmful” than cigarettes when using a direct comparative risk measure versus 73% when using an indirect measure. Agreement between measure types was fair (Cohen’s Kappa=0.45) and was lower for males, Blacks, older and less educated smokers. Conclusions E-cigarettes were more likely to be rated by smokers as less harmful than cigarettes when using indirect versus direct measures. Additional methodology research into this area is warranted given the importance of risk perceptions to tobacco control interventions, communications, policy-making and regulation. PMID:26855966

  6. A Comparison of Activity-Based Intervention and Embedded Direct Instruction When Teaching Emergent Literacy Skills

    ERIC Educational Resources Information Center

    Botts, Dawn C.; Losardo, Angela S.; Tillery, Christina Y.; Werts, Margaret G.

    2014-01-01

    This replication study focused on the effectiveness of two different intervention approaches, activity-based intervention and embedded direct instruction, on the acquisition, generalization, and maintenance of phonological awareness, a key area of emergent literacy, by preschool children with language delays. Five male preschool participants with…

  7. Comparison of CaOH with MTA for Direct Pulp Capping

    PubMed Central

    Hilton, T.J.; Ferracane, J.L.; Mancl, L.; Baltuck, C.

    2013-01-01

    This practice-based, randomized clinical trial evaluated and compared the success of direct pulp capping in permanent teeth with MTA (mineral trioxide aggregate) or CaOH (calcium hydroxide). Thirty-five practices in Northwest PRECEDENT were randomized to perform direct pulp caps with either CaOH (16 practices) or MTA (19 practices). Three hundred seventy-six individuals received a direct pulp cap with CaOH (n = 181) or MTA (n = 195). They were followed for up to 2 yrs at regular recall appointments, or as dictated by tooth symptoms. The primary outcomes were the need for extraction or root canal therapy. Teeth were also evaluated for pulp vitality, and radiographs were taken at the dentist’s discretion. The probability of failure at 24 mos was 31.5% for CaOH vs. 19.7% for MTA (permutation log-rank test, p = .046). This large randomized clinical trial provided confirmatory evidence for a superior performance with MTA as a direct pulp-capping agent as compared with CaOH when evaluated in a practice-based research network for up to 2 yrs (ClinicalTrials.gov NCT00812887). PMID:23690353

  8. Comparison of direct and indirect methods of measuring airborne chrysotile fibre concentration.

    PubMed

    Eypert-Blaison, Celine; Veissiere, Sylvie; Rastoix, Olivier; Kauffer, Edmond

    2010-01-01

    Transmission electron microscopy observations most frequently form a basis for estimating asbestos fibre concentration in the environment and in buildings with asbestos-containing materials. Sampled fibres can be transferred to microscope grids by applying either a direct [ISO (1995) Draft International ISO/DIS 10312. Ambient air. Determination of asbestos fibres. Direct transfer transmission electron microscopy procedure. Geneva, Switzerland: International Standardization Organization] or an indirect [AFNOR (1996) Détermination de la concentration en fibres d'amiante par microscopie électronique à transmission-Méthode indirecte. Cedex, France: AFNOR, p. 42; ISO (1997) Draft International ISO/DIS 13794. Ambient air. Determination of asbestos fibres. Indirect-transfer transmission electron microscopy procedure. Geneva, Switzerland: International Standardization Organization] method. In the latter case, ISO Standard 13794 recommends filtering calcination residues either on a polycarbonate (PC) filter (PC indirect method) or on a cellulose ester (CE) membrane (CE indirect method). The PC indirect method requires that fibres deposited on a PC filter be covered by a carbon layer, whereas in the CE indirect method, the CE membrane has to be directly processed using a method described in ISO Standard 10312. The purpose of this study was to compare results obtained using, on the one hand, direct preparation methods and, on the other hand, PC indirect or CE indirect methods, for counting asbestos fibres deposited on filters as a result of liquid filtration or air sampling. In direct method-based preparation, we observed that an etching time of 6-14 min does not affect the measured densities, except for fibres <1 microm deposited by liquid filtration. Moreover, in all cases, the direct method gives higher densities than the PC indirect method because of possible fibre disappearance when using the carbon evaporator implemented in the PC indirect method. The CE membrane

  9. Comparison of direct and geodetic mass balances on a multi-annual time scale

    NASA Astrophysics Data System (ADS)

    Fischer, A.

    2011-02-01

    The geodetic mass balances of six Austrian glaciers over 19 periods between 1953 and 2006 are compared to the direct mass balances over the same periods. For two glaciers, Hintereisferner and Kesselwandferner, case studies showing possible reasons for discrepancies between the geodetic and the direct mass balance are presented. The mean annual geodetic mass balance for all periods is -0.5 m w.e. a-1, the mean annual direct mass balance -0.4 m w.e. a-1. The mean cumulative difference is -0.6 m w.e., the minimum -7.3 m w.e., and the maximum 5.6 m w.e. The accuracy of geodetic mass balance may depend on the accuracy of the DEMs, which ranges from 2 m w.e. for photogrammetric data to 0.02 m w.e. for airborne laser scanning (LiDAR) data. Basal melt, seasonal snow cover, and density changes of the surface layer also contribute up to 0.7 m w.e. to the difference between the two methods over the investigated period of 10 yr. On Hintereisferner, the fraction of area covered by snow or firn has been changing within 1953-2006. The accumulation area is not identical with the firn area, and both are not coincident with areas of volume gain. Longer periods between the acquisition of the DEMs do not necessarily result in a higher accuracy of the geodetic mass balance. Trends in the difference between the direct and the geodetic data vary from glacier to glacier and can differ systematically for specific glaciers under specific types of climate forcing. Ultimately, geodetic and direct mass balance data are complementary, and great care must be taken when attempting to combine them.

  10. Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA.

    PubMed

    Musselman, Catherine; Zhang, Qi; Al-Hashimi, Hashim; Andricioaei, Ioan

    2010-01-21

    Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations are both techniques that can be used to characterize the structural dynamics of biomolecules and their underlying time scales. Comparison of relaxation parameters obtained through each methodology allows for cross validation of techniques and for complementarity in the analysis of dynamics. Here we present a combined NMR/MD study of the dynamics of HIV-1 transactivation response (TAR) RNA. We compute relaxation constants (R(1), R(2), and NOE) and model-free parameters (S(2) and tau) from a 65 ns molecular dynamics (MD) trajectory and compare them with the respective parameters measured in a domain-elongation NMR experiment. Using the elongated domain as the frame of reference for all computed parameters allows for a direct comparison between experiment and simulation. We see good agreement for many parameters and gain further insight into the nature of the local and global dynamics of TAR, which are found to be quite complex, spanning multiple time scales. For the few cases where agreement is poor, comparison of the dynamical parameters provides insight into the limits of each technique. We suggest a frequency-matching procedure that yields an upper bound for the time scale of dynamics to which the NMR relaxation experiment is sensitive.

  11. Quantifying contingent relations from direct observation data: transitional probability comparisons versus Yule's Q.

    PubMed

    Lloyd, Blair P; Kennedy, Craig H; Yoder, Paul J

    2013-01-01

    Measuring contingencies or sequential associations may be applied to a broad range of response-stimulus, stimulus-stimulus, or response-response relations. Within behavior analysis, response-stimulus contingencies have been quantified by comparing 2 transitional probabilities and plotting them in contingency space. Within and outside behavior analysis, Yule's Q has become a recommended statistic used to quantify sequential associations between 2 events. In the current paper, we identify 2 methods of transitional probability comparisons used in the behavior-analytic literature to estimate contingencies in natural settings. We compare each of these methods to the more established Yule's Q statistic and evaluate relations between each pair of indices. Advantages and disadvantages of each method are identified, with recommendations as to which approach may be most appropriate for measuring contingencies.

  12. [Comparison of direct microscopy, culture and polymerase chain reaction methods for the diagnosis of cutaneous leishmaniasis].

    PubMed

    Ertabaklar, Hatice; Özlem Çalışkan, Serçin; Boduç, Erengül; Ertuğ, Sema

    2015-01-01

    Cutaneous leishmaniasis (CL) is an endemic disease especially in Southeastern Anatolia of Turkey and recently shows a trend for spread to other regions of the country including the Aegean region. The diagnosis of CL is based on combined evaluation of epidemiological data with the clinical symptoms and laboratory findings. Direct microscopic examination and culture methods are mainly used in the routine diagnosis of CL, while molecular methods are mainly used for research. The aim of this study was to detect the presence of Leishmania spp. in samples obtained from CL-suspected patients by using direct microscopy, culture and polymerase chain reaction (PCR) methods and to compare the results. A total of 55 patients who were admitted to Parasitology Laboratory of Adnan Menderes University Hospital, Aydin (located at Aegean region in Turkey), between 2012-2014 were included in the study. Smear preparations from the skin lesions of cases were fixed and stained with Giemsa, and the presence of amastigote forms were evaluated by direct microscopy. NNN medium was used for the cultivation of samples. Total genomic DNA of Leishmania from the samples were extracted with a commercial kit (NucleoSpin Tissue(®) Kit, Macherey-Nagel, Germany) and PCR was performed by using 13A and 13B primers to amplify the 116 base pair fragment of Leishmania spp. specific kinetoplast DNA. Amastigotes were observed in 29 (53%) of the 55 samples by direct microscopy, promastigotes were detected among 34 (62%) samples in culture, and parasite-specific amplicons were revealed in 30 (55%) samples by PCR. All assays were positive in 24 patients while in 18 patients all of the tests yielded negative results. Thirty-seven (67%) out of 55 cases were diagnosed as CL when reactivity in at least one of these three methods were considered as positive. Accordingly the positivity rates of the methods were 78.4% (29/37) for direct microscopy, 92% (34/37) for culture and 81.1% (30/37) for PCR in CL

  13. A direct time series comparison between the La Jolla and Belfast radiocarbon records

    NASA Technical Reports Server (NTRS)

    Sonett, C. P.; Suess, H. E.

    1986-01-01

    For many years it has been widely assumed that the variations in the level of atmospheric carbon-14 were due to statistical fluctuations arising from experimental error. This is understandable since the signal/noise ratio is very low and the time sequences representing the variations are strongly stochastic. Interlaboratory comparisons show that baseline variations in the absolute value of the carbon-14 concentration do exist. However, assuming linearity, the delta 14C values are independent of these. The importance of assessing the quantitive reality of the delta 14C values is based upon their expression of the interplanetary cosmic ray source function, because in the range of 100 to 1000 year periods, there appears to be no evidence that the Earth's magnetic field is the source modulating function. Therefore the modulation is either due to changes in the solar atmosphere propagated out into the solar wind, or extra-heliospheric pressure effects, but these appear to be unlikely for the periods noted here. The recent availability of the new high quality Belfast time sequence of delta 14C now permits a simple mutual assessment of the several sequences which are available. Since the La Jolla record has been a standard for many years , these two were chosen for a simple comparison. Although differences exist, the close agreement between these two sequences, one carried out on White mountain Bristlecone pines, and the other done using Irish peat bog wood, is striking. This correlation between the two strongly reinforces the statistical view that the delta 14C record is that of real interplanetary modulation of the cosmic ray source leading to the generation of atmospheric 14C.

  14. Isolation of human minisatellite loci detected by synthetic tandem repeat probes: direct comparison with cloned DNA fingerprinting probes.

    PubMed

    Armour, J A; Vergnaud, G; Crosier, M; Jeffreys, A J

    1992-08-01

    As a direct comparison with cloned 'DNA fingerprinting' probes, we present the results of screening an ordered array Charomid library for hypervariable human loci using synthetic tandem repeat (STR) probes. By recording the coordinates of positive hybridization signals, the subset of clones within the library detected by each STR probe can be defined, and directly compared with the set of clones detected by naturally occurring (cloned) DNA fingerprinting probes. The STR probes vary in the efficiency of detection of polymorphic minisatellite loci; among the more efficient probes, there is a strong overlap with the sets of clones detected by the DNA fingerprinting probes. Four new polymorphic loci were detected by one or more of the STR probes but not by any of the naturally occurring repeats. Sequence comparisons with the probe(s) used to detect the locus suggest that a relatively poor match, for example 10 out of 14 bases in a limited region of each repeat, is sufficient for the positive detection of tandem repeats in a clone in this type of library screening by hybridization. These results not only provide a detailed evaluation of the usefulness of STR probes in the isolation of highly variable loci, but also suggest strategies for the use of these multi-locus probes in screening libraries for clones from hypervariable loci.

  15. Comparison of direct and indirect pyrolysis of micro-algae Isochrysis.

    PubMed

    Wang, Xin; Zhao, Bingwei; Tang, Xiaohan; Yang, Xiaoyi

    2015-03-01

    Yield and composition of pyrolysis oil in direct and indirect pyrolysis process were investigated which indicated that pyrolysis of defatted microalgae provided a potential way to convert protein and carbohydrate to biofuels. Defatted microalgae pyrolysis with lipid extraction has higher total oil yield than only microalgae direct pyrolysis. There was an increase for N-heterocyclic compounds and phenols and a decrease for hydrocarbons in defatted microalgae pyrolysis oil. There is an apparent decrease from C12 to C16 and nearly no carbon distribution from C17 to C22 for defatted microalgae pyrolysis. Based on composition of pyrolysis feedstock, pyrolysis oil yields were simulated by Compounds Biofuel Model and their accuracy was less than ±4.4%. Considering total oil yield and characteristics, microalgae pyrolysis after lipid extraction process is a promising way for microalgae utilization.

  16. Testing reciprocity in social interactions: a comparison between the directional consistency and skew-symmetry statistics.

    PubMed

    Leiva, David; Solanas, Antonio; Salafranca, Lluís

    2008-05-01

    In the present article, we focus on two indices that quantify directionality and skew-symmetrical patterns in social interactions as measures of social reciprocity: the directional consistency (DC) and skew-symmetry indices. Although both indices enable researchers to describe social groups, most studies require statistical inferential tests. The main aims of the present study are first, to propose an overall statistical technique for testing null hypotheses regarding social reciprocity in behavioral studies, using the DC and skew-symmetry statistics (Phi) at group level; and second, to compare both statistics in order to allow researchers to choose the optimal measure depending on the conditions. In order to allow researchers to make statistical decisions, statistical significance for both statistics has been estimated by means of a Monte Carlo simulation. Furthermore, this study will enable researchers to choose the optimal observational conditions for carrying out their research, since the power of the statistical tests has been estimated.

  17. A comparison of RNA with DNA in template-directed synthesis

    NASA Technical Reports Server (NTRS)

    Zielinski, M.; Kozlov, I. A.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    2000-01-01

    Nonenzymatic template-directed copying of RNA sequences rich in cytidylic acid using nucleoside 5'-(2-methylimidazol-1-yl phosphates) as substrates is substantially more efficient than the copying of corresponding DNA sequences. However, many sequences cannot be copied, and the prospect of replication in this system is remote, even for RNA. Surprisingly, wobble-pairing leads to much more efficient incorporation of G opposite U on RNA templates than of G opposite T on DNA templates.

  18. Feedback in formative OSCEs: comparison between direct observation and video-based formats

    PubMed Central

    Junod Perron, Noëlle; Louis-Simonet, Martine; Cerutti, Bernard; Pfarrwaller, Eva; Sommer, Johanna; Nendaz, Mathieu

    2016-01-01

    Introduction Medical students at the Faculty of Medicine, University of Geneva, Switzerland, have the opportunity to practice clinical skills with simulated patients during formative sessions in preparation for clerkships. These sessions are given in two formats: 1) direct observation of an encounter followed by verbal feedback (direct feedback) and 2) subsequent review of the videotaped encounter by both student and supervisor (video-based feedback). The aim of the study was to evaluate whether content and process of feedback differed between both formats. Methods In 2013, all second- and third-year medical students and clinical supervisors involved in formative sessions were asked to take part in the study. A sample of audiotaped feedback sessions involving supervisors who gave feedback in both formats were analyzed (content and process of the feedback) using a 21-item feedback scale. Results Forty-eight audiotaped feedback sessions involving 12 supervisors were analyzed (2 direct and 2 video-based sessions per supervisor). When adjusted for the length of feedback, there were significant differences in terms of content and process between both formats; the number of communication skills and clinical reasoning items addressed were higher in the video-based format (11.29 vs. 7.71, p=0.002 and 3.71 vs. 2.04, p=0.010, respectively). Supervisors engaged students more actively during the video-based sessions than during direct feedback sessions (self-assessment: 4.00 vs. 3.17, p=0.007; active problem-solving: 3.92 vs. 3.42, p=0.009). Students made similar observations and tended to consider that the video feedback was more useful for improving some clinical skills. Conclusion Video-based feedback facilitates discussion of clinical reasoning, communication, and professionalism issues while at the same time actively engaging students. Different time and conceptual frameworks may explain observed differences. The choice of feedback format should depend on the educational

  19. Feedback in formative OSCEs: comparison between direct observation and video-based formats.

    PubMed

    Perron, Noëlle Junod; Louis-Simonet, Martine; Cerutti, Bernard; Pfarrwaller, Eva; Sommer, Johanna; Nendaz, Mathieu

    2016-01-01

    Introduction Medical students at the Faculty of Medicine, University of Geneva, Switzerland, have the opportunity to practice clinical skills with simulated patients during formative sessions in preparation for clerkships. These sessions are given in two formats: 1) direct observation of an encounter followed by verbal feedback (direct feedback) and 2) subsequent review of the videotaped encounter by both student and supervisor (video-based feedback). The aim of the study was to evaluate whether content and process of feedback differed between both formats. Methods In 2013, all second- and third-year medical students and clinical supervisors involved in formative sessions were asked to take part in the study. A sample of audiotaped feedback sessions involving supervisors who gave feedback in both formats were analyzed (content and process of the feedback) using a 21-item feedback scale. Results Forty-eight audiotaped feedback sessions involving 12 supervisors were analyzed (2 direct and 2 video-based sessions per supervisor). When adjusted for the length of feedback, there were significant differences in terms of content and process between both formats; the number of communication skills and clinical reasoning items addressed were higher in the video-based format (11.29 vs. 7.71, p=0.002 and 3.71 vs. 2.04, p=0.010, respectively). Supervisors engaged students more actively during the video-based sessions than during direct feedback sessions (self-assessment: 4.00 vs. 3.17, p=0.007; active problem-solving: 3.92 vs. 3.42, p=0.009). Students made similar observations and tended to consider that the video feedback was more useful for improving some clinical skills. Conclusion Video-based feedback facilitates discussion of clinical reasoning, communication, and professionalism issues while at the same time actively engaging students. Different time and conceptual frameworks may explain observed differences. The choice of feedback format should depend on the educational

  20. a Systematic Comparison of Direct and Image-Based Georeferencing in Challenging Urban Areas

    NASA Astrophysics Data System (ADS)

    Cavegn, S.; Nebiker, S.; Haala, N.

    2016-06-01

    Image-based mobile mapping systems enable an efficient acquisition of georeferenced image sequences, which can be used for geo-data capture in subsequent steps. In order to provide accurate measurements in a given reference frame while e.g. aiming at high fidelity 3D urban models, high quality georeferencing of the captured multi-view image sequences is required. Moreover, sub-pixel accurate orientations of these highly redundant image sequences are needed in order to optimally perform steps like dense multi-image matching as a prerequisite for 3D point cloud and mesh generation. While direct georeferencing of image-based mobile mapping data performs well in open areas, poor GNSS coverage in urban canyons aggravates fulfilling these high accuracy requirements, even with high-grade inertial navigation equipment. Hence, we conducted comprehensive investigations aiming at assessing the quality of directly georeferenced sensor orientations as well as the expected improvement by image-based georeferencing in a challenging urban environment. Our study repeatedly delivered mean trajectory deviations of up to 80 cm. By performing image-based georeferencing using bundle adjustment for a limited set of cameras and a limited number of ground control points, mean check point residuals could be lowered from approx. 40 cm to 4 cm. Furthermore, we showed that largely automated image-based georeferencing is capable of detecting and compensating discontinuities in directly georeferenced trajectories.

  1. Comparison of stopped Cox regression with direct methods such as pseudo-values and binomial regression.

    PubMed

    van Houwelingen, Hans C; Putter, Hein

    2015-04-01

    By far the most popular model to obtain survival predictions for individual patients is the Cox model. The Cox model does not make any assumptions on the underlying hazard, but it relies heavily on the proportional hazards assumption. The most common ways to circumvent this robustness problem are 1) to categorize patients based on their prognostic risk score and to base predictions on Kaplan-Meier curves for the risk categories, or 2) to include interactions with the covariates and suitable functions of time. Robust estimators of the t(0)-year survival probabilities can also be obtained from a "stopped Cox" regression model, in which all observations are administratively censored at t(0). Other recent approaches to solve this robustness problem, originally proposed in the context of competing risks, are pseudo-values and direct binomial regression, based on unbiased estimating equations. In this paper stopped Cox regression is compared with these direct approaches. This is done by means of a simulation study to assess the biases of the different approaches and an analysis of breast cancer data to get some feeling for the performance in practice. The tentative conclusion is that stopped Cox and direct models agree well if the follow-up is not too long. There are larger differences for long-term follow-up data. There stopped Cox might be more efficient, but less robust.

  2. A comparison of directed search target detection versus in-scene target detection in Worldview-2 datasets

    NASA Astrophysics Data System (ADS)

    Grossman, S.

    2015-05-01

    Since the events of September 11, 2001, the intelligence focus has moved from large order-of-battle targets to small targets of opportunity. Additionally, the business community has discovered the use of remotely sensed data to anticipate demand and derive data on their competition. This requires the finer spectral and spatial fidelity now available to recognize those targets. This work hypothesizes that directed searches using calibrated data perform at least as well as inscene manually intensive target detection searches. It uses calibrated Worldview-2 multispectral images with NEF generated signatures and standard detection algorithms to compare bespoke directed search capabilities against ENVI™ in-scene search capabilities. Multiple execution runs are performed at increasing thresholds to generate detection rates. These rates are plotted and statistically analyzed. While individual head-to-head comparison results vary, 88% of the directed searches performed at least as well as in-scene searches with 50% clearly outperforming in-scene methods. The results strongly support the premise that directed searches perform at least as well as comparable in-scene searches.

  3. [Comparison of direct microscopy, culture, ELISA and molecular methods for diagnosis of Entamoeba histolytica].

    PubMed

    Tüzemen, Nazmiye Ulkü; Doğan, Nihal

    2014-01-01

    Amebiasis, a parasitic infection caused by Entamoeba histolytica, is one of the most common parasitic infections worldwide. Since it is still an important public health problem in developing countries, rapid differential diagnosis of amebiasis is crucial in terms of treatment. The most frequently used method for laboratory diagnosis is direct microscopy, however more reliable and specific methods are needed in order to differentiate the apathogenic Entamoeba dispar under the microscope. This study was conducted to compare the results of different methods namely, direct microscopy, culture, ELISA and PCR for the detection of E.histolytica in stool samples and to evaluate the performances of those methods. A total of 1049 stool samples collected from pediatric and adult patients who were admitted to hospital with diarrhea complaint between January 2011-March 2013, and randomly selected samples from primary school children, were included in the study. Direct microscopic examination was performed by native-lugol, physiological saline, modified formol-ethyl acetate sedimentation and trichrome staining methods. The stool samples were also inoculated into TYI-S-33 media for axenic cultivation of amoeba. The presence of amebic antigens in the samples were screened by a commercial ELISA kit (TechLab, E.histolytica II, USA). For the molecular diagnosis, a multiplex tandem real-time PCR (MT-PCR) kit (AusDiagnostics Pty Ltd, Australia) was used, after the extraction of DNAs with QIAamp DNA Stool Mini Kit (Qiagen, USA). A total of 354 samples which could be evaluated by all of the methods, were included in the study. Of the 354 stool samples, 84 (23.7%) were found E.histolytica/E.dispar positive by direct microscopy, 61 (17.2%) by trichrome staining, 46 (12.9%) by culture, 31 (8.7%) by ELISA and 9 (2.5%) by MT-PCR. Of direct microscopy positive samples 54.7% (46/84) were also positive with trichrome staining, 39.3% (33/84) with culture, 15.5% (13/84) with ELISA and 7.1% (6

  4. Sport Education and Direct Instruction Units: Comparison of Student Knowledge Development in Athletics

    PubMed Central

    Pereira, José; Araújo, Rui; Farias, Cláudio; Bessa, Cristiana; Mesquita, Isabel

    2016-01-01

    This study conducted a comparative analysis of students’ knowledge development on athletics in Sport Education and in a Direct Instruction unit taking into account sex and initial skill level. The participants were an experienced Physical Education teacher and two sixth-grade classes totaling 47 students (25 boys and 22 girls). Each class was randomly placed in either Sport Education or Direct Instruction classes and participated in 20, 45-minutes lessons focused on shot put, hurdles and triple jump. Knowledge on athletics was assessed through a 25-items written and video-based test. The inter-group differences and improvements across time in the knowledge test were analyzed through the Mann-Whitney and Wilcoxon tests, respectively. There were significant knowledge improvements in both instructional approaches irrespective of students’ gender and skill level. In Direct Instruction, the type of task organization, the high rates of repetition of movement patterns and feedback by the teacher were beneficial to student learning. In Sport Education, the autonomy granted to students in the control of the pace of task transitions by making on-going judgments on achievement of performance criteria, implicated students affectively and cognitively with the learning content. It was further supported that several models and teaching strategies should be taken into consideration when teaching Physical Education. Different approaches should be perceived as alternatives and teachers should retain the best in each according with the moment in the unit, student developmental stage, and the specific learning objectives in the task. Key points The results in this study showed that regardless of students’ sex, both DI and SE were efficient in the promotion of improvements in students’ content knowledge of athletics. Both boys and girls improved from the pre-test to the post-test in SE and DI. SE was particularly beneficial to lower skill-level. On the contrary, in the DI unit

  5. A comparison of microwave versus direct solar heating for lunar brick production

    NASA Technical Reports Server (NTRS)

    Yankee, S. J.; Strenski, D. G.; Pletka, B. J.; Patil, D. S.; Mutsuddy, B. C.

    1990-01-01

    Two processing techniques considered suitable for producing bricks from lunar regolith are examined: direct solar heating and microwave heating. An analysis was performed to compare the two processes in terms of the amount of power and time required to fabricate bricks of various sizes. Microwave heating was shown to be significantly faster than solar heating for rapid production of realistic-size bricks. However, the relative simplicity of the solar collector(s) used for the solar furnace compared to the equipment necessary for microwave generation may present an economic tradeoff.

  6. A direct interaction approximation treatment of high Rayleigh number convective turbulence and comparison with experiment

    NASA Technical Reports Server (NTRS)

    Hartke, Gregory J.; Canuto, V. M.; Dannevik, William P.

    1988-01-01

    A method is proposed for treating steady-state, thermally driven convection using the full direct interaction approximation to treat the nonlinear energy transfer and a prescribed instability function to model the eenrgy input. The instability function used is the growth rate of the mechanism generating the turbulence. This methodology can be easily generalized and applied to other driving mechanisms. The 1/3 power law form of the N vs. R relation for water is duplicated here and the coefficient is computed, using a two-point closure, to be less than about 0.08.

  7. Directionally Solidified Aluminum - 7 wt% Silicon Alloys: Comparison of Earth and International Space Station Processed Samples

    NASA Technical Reports Server (NTRS)

    Grugel, Richard N,; Tewari, Surendra; Rajamure, R. S.; Erdman, Robert; Poirier, David

    2012-01-01

    Primary dendrite arm spacings of Al-7 wt% Si alloy directionally solidified in low gravity environment of space (MICAST-6 and MICAST-7: Thermal gradient approx. 19 to 26 K/cm, Growth speeds varying from 5 to 50 microns/s show good agreement with the Hunt-Lu model. Primary dendrite trunk diameters of the ISS processed samples show a good fit with a simple analytical model based on Kirkwood s approach, proposed here. Natural convection, a) decreases primary dendrite arm spacing. b) appears to increase primary dendrite trunk diameter.

  8. Direct comparison of statistical damage frequency method and raster scan procedure

    NASA Astrophysics Data System (ADS)

    Batavičiūtė, G.; Ščiuka, M.; Plerpaitė, V.; Melninkaitis, A.

    2015-11-01

    Presented study addresses the nano-size defects acting as damage precursors in nanosecond laser pulse irradiation regime. Defects embedded within the surface of glass are investigated in terms of defect ensembles. Damage frequency method and raster scan procedure are directly compared on the set of two samples: uncoated fused silica substrates and SiO2 monolayer films. The extracted defect ensembles appear to be different from each other. The limitations of compared methods such as pulse-to-pulse variation of laser intensity and sample contamination induced by laser ablation were identified as the main causes of observed differences.

  9. First direct comparison of high and low ionization line kinematics in active galactic nuclei

    NASA Technical Reports Server (NTRS)

    Sulentic, J. W.; Marziani, P.; Dultzin-Hacyan, D.; Calvani, M.; Moles, M.

    1995-01-01

    We present first results of a comparison of emission line shift properties for the high (HILs) and low (LILs) ionization lines in 43 low-reshift quasars. We identify a core sample of C IV lambda 1549 and hydrogen beta profiles with a wide distribution of red- and blueshifts (less than or equal to +/- 1000 km/sec). We also identify two tails in this distribution: one with large hydrogen beta redshifts (greater than or equal to 2000 km/sec) and another with large C IV blueshifts (greater than or equal to 1500 km/sec). The tails are mutually exclusive. All objects with extreme hydrogen beta redshift are radio loud, and all objects with extreme C IV blueshift are radio quiet. The core samples of smaller shifts can be most simply divided into: (1) hydrogen beta - a redshifted radio-loud population (related to the tail) and a radio-quiet population with mean shift near zero, and (2) C IV - a blueshifted radio-quiet population (related to the tail) and a radio-loud population with mean shift near zero. The results suggest fundamentally different kinematics for the HILs and LILs. They also suggest very different kinematics for radio-loud and radio-quiet active galactic nuclei. They also favor a predominance of radial motion in a large fraction of the sample.

  10. A performance comparison of different graphics processing units running direct N-body simulations

    NASA Astrophysics Data System (ADS)

    Capuzzo-Dolcetta, R.; Spera, M.

    2013-11-01

    Hybrid computational architectures based on the joint power of Central Processing Units (CPUs) and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering, physics, etc. In this paper we present a performance comparison of various GPUs available on market when applied to the numerical integration of the classic, gravitational, N-body problem. To do this, we developed an OpenCL version of the parallel code HiGPUs used for these tests, because this portable version is the only apt to work on GPUs of different makes. The main general result is that we confirm the reliability, speed and cheapness of GPUs when applied to the examined kind of problems (i.e. when the forces to evaluate are dependent on the mutual distances, as it happens in gravitational physics and molecular dynamics). More specifically, we find that also the cheap GPUs built to be employed just for gaming applications are very performant in terms of computing speed also in scientific applications and, although with some limitations concerning on-board memory, can be a good choice to build a cheap and efficient machine for scientific applications.

  11. Functional comparison of annexin V analogues labeled indirectly and directly with iodine-124.

    PubMed

    Dekker, Bronwen; Keen, Heather; Shaw, David; Disley, Lynn; Hastings, David; Hadfield, John; Reader, Andrew; Allan, Donald; Julyan, Peter; Watson, Alastair; Zweit, Jamal

    2005-05-01

    We are interested in imaging cell death in vivo using annexin V radiolabeled with (124)I. In this study, [(124)I]4IB-annexin V and [(124)I]4IB-ovalbumin were made using [(124)I]N-hydroxysuccinimidyl-4-iodobenzoate prepared by iododestannylation of N-hydroxysuccinimidyl-4-(tributylstannyl)benzoate. [(124)I]4IB-annexin V binds to phosphatidylserine-coated microtiter plates and apoptotic Jurkat cells and accumulates in hepatic apoptotic lesions in mice treated with anti-Fas antibody, while [(124)I]4IB-ovalbumin does not. In comparison with (124)I-annexin V, [(124)I]4IB-annexin V has a higher rate of binding to phosphatidylserine in vitro, a higher kidney and urine uptake, a lower thyroid and stomach content uptake, greater plasma stability and a lower rate of plasma clearance. Binding of radioactivity to apoptotic cells relative to normal cells in vitro and in vivo appears to be lower for [(124)I]4IB-annexin V than for (124)I-annexin V.

  12. Direct imaging with a dense aperture masking in comparison with a telescope or a hypertelelescope

    NASA Astrophysics Data System (ADS)

    Patru, Fabien; Antichi, Jacopo; Girard, Julien

    2011-10-01

    Dense Aperture Masking (DAM) is a new interferometric technique allowing high-angular resolution over a narrow field of view (FOV) imaged by the present class of mono-pupil telescopes equipped with adaptive optics (AO). DAM is realized by a suited afocal double lenslet array (BIGRE), remapping the entrance aperture (telescope pupil) into coherent sub-apertures (sub-pupils), and adopted as sub-pupils spatial filter and re-imager.We focus our attention on the point spread function (PSF) properties of DAM, highlighting those related to spatial sampling and filtering of the frequency coverage of the entrance pupil.We stress why the high spatial frequency sampling of the pupil and the low spatial frequency filtering of the sub-pupils are consistent with both a mono-pupil (telescope) and an array of sub-pupils (hypertelescope). We explain how DAM provides high Strehl and high-angular resolution images, first by filtering the low frequencies, which in turn are not so well corrected with a standard AO, second by preserving an object-image convolution relation over a narrow FOV. Finally, we make a comparison with the imaging properties of a telescope and a hypertelescope with the aim to show the complementary of DAM with other techniques adopted in high-contrast imaging.

  13. Comparison of direct-plating and enrichment methods for isolation of Vibrio cholerae from diarrhea patients.

    PubMed Central

    Lesmana, M; Richie, E; Subekti, D; Simanjuntak, C; Walz, S E

    1997-01-01

    A direct-plating method on thiosulfate citrate bile salts sucrose agar (DIR-TCBS) in conjunction with enrichment in alkaline peptone water (APW) incubated for both 6 h and 24 h followed by subculture onto TCBS (APW6h-TCBS and APW24h-TCBS, respectively) was performed on 16,034 rectal swab samples for isolating Vibrio cholerae. A total of 2,932 (18.3%) rectal swab samples were positive for V. cholerae O1 biotype El Tor, with the Ogawa serotype constituting 99.2% of the isolates. There were no significant differences in V. cholerae O1 isolation rates between the three culture systems nor between the combinations of any two systems. However, direct plating plus enrichment demonstrated a significantly higher V. cholerae O1 isolation rate than DIR-TCBS alone (P < 0.02). Conversely, enrichment procedure, alone or in combination with DIR-TCBS, yielded significantly more (P < 0.0001) V. cholerae non-O1 isolates than DIR-TCBS alone. The length of incubation time of the enrichment broth, 6 h, offers no significant advantages over 24 h for the isolation of V. cholerae O1 and non-O1. A 24-h enrichment broth incubation period has the practical advantage of being easy to integrate into a normal laboratory workday, whereas 6-h broth enrichment, although more commonly recommended, requires that arrangements be made for after-hours subculture. PMID:9196208

  14. A Comparison of Three Second-generation Swirl-Venturi Lean Direct Injection Combustor Concepts

    NASA Technical Reports Server (NTRS)

    Tacina, Kathleen M.; Podboy, Derek P.; He, Zhuohui Joe; Lee, Phil; Dam, Bidhan; Mongia, Hukam

    2016-01-01

    Three variations of a low emissions aircraft gas turbine engine combustion concept were developed and tested. The concept is a second generation swirl-venturi lean direct injection (SV-LDI) concept. LDI is a lean-burn combustion concept in which the fuel is injected directly into the flame zone. All three variations were based on the baseline 9- point SV-LDI configuration reported previously. The three second generation SV-LDI variations are called the 5-recess configuration, the flat dome configuration, and the 9- recess configuration. These three configurations were tested in a NASA Glenn Research Center medium pressure flametube. All three second generation variations had better low power operability than the baseline 9-point configuration. All three configurations had low NO(sub x) emissions, with the 5-recess configuration generally having slightly lower NO(x) than the flat dome or 9-recess configurations. Due to the limitations of the flametube that prevented testing at pressures above 20 atm, correlation equations were developed for the at dome and 9-recess configurations so that the landing-takeoff NO(sub x) emissions could be estimated. The flat dome and 9-recess landing-takeoff NO(x) emissions are estimated to be 81-88% below the CAEP/6 standards, exceeding the project goal of 75% reduction.

  15. Comparison of commercial uv lamps for radical oxidation and direct photolysis in water

    SciTech Connect

    Haag, W; Wang, F T

    1999-08-01

    Lawrence Livermore National Laboratory (LLNL) is charged with developing methods for treating contaminated sites and destroying waste organic compounds that are currently being accumulated, including Trimsol (machining oil), trichloroethene (ICE), tributyl phosphate (TBP), kerosene, and many other organics. These organics are sometimes present mixed with radioactive waste, and in these cases it is important to destroy the organics in such a way as to not increase the total volume of the waste and to ensure that no radioactivity is released in the process. Among the most promising techniques for treating aqueous mixed wastes are ultraviolet light (UV) oxidation and the molten salt process, as opposed to methods like incineration or supercritical water oxidation that might lead to air emissions of radioactivity if not very carefully controlled. The purpose of the present study was to compare the energy efficiency of various commercial UV lamp systems designed for photooxidation. Two type of tests were conducted: (1) direct photolysis of a chlorinated compound and (2) photolysis of hydrogen peroxide, which is an additive often used to photooxidize compounds that are not amenable to direct photolysis. The results should allow LLNL to select the most cost-effective system for treating wastes by UV- enhanced radical oxidation processes.

  16. A comparison of bond strength between direct- and indirect-bonding methods.

    PubMed

    Linn, Brandon James; Berzins, David W; Dhuru, Virendra B; Bradley, Thomas Gerard

    2006-03-01

    The purpose of this study was to evaluate and compare the shear bond strength and the sites of bond failure for brackets bonded to teeth, using two indirect-bonding material protocols and a direct-bonding technique. Sixty extracted human premolars were collected and randomly divided into three groups. The direct-bonded group (group 1) used a light-cured adhesive and primer (Transbond XT). One indirect-bonded group (group 2) consisted of a chemical-cured primer (Sondhi Rapid Set) and light-cured adhesive (Transbond XT), whereas the other group (group 3) used a light-cured primer (Orthosolo) and adhesive (Enlight LV). Forty hours after bonding, the samples were debonded. Mean shear bond strengths were 16.27, 13.83, and 14.76 MPa for groups 1, 2, and 3, respectively. A one-way analysis of variance showed no significant difference in mean bond strength between groups (P = .21). Furthermore, a Weibull analysis showed all three groups tested provided over a 90% survival rate at normal masticatory and orthodontic force levels. For each tooth, an Adhesive Remnant Index (ARI) score was determined. Group 2 was found to have a significantly lower ARI score (P < .05) compared with groups 1 and 3. In addition, Pearson correlation coefficients indicated no strong correlation between bond strength and ARI score within or across all groups.

  17. Phenotypic and Genetic Characterization of Lactococcus garvieae Isolated in Spain from Lactococcosis Outbreaks and Comparison with Isolates of Other Countries and Sources

    PubMed Central

    Vela, A. I.; Vázquez, J.; Gibello, A.; Blanco, M. M.; Moreno, M. A.; Liébana, P.; Albendea, C.; Alcalá, B.; Mendez, A.; Domínguez, L.; Fernández-Garayzábal, J. F.

    2000-01-01

    The phenotypic and genetic analysis results for 84 isolates of Lactococcus garvieae (including 62 strains from trout with lactococcosis from four different countries, 7 strains from cows and water buffalos with subclinical mastitis, 3 from water, and 10 from human clinical samples) are presented. There was great phenotypic heterogeneity (13 different biotypes) based on the acidification of saccharose, tagatose, mannitol, and cyclodextrin and the presence of the enzymes pyroglutamic acid arylamidase and N-acetyl-β-glucosaminidase. L. garvieae also exhibited high genetic diversity by pulsed-field gel electrophoresis (PFGE), with 19 different pulsotypes among the isolates of L. garvieae studied. Only epidemiologically related strains, like the Spanish and Italian fish isolates and the cow and water buffalo isolates, displayed a close genetic relationship by PFGE, while the strains isolated from sporadic clinical cases, like the human isolates, were genetically unrelated. Overall, a general correlation between phenotypic and genetic data was observed. Epidemiological analysis of biotype and PFGE results indicated that the trout lactococcosis outbreaks in Spain and Portugal and those in France and Italy were produced by genetically unrelated clones. In Spain, two different clones were detected; the outbreaks diagnosed from 1995 onward were produced by a clone (biotype 2, pulsotype A1) which, although genetically related, was different from the one that was responsible for the outbreaks studied between 1991 and 1994 (biotype 1, pulsotype B). The Portuguese isolate had a biochemical profile identical to that of the Spanish strain isolated from 1995 onward and is also genetically closely related to this strain (pulsotype A2). There was a close relationship between the two pulsotypes (E and F) found in the Italian isolates. The French isolate (biotype 3, pulsotype D) was not genetically related to any other L. garvieae fish isolate. These results suggest the existence of

  18. Direct comparison of amphipod sensitivities to dredged sediments from Spanish ports.

    PubMed

    Casado-Martinez, M C; Forja, J M; DelValls, T A

    2007-06-01

    The sensitivity of the benthic amphipod species Ampelisca brevicornis and Corophium volutator to dredged sediments was compared through simultaneous testing on the standard 10 days sediment toxicity test. The results of mortality obtained for 22 harbor sediments sampled at several Spanish ports were studied together with the physico-chemical characteristics of the samples to obtain the incidence of toxicity in terms of dredged material categories and to identify possible differences in the amphipod mortality results when using one or another test species. The results showed a similar incidence of toxicity for medium-high and highly contaminated sediments for both amphipod species, similar to that obtained through the comparison of the chemical concentrations measured in sediments with the single limit values used in Spain for dredged material characterization and management. On the contrary, C. volutator presented a higher mortality and a higher incidence of toxicity when exposed to low and medium-low contaminated sediments, which may have been caused by the lower sensitivity of A. brevicornis when exposed to sediments from its natural environment. When compared to other amphipod species used for whole sediment toxicity assessment, both amphipod species used in this study reported slightly higher sensitivities although these differences could have been associated to the different set of chemical compounds considered when characterizing the sediment samples. In this sense, the amphipod mortality results were better predicted through the use of mean quotients than just by comparing the measured chemical concentrations with the single limit values used in Spain, which indicates that the toxic response of both species was caused by the cocktail of contaminants present in the sediments. Finally, the correlation analysis identified a higher association between A. brevicornis mortality and the metallic contaminants while C. volutator was more correlated with the organic

  19. The boundary currents east and north of Madagascar: 2. Direct measurements and model comparisons

    NASA Astrophysics Data System (ADS)

    Schott, Friedrich; Fieux, MichèLe; Kindle, John; Swallow, John; Zantopp, Rainer

    1988-05-01

    Moored current measurements of 11-month duration were carried out in the boundary currents east of Madagascar, near 12°S at Cape Amber where the mean current flows northwestward and near 23°S where the mean current flows approximately southward. Transports derived from the moored current measurements in the depth range 150-1100 m compare reasonably well with those derived from ship sections by Swallow et al. (this issue). At 12°S, very energetic boundary current transport variations occur in the 40- to 55-day-period band, contributing about 40% to the total transport variance, while at 23°S the 40- to 55-day-period band fluctuations contribute only 15% to the total transport variance. The fluctuations near 12°S do not seem to be caused by local wind forcing, which does not show an energy peak in this period band. A significant annual cycle cannot be detected in the moored current and transport time series despite significant variation of wind forcing over the subtropical Indian Ocean. A comparison of the observations is carried out with two different numerical Indian Ocean models, both forced by the seasonally varying winds of Hellerman and Rosenstein (1983). A reduced-gravity model gives mean boundary current transports which compare well with the observations and also shows a negligible seasonal cycle. The multilayer Geophysical Fluid Dynamics Laboratory model also shows a small seasonal cycle. The observational evidence from the western subtropical Indian Ocean appears to be similar to that from the subtropical North Atlantic east of the Bahamas-Antilles arc where also no significant seasonal boundary current response was detected, despite large annual variation of wind forcing over the ocean. The two observational situations and numerical model results for both oceans are compared.

  20. Impression techniques for multiple implants: a photoelastic analysis. Part I: comparison of three direct methods.

    PubMed

    Lopes-Júnior, Itamar; de Lima Lucas, Barbara; Gomide, Henner Alberto; Gomes, Vanderlei Luiz

    2013-10-01

    The purpose of this article was to compare through photoelastic analysis the stress distribution in 3 direct transfer techniques for implants with splinting. Three photoelastic resin blocks were made with 2 implants placed parallel to each other and 2 square transfer copings splinted. Both transfers were splinted with acrylic resin chemically activated in 3 different techniques: metallic sticks (T1), prefabricated acrylic bars (T2), or dental floss (T3). A circular polariscope was used, and the distortion energy (E) was calculated in 4 periods: 20 minutes and 3, 24, and 36 hours. Statistically significant differences were found among the 3 techniques (P < .05). The dental floss presented the greatest distortion energy values (T3 = 0.469 Kgf/mm(2)) and the metallic sticks the lowest values (T1 = 0.0 Kgf/mm(2)). Thus, the metallic sticks technique (T1) appears to be the most accurate protocol to be used for implant-supported prosthesis with multiple abutments.

  1. COMPARISON OF DIRECT PLATING MEDIA FOR THE ISOLATION AND ENUMERATION OF ENTEROCOCCI IN CERTAIN FROZEN FOODS.

    PubMed

    BURKWALL, M K; HARTMAN, P A

    1964-01-01

    A total of 15 agar media were examined for their yield, selectivity, readability, and simplicity of preparation and use. A thallium medium of Barnes was selected as the better of the high yield-fair selectivity type of medium and an azide-citrate medium of Reinbold appeared to be the better of the low yield-high selectivity type of medium. Sodium carbonate (optimal concentration, 0.20%) was found to increase recovery substantially when added to certain media, especially in the presence of 0.05% Tween 80. When these two ingredients were incorporated into a medium modified after Slanetz and Bartley, the resultant medium was superior to other media for the isolation and enumeration of enterococci in certain frozen foods, such as peas and hamburger, by the direct plating method.

  2. Comparison of Direct Eulerian Godunov and Lagrange Plus Remap, Artificial Viscosity Schemes

    SciTech Connect

    Pember, R B; Anderson, R W

    2001-03-30

    The authors compare two algorithms for solving the equations of unsteady inviscid compressible flow in an Eulerian frame: a staggered grid, Lagrange plus remap artificial viscosity scheme and a cell-centered, direct Eulerian higher-order Godunov scheme. They use the two methods to compute solutions to a number of one- and two-dimensional problems. The results show the accuracy of the two schemes to be generally equivalent. In a 1984 survey paper by Woodward and Colella, the Lagrange plus remap approach did not compare favorably with the higher-order Godunov methodology. They examine, therefore, how certain features of the staggered grid scheme considered here contribute to its improved accuracy. The critical features are shown to be the use of a monotonic artificial viscosity in the Lagrange step and, in the remap step, the use of a corner transport upwind scheme with van Leer limiters in conjunction with separate advection of internal and kinetic energies.

  3. A Comparison Between Structure from Motion and Direct Survey Methodologies on the Warwick

    NASA Astrophysics Data System (ADS)

    Bojakowski, Piotr; Bojakowski, Katie Custer; Naughton, Perry

    2015-08-01

    Structure from Motion, the process of turning two-dimensional digital images into a three-dimensional digital model, is recognized as an emerging method in archaeological research. While some of the previous studies of Structure from Motion applied to underwater projects showed promise as an information rich and affordable survey method, the issue of accuracy remains. This study examined the efficacy of this new technology as a post-processing analytical tool on the early seventeenth-century shipwreck site, Warwick, from Bermuda. Using original digital images from the archaeological excavations, Structure from Motion was tested for suitability and accuracy, and the results compared against the Direct Survey Method. The outcome was an interdisciplinary effort that allowed for a better understanding of the process and the resulting limitations of Structure from Motion for underwater surveys and excavations.

  4. Comparison of direct, rehalogenating, and solvent bleaching processes with BB-640 plates

    NASA Astrophysics Data System (ADS)

    Ulibarrena, Manuel; Mendez, Maria J.; Carretero, Luis; Madrigal, Roque; Fimia, Antonio

    2002-07-01

    Bleaching is one of the key processes in the production of phase holograms with fine grain silver halide emulsions. This step was widely studied for discontinued Kodak, Agfa, and Ilford emulsions, and most of those results have been optimized with small changes for presently available holographic emulsions. A study of the different bleaching techniques with BB-640 holographic emulsions is presented. Some interesting new features found are the high-diffraction efficiencies achieved with direct rehalogenating bleaching and with reversal bleaching, with higher values and better sensitivities than those of classical fixation-free rehalogenating bleaching. In particular, we have found that the highest diffraction efficiency and the lowest scattering is obtained with AAC developer and reversal bleach R-9, with diffraction efficiency values of 82%.

  5. Accurate Clock Period Comparison for PLL Using Phase-Shift Direction Detector

    NASA Astrophysics Data System (ADS)

    Makihara, Yukinobu; Ikebe, Masayuki; Motohisa, Junichi; Sano, Eiichi

    We proposed a new architecture for a phase-locked loop (PLL) obtained by comparing clock periods. We evaluated the use of a clock-period comparator (CPC) for the digitally controlled PLL we propose, where only the frequency should be locked. However, frequency control with the CPC resulted in the phase being locked. Thus, phase-lock operation was also achieved. The theoretical analysis of the phase-lock mechanism was confirmed through system simulations. We discussed about dead-zone problem caused by a time delay of circuits. We evaluated phase-shift direction detector to solve the dead zone problem. We designed the element blocks of the new PLL using a 0.25-μm CMOS process. We confirmed phase-lock operation through SPICE simulations of the MOSFET level. Moreover, we manufactured a trial circuit for the new PLL. We also confirmed phase-lock operation in the proposed PLL through measurements.

  6. Comparison of transcatheter laser and direct-current shock ablation of endocardium near tricuspid anulus

    NASA Astrophysics Data System (ADS)

    Zhang, Yu-Zhen; Wang, Shi-Wen; Li, Junheng

    1993-03-01

    Forty to eighty percent of the patients with accessory pathways (APs) manifest themselves by tachyarrhythmias. Many of these patients needed either life-long medical therapy or surgery. In order to avoid the discomfort and expenses in surgical procedures, closed chest percutaneous catheter ablation of APs became a potentially desirable therapeutic approach. Many investigations indicated that ablation of right APs by transcatheter direct current (dc) shock could cause life-threatening arrhythmias, right coronary arterical (RCA) spasm, etc. With the development of transcatheter laser technique, it has been used in drug-incurable arrhythmias. The results show that laser ablation is much safer than surgery and electric shock therapy. The purpose of this study is to explore the effectiveness, advantages, and complications with transcatheter Nd:YAG laser and dc shock in the ablation of right atrioventricular accessory pathways in the atrium near the tricuspid annulus (TA) in 20 dogs.

  7. Performance analysis and comparison of a minimum interconnections direct storage model with traditional neural bidirectional memories.

    PubMed

    Bhatti, A Aziz

    2009-12-01

    This study proposes an efficient and improved model of a direct storage bidirectional memory, improved bidirectional associative memory (IBAM), and emphasises the use of nanotechnology for efficient implementation of such large-scale neural network structures at a considerable lower cost reduced complexity, and less area required for implementation. This memory model directly stores the X and Y associated sets of M bipolar binary vectors in the form of (MxN(x)) and (MxN(y)) memory matrices, requires O(N) or about 30% of interconnections with weight strength ranging between +/-1, and is computationally very efficient as compared to sequential, intraconnected and other bidirectional associative memory (BAM) models of outer-product type that require O(N(2)) complex interconnections with weight strength ranging between +/-M. It is shown that it is functionally equivalent to and possesses all attributes of a BAM of outer-product type, and yet it is simple and robust in structure, very large scale integration (VLSI), optical and nanotechnology realisable, modular and expandable neural network bidirectional associative memory model in which the addition or deletion of a pair of vectors does not require changes in the strength of interconnections of the entire memory matrix. The analysis of retrieval process, signal-to-noise ratio, storage capacity and stability of the proposed model as well as of the traditional BAM has been carried out. Constraints on and characteristics of unipolar and bipolar binaries for improved storage and retrieval are discussed. The simulation results show that it has log(e) N times higher storage capacity, superior performance, faster convergence and retrieval time, when compared to traditional sequential and intraconnected bidirectional memories.

  8. A Comparison of Direct Heating During Radiofrequency and Microwave Ablation in Ex Vivo Liver

    SciTech Connect

    Andreano, Anita; Brace, Christopher L.

    2013-04-15

    This study was designed to determine the magnitude and spatial distribution of temperature elevations when using 480 kHz RF and 2.45 GHz microwave energy in ex vivo liver models. A total of 60 heating cycles (20 s at 90 W) were performed in normal, RF-ablated, and microwave-ablated liver tissues (n = 10 RF and n = 10 microwave in each tissue type). Heating cycles were performed using a 480-kHz generator and 3-cm cooled-tip electrode (RF) or a 2.45-GHz generator and 14-gauge monopole (microwave) and were designed to isolate direct heating from each energy type. Tissue temperatures were measured by using fiberoptic thermosensors 5, 10, and 15 mm radially from the ablation applicator at the depth of maximal heating. Power delivered, sensor location, heating rates, and maximal temperatures were compared using mixed effects regression models. No significant differences were noted in mean power delivered or thermosensor locations between RF and microwave heating groups (P > 0.05). Microwaves produced significantly more rapid heating than RF at 5, 10, and 15 mm in normal tissue (3.0 vs. 0.73, 0.85 vs. 0.21, and 0.17 vs. 0.09 Degree-Sign C/s; P < 0.05); and at 5 and 10 mm in ablated tissues (2.3 {+-} 1.4 vs. 0.7 {+-} 0.3, 0.5 {+-} 0.3 vs. 0.2 {+-} 0 Degree-Sign C/s, P < 0.05). The radial depth of heating was {approx}5 mm greater for microwaves than RF. Direct heating obtained with 2.45-GHz microwave energy using a single needle-like applicator is faster and covers a larger volume of tissue than 480-kHz RF energy.

  9. Comparison of indirect and direct quantification of esters of monochloropropanediol in vegetable oil.

    PubMed

    Dubois, Mathieu; Tarres, Adrienne; Goldmann, Till; Empl, Anna Maria; Donaubauer, Alfred; Seefelder, Walburga

    2012-05-04

    The presence of fatty acid esters of monochloropropanediol (MEs) in food is a recent concern raised due to the carcinogenicity of their hydrolysable moieties 2- and 3-monochloropropanediol (2- and 3-MCPD). Several indirect methods for the quantification of MEs have been developed and are commonly in use until today, however significant discrepancies among analytical results obtained are challenging their reliability. The aim of the present study was therefore to test the trueness of an indirect method by comparing it to a newly developed direct method using palm oil and palm olein as examples. The indirect method was based on ester cleavage under acidic conditions, derivatization of the liberated 2- and 3-MCPD with heptafluorobutyryl imidazole and GC-MS determination. The direct method was comprised of two extraction procedures targeting 2-and 3-MCPD mono esters (co-extracting as well glycidyl esters) by the use of double solid phase extraction (SPE), and 2- and 3-MCPD di-esters by the use of silica gel column, respectively. Detection was carried out by liquid chromatography coupled to time of flight mass spectrometry (LC-ToF-MS). Accurate quantification of the intact compounds was assured by means of matrix matched standard addition on extracts. Analysis of 22 palm oil and 7 palm olein samples (2- plus 3-MCPD contamination ranged from 0.3 to 8.8 μg/g) by both methods revealed no significant bias. Both methods were therefore considered as comparable in terms of results; however the indirect method was shown to require less analytical standards, being less tedious and furthermore applicable to all type of different vegetable oils and hence recommended for routine application.

  10. Comparison between direct and predicted maximal oxygen uptake measurement during cycling.

    PubMed

    Santtila, Matti; Häkkinen, Keijo; Pihlainen, Kai; Kyröläinen, Heikki

    2013-02-01

    Predicted maximal oxygen uptake (VO2max) measurements are based on the assumption of linear relationship between heart rate or power output and oxygen consumption during various intensities. To develop more reliable predicted test for soldiers, the purpose of the present study was to compare the results of direct measurements of VO2max to respective predicted values in cycling (military fitness test). The predicted mean (+/- SD) peak oxygen uptake (VO2peak) value was 45.2 +/- 7.7 mL kg(-1) min(-1) during first week, whereas the respective direct value was 44.8 +/- 8.5 mL kg(-1) min(-1). During the ninth week, the predicted and measured mean (+/-SD) VO2max values were 47.4 +/- 6.7 mL kg(-1) min(-1) and 48.7 +/- 7.3 mL kg(-1) min(-1), respectively. The absolute differences between the methods were -0.42 mL kg(-1) min(-1) (p = 0.46) and 1.28 mL kg(-1) min(-1) (p < 0.05), which correspond to relative values of 0.9% and 2.7%, respectively. A Bland-Altman plot of measured VO2max and predicted VO2max showed no significant trend between the mean and the difference of the 2 methods either before (r = 0.14, p = 0.24) or after the basic military training period (r = 0.11, p = 0.36). Intraclass correlation coefficient varied between r = 0.82 to 0.94. In conclusion, the predicted protocol is fairly accurate (+/-3%) and reliable to predict VO2max values in male soldiers but the use for clinical purposes should be considered individually.

  11. Direct comparison of the magnetic and electronic properties of samarocene and ytterbocene terpyridine complexes.

    PubMed

    Veauthier, Jacqueline M; Schelter, Eric J; Carlson, Christin N; Scott, Brian L; Da Re, Ryan E; Thompson, J D; Kiplinger, Jaqueline L; Morris, David E; John, Kevin D

    2008-07-07

    A new complex, Cp* 2Sm(tpy) ( 1, where Cp* = C 5Me 5, tpy = 2,2':6',2''-terpyridine) and its one-electron oxidized congener [Cp* 2Sm(tpy)]PF 6 ([ 1] (+)) have been synthesized and characterized with the aim of comparing their electronic and magnetic behavior to the known ytterbium analogues: Cp* 2Yb(tpy) ( 2) and [Cp* 2Yb(tpy)]OTf ([ 2] ( + )). These new samarium complexes have been characterized using single-crystal X-ray diffraction, (1)H NMR spectroscopy, cyclic voltammetry, optical spectroscopy, and bulk magnetic susceptibility measurements. All data for 1 indicate a Sm(III)-tpy* (-)[(4f) (5)-(pi*) (1)] ground-state electronic configuration similar to that found previously for 2 [(4f) (13)-(pi*) (1)]. Structural comparisons reveal that there are no significant changes in the overall geometries associated with the neutral and cationic samarium and ytterbium congeners aside from those anticipated based upon the lanthanide contraction. The redox potentials for the divalent Cp* 2Ln(THF) n precursors ( E 1/2(Sm (2+)) = -2.12 V, E 1/2(Yb (2+)) = -1.48 V) are consistent with established trends, the redox potentials (metal-based reduction and ligand-based oxidation) for 1 are nearly identical to those for 2. The correlation in the optical spectra of 1 and 2 is excellent, as expected for this ligand-radical based electronic structural assignment, but there does appear to be a red-shift ( approximately 400 cm (-1)) in all of the bands of 1 relative to those of 2 that suggests a slightly greater stabilization of the pi* level(s) in the samarium(III) complex compared to that in the ytterbium(III) complex. Similar spectroscopic overlap is observed for the monocationic complexes [ 1] (+) and [ 2] (+). Bulk magnetic susceptibility measurements for 1 reveal significantly different behavior than that of 2 due to differences in the electronic-state structure of the two metal ions. The implications of these differences in magnetic behavior are discussed.

  12. Direct comparison of three different methods of volcanic edifice identification from bathymetry maps

    NASA Astrophysics Data System (ADS)

    Howell, J.; White, S. M.; Bohnenstiehl, D. R.; Miller, D.

    2009-12-01

    The detection of volcanic edifices from bathymetric sonar data is often used in studies of seamount distribution near arcs, ridges and hotspots to interpret volcanic spacing and alignment. Such studies form the basis for the ongoing debate on the structural controls on volcanism and our understanding of linkages between tectonics and volcanism. Until recently, manually picking closed-contour peaks from maps was the only method of volcanic edifice identification, however this can be subjective and time consuming. In this study we have compared the results from three separate methods: manually picking closed contours, using a peakshed method based on a widely used algorithm for detecting sinkholes in topographic data, and a closed-contour picking computer algorithm. Bathymetry from the western Aleutian backarc collected in 2005, the Galapagos Spreading Centers collected in 2006 and the Mid-Atlantic Ridge collected in 1990 was used as the comparison data. To each dataset, we applied a common set of criteria: minimum peak to base heights must be greater than 25 meters and aspect ratios (long to short axis of the basal contour) must be less than 1.5. The peakshed method begins by looking for local bathymetric peaks remaining after removing regional bathymetry using a median filter. The median filtered bathymetry grid was subtracted from the original bathymetric grid to obtain the residual bathymetry representing the volcanic edifices. We use a novel application of the method used to detect and remove local sinkholes from digital terrain models to define the basal boundary of each edifice. The residual bathymetry is first inverted, so that local peaks become local sinks, and then the area of the basin that drains into each sink is calculated using a GIS algorithm and returned as a closed polygon that represents the basal area of each edifice. This method has the advantage of using the full resolution of the gridded data to determine the volume of an edifice. The closed

  13. Direct Phenotypic Screening in Mice: Identification of Individual, Novel Antinociceptive Compounds from a Library of 734 821 Pyrrolidine Bis-piperazines

    PubMed Central

    2015-01-01

    The hypothesis in the current study is that the simultaneous direct in vivo testing of thousands to millions of systematically arranged mixture-based libraries will facilitate the identification of enhanced individual compounds. Individual compounds identified from such libraries may have increased specificity and decreased side effects early in the discovery phase. Testing began by screening ten diverse scaffolds as single mixtures (ranging from 17 340 to 4 879 681 compounds) for analgesia directly in the mouse tail withdrawal model. The “all X” mixture representing the library TPI-1954 was found to produce significant antinociception and lacked respiratory depression and hyperlocomotor effects using the Comprehensive Laboratory Animal Monitoring System (CLAMS). The TPI-1954 library is a pyrrolidine bis-piperazine and totals 738 192 compounds. This library has 26 functionalities at the first three positions of diversity made up of 28 392 compounds each (26 × 26 × 42) and 42 functionalities at the fourth made up of 19 915 compounds each (26 × 26 × 26). The 120 resulting mixtures representing each of the variable four positions were screened directly in vivo in the mouse 55 °C warm-water tail-withdrawal assay (ip administration). The 120 samples were then ranked in terms of their antinociceptive activity. The synthesis of 54 individual compounds was then carried out. Nine of the individual compounds produced dose-dependent antinociception equivalent to morphine. In practical terms what this means is that one would not expect multiexponential increases in activity as we move from the all-X mixture, to the positional scanning libraries, to the individual compounds. Actually because of the systematic formatting one would typically anticipate steady increases in activity as the complexity of the mixtures is reduced. This is in fact what we see in the current study. One of the final individual compounds identified, TPI 2213-17, lacked significant

  14. Direct Phenotypic Screening in Mice: Identification of Individual, Novel Antinociceptive Compounds from a Library of 734,821 Pyrrolidine Bis-piperazines.

    PubMed

    Houghten, Richard A; Ganno, Michelle L; McLaughlin, Jay P; Dooley, Colette T; Eans, Shainnel O; Santos, Radleigh G; LaVoi, Travis; Nefzi, Adel; Welmaker, Greg; Giulianotti, Marc A; Toll, Lawrence

    2016-01-11

    The hypothesis in the current study is that the simultaneous direct in vivo testing of thousands to millions of systematically arranged mixture-based libraries will facilitate the identification of enhanced individual compounds. Individual compounds identified from such libraries may have increased specificity and decreased side effects early in the discovery phase. Testing began by screening ten diverse scaffolds as single mixtures (ranging from 17,340 to 4,879,681 compounds) for analgesia directly in the mouse tail withdrawal model. The "all X" mixture representing the library TPI-1954 was found to produce significant antinociception and lacked respiratory depression and hyperlocomotor effects using the Comprehensive Laboratory Animal Monitoring System (CLAMS). The TPI-1954 library is a pyrrolidine bis-piperazine and totals 738,192 compounds. This library has 26 functionalities at the first three positions of diversity made up of 28,392 compounds each (26 × 26 × 42) and 42 functionalities at the fourth made up of 19,915 compounds each (26 × 26 × 26). The 120 resulting mixtures representing each of the variable four positions were screened directly in vivo in the mouse 55 °C warm-water tail-withdrawal assay (ip administration). The 120 samples were then ranked in terms of their antinociceptive activity. The synthesis of 54 individual compounds was then carried out. Nine of the individual compounds produced dose-dependent antinociception equivalent to morphine. In practical terms what this means is that one would not expect multiexponential increases in activity as we move from the all-X mixture, to the positional scanning libraries, to the individual compounds. Actually because of the systematic formatting one would typically anticipate steady increases in activity as the complexity of the mixtures is reduced. This is in fact what we see in the current study. One of the final individual compounds identified, TPI 2213-17, lacked significant respiratory

  15. Comparison of Chemical Sensitivity of Fresh and Long-Stored Heat Resistant Neosartorya fischeri Environmental Isolates Using BIOLOG Phenotype MicroArray System

    PubMed Central

    Panek, Jacek; Frąc, Magdalena; Bilińska-Wielgus, Nina

    2016-01-01

    Spoilage of heat processed food and beverage by heat resistant fungi (HRF) is a major problem for food industry in many countries. Neosartorya fischeri is the leading source of spoilage in thermally processed products. Its resistance to heat processing and toxigenicity makes studies about Neosartorya fischeri metabolism and chemical sensitivity essential. In this study chemical sensitivity of two environmental Neosartorya fischeri isolates were compared. One was isolated from canned apples in 1923 (DSM3700), the other from thermal processed strawberry product in 2012 (KC179765), used as long-stored and fresh isolate, respectively. The study was conducted using Biolog Phenotype MicroArray platforms of chemical sensitivity panel and traditional hole-plate method. The study allowed for obtaining data about Neosartorya fischeri growth inhibitors. The fresh isolate appeared to be much more resistant to chemical agents than the long-stored isolate. Based on phenotype microarray assay nitrogen compounds, toxic cations and membrane function compounds were the most effective in growth inhibition of N. fischeri isolates. According to the study zaragozic acid A, thallium(I) acetate and sodium selenate were potent and promising N. fischeri oriented fungicides which was confirmed by both chemical sensitivity microplates panel and traditional hole-plate methods. PMID:26815302

  16. Gaussian variational ansatz in the problem of anomalous sea waves: Comparison with direct numerical simulation

    SciTech Connect

    Ruban, V. P.

    2015-05-15

    The nonlinear dynamics of an obliquely oriented wave packet on a sea surface is analyzed analytically and numerically for various initial parameters of the packet in relation to the problem of the so-called rogue waves. Within the Gaussian variational ansatz applied to the corresponding (1+2)-dimensional hyperbolic nonlinear Schrödinger equation (NLSE), a simplified Lagrangian system of differential equations is derived that describes the evolution of the coefficients of the real and imaginary quadratic forms appearing in the Gaussian. This model provides a semi-quantitative description of the process of nonlinear spatiotemporal focusing, which is one of the most probable mechanisms of rogue wave formation in random wave fields. The system of equations is integrated in quadratures, which allows one to better understand the qualitative differences between linear and nonlinear focusing regimes of a wave packet. Predictions of the Gaussian model are compared with the results of direct numerical simulation of fully nonlinear long-crested waves.

  17. Comparison of direct measurement methods for headset noise exposure in the workplace

    PubMed Central

    Nassrallah, Flora G.; Giguère, Christian; Dajani, Hilmi R.; Ellaham, Nicolas N.

    2016-01-01

    The measurement of noise exposure from communication headsets poses a methodological challenge. Although several standards describe methods for general noise measurements in occupational settings, these are not directly applicable to noise assessments under communication headsets. For measurements under occluded ears, specialized methods have been specified by the International Standards Organization (ISO 11904) such as the microphone in a real ear and manikin techniques. Simpler methods have also been proposed in some national standards such as the use of general purpose artificial ears and simulators in conjunction with single number corrections to convert measurements to the equivalent diffuse field. However, little is known about the measurement agreement between these various methods and the acoustic manikin technique. Twelve experts positioned circum-aural, supra-aural and insert communication headsets on four different measurement setups (Type 1, Type 2, Type 3.3 artificial ears, and acoustic manikin). Fit-refit measurements of four audio communication signals were taken under quiet laboratory conditions. Data were transformed into equivalent diffuse-field sound levels using third-octave procedures. Results indicate that the Type 1 artificial ear is not suited for the measurement of sound exposure under communication headsets, while Type 2 and Type 3.3 artificial ears are in good agreement with the acoustic manikin technique. Single number corrections were found to introduce a large measurement uncertainty, making the use of the third-octave transformation preferable. PMID:26960783

  18. Comparison of directed and weighted co-occurrence networks of six languages

    NASA Astrophysics Data System (ADS)

    Gao, Yuyang; Liang, Wei; Shi, Yuming; Huang, Qiuling

    2014-01-01

    To study commonalities and differences among different languages, we select 100 reports from the documents of the United Nations, each of which was written in Arabic, Chinese, English, French, Russian and Spanish languages, separately. Based on these corpora, we construct 6 weighted and directed word co-occurrence networks. Besides all the networks exhibit scale-free and small-world features, we find several new non-trivial results, including connections among English words are denser, and the expression of English language is more flexible and powerful; the connection way among Spanish words is more stringent and this indicates that the Spanish grammar is more rigorous; values of many statistical parameters of the French and Spanish networks are very approximate and this shows that these two languages share many commonalities; Arabic and Russian words have many varieties, which result in rich types of words and a sparse connection among words; connections among Chinese words obey a more uniform distribution, and one inclines to use the least number of Chinese words to express the same complex information as those in other five languages. This shows that the expression of Chinese language is quite concise. In addition, several topics worth further investigating by the complex network approach have been observed in this study.

  19. Gaussian variational ansatz in the problem of anomalous sea waves: Comparison with direct numerical simulation

    NASA Astrophysics Data System (ADS)

    Ruban, V. P.

    2015-05-01

    The nonlinear dynamics of an obliquely oriented wave packet on a sea surface is analyzed analytically and numerically for various initial parameters of the packet in relation to the problem of the so-called rogue waves. Within the Gaussian variational ansatz applied to the corresponding (1+2)-dimensional hyperbolic nonlinear Schrödinger equation (NLSE), a simplified Lagrangian system of differential equations is derived that describes the evolution of the coefficients of the real and imaginary quadratic forms appearing in the Gaussian. This model provides a semi-quantitative description of the process of nonlinear spatiotemporal focusing, which is one of the most probable mechanisms of rogue wave formation in random wave fields. The system of equations is integrated in quadratures, which allows one to better understand the qualitative differences between linear and nonlinear focusing regimes of a wave packet. Predictions of the Gaussian model are compared with the results of direct numerical simulation of fully nonlinear long-crested waves.

  20. Development of reference assignment in children: a direct comparison to the performance of cognitive shift.

    PubMed

    Murakami, Taro; Hashiya, Kazuhide

    2014-01-01

    The referent of a deictic embedded in a particular utterance or sentence is often ambiguous. Reference assignment is a pragmatic process that enables the disambiguation of such a referent. Previous studies have demonstrated that receivers use social-pragmatic information during referent assignment; however, it is still unclear which aspects of cognitive development affect the development of referential processing in children. The present study directly assessed the relationship between performance on a reference assignment task (Murakami and Hashiya, in preparation) and the dimensional change card sort task (DCCS) in 3- and 5-years-old children. The results indicated that the 3-years-old children who passed DCCS showed performance above chance level in the event which required an explicit (cognitive) shift, while the performance of the children who failed DCCS remained in the range of chance level; however, such a tendency was not observed in the 5-years-old, possibly due to a ceiling effect. The results indicated that, though the development of skills that mediate cognitive shifting might adequately explain the explicit shift of attention in conversation, the pragmatic processes underlying the implicit shift, which requires reference assignment, might follow a different developmental course.

  1. Comparison of Direct and Indirect Laryngoscopes in Vomitus and Hematemesis Settings: A Randomized Simulation Trial

    PubMed Central

    Mihara, Ryosuke; Komasawa, Nobuyasu; Matsunami, Sayuri; Minami, Toshiaki

    2015-01-01

    Background. Videolaryngoscopes may not be useful in the presence of hematemesis or vomitus. We compared the utility of the Macintosh laryngoscope (McL), which is a direct laryngoscope, with that of the Pentax-AWS Airwayscope (AWS) and McGRATH MAC (McGRATH), which are videolaryngoscopes, in simulated hematemesis and vomitus settings. Methods. Seventeen anesthesiologists with more than 1 year of experience performed tracheal intubation on an adult manikin using McL, AWS, and McGRATH under normal, hematemesis, and vomitus simulations. Results. In the normal setting, the intubation success rate was 100% for all three laryngoscopes. In the hematemesis settings, the intubation success rate differed significantly among the three laryngoscopes (P = 0.021). In the vomitus settings, all participants succeeded in tracheal intubation with McL or McGRATH, while five failed in the AWS trial with significant difference (P = 0.003). The intubation time did not significantly differ in normal settings, while it was significantly longer in the AWS trial compared to McL or McGRATH trial in the hematemesis or vomitus settings (P < 0.001, compared to McL or McGRATH in both settings). Conclusion. The performance of McGRATH and McL can be superior to that of AWS for tracheal intubation in vomitus and hematemesis settings in adults. PMID:26618177

  2. Sputtering and redeposition of ion irradiated Au nanoparticle arrays: direct comparison of simulations to experiments

    NASA Astrophysics Data System (ADS)

    Holland-Moritz, Henry; Ilinov, Andrey; Djurabekova, Flyura; Nordlund, Kai; Ronning, Carsten

    2017-01-01

    Ion beam processing of surfaces is well known to lead to sputtering, which conventionally is associated only with erosion of atoms from the material. We show here, by combination of experiments and a newly developed Monte Carlo algorithm, that in the case of nanoparticles in a regular two-dimensional array on surfaces, the redeposition of sputtered atoms may play a significant role on the system development. The simulations are directly compared to in situ experiments obtained using a dual focused Ga+ ion beam system and high resolution scanning electron microscopy, and explain the size evolution by a combination of sputtering and redeposition of sputtered material on neighboring particles. The effect is found to be dependent on the size of the nanoparticles: if the nanoparticle size is comparable to the ion range, the reposition is negligible. For larger nanoparticles the redeposition becomes significant and is able to compensate up to 20% of the sputtered material, effectively reducing the process of sputtering. The redeposition may even lead to significant growth: this was seen for the nanoparticles with the sizes much smaller than the ion range. Furthermore, the algorithm shows that significant redeposition is possible when the large size neighboring nanoparticles are present.

  3. Comparison of Directionally Solidified Samples Solidified Terrestrially and Aboard the International Space Station

    NASA Technical Reports Server (NTRS)

    Angart, S.; Lauer, M.; Tewari, S. N.; Grugel, R. N.; Poirier, D. R.

    2014-01-01

    This article reports research that has been carried out under the aegis of NASA as part of a collaboration between ESA and NASA for solidification experiments on the International Space Station (ISS). The focus has been on the effect of convection on the microstructural evolution and macrosegregation in hypoeutectic Al-Si alloys during directional solidification (DS). Terrestrial DS-experiments have been carried out at Cleveland State University (CSU) and under microgravity on the International Space Station (ISS). The thermal processing-history of the experiments is well defined for both the terrestrially processed samples and the ISS-processed samples. As of this writing, two dendritic metrics was measured: primary dendrite arm spacings and primary dendrite trunk diameters. We have observed that these dendrite-metrics of two samples grown in the microgravity environment show good agreements with models based on diffusion controlled growth and diffusion controlled ripening, respectively. The gravity-driven convection (i.e., thermosolutal convection) in terrestrially grown samples has the effect of decreasing the primary dendrite arm spacings and causes macrosegregation. Dendrite trunk diameters also show differences between the earth- and space-grown samples. In order to process DS-samples aboard the ISS, the dendritic seed crystals were partially remelted in a stationary thermal gradient before the DS was carried out. Microstructural changes and macrosegregation effects during this period are described and have modeled.

  4. Comparison of direct measurement methods for headset noise exposure in the workplace.

    PubMed

    Nassrallah, Flora G; Giguere, Christian; Dajani, Hilmi R; Ellaham, Nicolas N

    2016-01-01

    The measurement of noise exposure from communication headsets poses a methodological challenge. Although several standards describe methods for general noise measurements in occupational settings, these are not directly applicable to noise assessments under communication headsets. For measurements under occluded ears, specialized methods have been specified by the International Standards Organization (ISO 11904) such as the microphone in a real ear and manikin techniques. Simpler methods have also been proposed in some national standards such as the use of general purpose artificial ears and simulators in conjunction with single number corrections to convert measurements to the equivalent diffuse field. However, little is known about the measurement agreement between these various methods and the acoustic manikin technique. Twelve experts positioned circum-aural, supra-aural and insert communication headsets on four different measurement setups (Type 1, Type 2, Type 3.3 artificial ears, and acoustic manikin). Fit-refit measurements of four audio communication signals were taken under quiet laboratory conditions. Data were transformed into equivalent diffuse-field sound levels using third-octave procedures. Results indicate that the Type 1 artificial ear is not suited for the measurement of sound exposure under communication headsets, while Type 2 and Type 3.3 artificial ears are in good agreement with the acoustic manikin technique. Single number corrections were found to introduce a large measurement uncertainty, making the use of the third-octave transformation preferable.

  5. A direct comparison of helix propensity in proteins and peptides

    PubMed Central

    Myers, Jeffrey K.; Pace, C. Nick; Scholtz, J. Martin

    1997-01-01

    α-Helical secondary structure occurs widely in globular proteins and its formation is a key step in their folding. As a consequence, understanding the energetics of helix formation is crucial to understanding protein folding and stability. We have measured the helix propensities of the nonpolar amino acids for an α-helix in an intact protein, ribonuclease T1, and for a 17-residue peptide with a sequence identical to that of the α-helix in the protein. The helix propensities are in excellent agreement. This shows that when compared in the same sequence context, the helix propensities of the nonpolar amino acids are identical in helical peptides and intact proteins, and that conclusions based on studies of the helix-to-coil transitions of peptides may, in favorable cases, be directly applicable to proteins. Our helix propensities based on ribonuclease T1 are in good agreement with those from similar studies of barnase and T4 lysozyme. In contrast, our helix propensities differ substantially from those derived from studies of alanine-stabilized or salt bridge-stabilized model α-helical peptides. PMID:9096306

  6. A Comparison of Alternating Current and Direct Current Electrospray Ionization for Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Sarver, Scott A.; Chetwani, Nishant; Dovichi, Norman J.; Go, David B.; Gartner, Carlos A.

    2014-04-01

    A series of studies comparing the performance of alternating current electrospray ionization (AC ESI) mass spectrometry (MS) and direct current electrospray ionization (DC ESI) MS have been conducted, exploring the absolute signal intensity and signal-to-background ratios produced by both methods using caffeine and a model peptide as targets. Because the high-voltage AC signal was more susceptible to generating gas discharges, the operating voltage range of AC ESI was significantly smaller than that for DC ESI, such that the absolute signal intensities produced by DC ESI at peak voltages were one to two orders of magnitude greater than those for AC ESI. Using an electronegative nebulizing gas, sulfur hexafluoride (SF6), instead of nitrogen (N2) increased the operating range of AC ESI by ~50 %, but did not appreciably improve signal intensities. While DC ESI generated far greater signal intensities, both ionization methods produced comparable signal-to-background noise, with AC ESI spectra appearing qualitatively cleaner. A quantitative calibration analysis was performed for two analytes, caffeine and the peptide MRFA. AC ESI utilizing SF6 outperforms all other techniques for the detection of MRFA, producing chromatographic limits of detection nearly one order of magnitude lower than that of DC ESI utilizing N2, and one-half that of DC ESI utilizing SF6. However, DC ESI outperforms AC ESI for the analysis of caffeine, indicating that improvements in spectral quality may benefit certain compounds or classes of compounds, on an individual basis.

  7. Comparison of Propane and Methane Performance and Emissions in a Turbocharged Direct Injection Dual Fuel Engine

    SciTech Connect

    Gibson, C. M.; Polk, A. C.; Shoemaker, N. T.; Srinivasan, K. K.; Krishnan, S. R.

    2011-01-01

    With increasingly restrictive NO x and particulate matter emissions standards, the recent discovery of new natural gas reserves, and the possibility of producing propane efficiently from biomass sources, dual fueling strategies have become more attractive. This paper presents experimental results from dual fuel operation of a four-cylinder turbocharged direct injection (DI) diesel engine with propane or methane (a natural gas surrogate) as the primary fuel and diesel as the ignition source. Experiments were performed with the stock engine control unit at a constant speed of 1800 rpm, and a wide range of brake mean effective pressures (BMEPs) (2.7-11.6 bars) and percent energy substitutions (PESs) of C 3 H 8 and CH 4. Brake thermal efficiencies (BTEs) and emissions (NO x, smoke, total hydrocarbons (THCs), CO, and CO 2) were measured. Maximum PES levels of about 80-95% with CH 4 and 40-92% with C 3 H 8 were achieved. Maximum PES was limited by poor combustion efficiencies and engine misfire at low loads for both C 3 H 8 and CH 4, and the onset of knock above 9 bar BMEP for C 3 H 8. While dual fuel BTEs were lower than straight diesel BTEs at low loads, they approached diesel BTE values at high loads. For dual fuel operation, NO x and smoke reductions (from diesel values) were as high as 66-68% and 97%, respectively, but CO and THC emissions were significantly higher with increasing PES at all engine loads

  8. Direct Chloroplast Sequencing: Comparison of Sequencing Platforms and Analysis Tools for Whole Chloroplast Barcoding

    PubMed Central

    Brozynska, Marta; Furtado, Agnelo; Henry, Robert James

    2014-01-01

    Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina) and Ion Torrent (Life Technology) sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare). Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis. PMID:25329378

  9. Direct Numerical Simulation of Pore-Scale Flow in a Bead Pack: Comparison with Magnetic Resonance Imaging Observations

    SciTech Connect

    Yang, Xiaofan; Scheibe, Timothy D.; Richmond, Marshall C.; Perkins, William A.; Vogt, Sarah J.; Codd, Sarah L.; Seymour, Joseph D.; Mckinley, Matthew I.

    2013-04-01

    A significant body of current research is aimed at developing methods for numerical simulation of flow and transport in porous media that explicitly resolve complex pore and solid geometries, and at utilizing such models to study the relationships between fundamental pore-scale processes and macroscopic manifestations at larger (i.e., Darcy) scales. A number of different numerical methods for pore-scale simulation have been developed, and have been extensively tested and validated for simplified geometries. However, validation of pore-scale simulations of fluid velocity for complex, three-dimensional (3D) pore geometries that are representative of natural porous media is challenging due to our limited ability to measure pore-scale velocity in such systems. Recent advances in magnetic resonance imaging (MRI) offer the opportunity to measure not only the pore geometry, but also local fluid velocities under steady-state flow conditions in 3D and with high spatial resolution. In this paper, we present a 3D velocity field measured at sub-pore resolution (tens of micrometers) over a centimeter-scale 3D domain using MRI methods. We have utilized the measured pore geometry to perform 3D simulations of Navier-Stokes flow over the same domain using direct numerical simulation techniques. We present a comparison of the numerical simulation results with the measured velocity field. It is shown that the numerical results match the observed velocity patterns well overall except for a variance and small systematic scaling which can be attributed to the known experimental error in the MRI measurements. The comparisons presented here provide strong validation of the pore-scale simulation methods and new insights for interpretation of uncertainty in MRI measurements of pore-scale velocity. This study also provides a potential benchmark for future comparison of other pore-scale simulation methods.

  10. Direct Signal-to-Noise Quality Comparison between an Electronic and Conventional Stethoscope aboard the International Space Station

    NASA Technical Reports Server (NTRS)

    Marshburn, Thomas; Cole, Richard; Ebert, Doug; Bauer, Pete

    2014-01-01

    believe the results are noteworthy. The electronic stethoscope out preformed the traditional stethoscope in each direct comparison. Consideration should be made to incorporate an electronic stethoscope into current and future space vehicle medical kits.

  11. Surface plasmon excitations in metal spheres: Direct comparison of light scattering and electron energy-loss spectroscopy by modal decomposition

    NASA Astrophysics Data System (ADS)

    Collins, Sean M.; Midgley, Paul A.

    2013-06-01

    In previous publications, qualitative agreement between studies of surface plasmon excitations in nanoparticles by near-field light scattering and electron energy-loss spectroscopy (EELS) has been found for experiments and simulations. Here, we present a quantitative method for the comparison of light scattering and EELS for surface plasmons in metal spheres. Defining the Fourier transform of the modal component of the scattered electric field along the equivalent electron trajectory enables a direct evaluation of the relative weighting factor for light- and electron-excited surface plasmon modes. This common quantity for light scattering and EELS is examined for size, composition, and trajectory dependencies, facilitating the analysis of key differences between light and electron excitation. A single functional dependence on Drude model plasmon energies is identified to explain the relative modal weighting factors for light scattering and EELS. This method represents an important step toward the complete spectral and spatial reconstruction of EELS maps from near-field light scattering calculations.

  12. A direct comparison between two independently calibrated time transfer techniques: T2L2 and GPS Common-Views

    NASA Astrophysics Data System (ADS)

    Rovera, G. D.; Abgrall, M.; Courde, C.; Exertier, P.; Fridelance, P.; Guillemot, Ph; Laas-Bourez, M.; Martin, N.; Samain, E.; Sherwood, R.; Torre, J.-M.; Uhrich, P.

    2016-06-01

    We present a direct comparison between two satellite time transfer techniques on independently calibrated links: Time Transfer by Laser Link (T2L2) and Common-Views (CV) of satellites from the Global Positioning System (GPS) constellation. The GPS CV and T2L2 links between three European laboratories where independently calibrated against the same reference point of the local timescales. For all the links the mean values of the differences between GPS CV and T2L2 are equal or below 240 ps, with standard deviations below 500 ps, mostly due to GPS CV. Almost all deviations from 0 ns are within the combined uncertainty estimates. Despite the weak number of common points obtained, due to the fact that T2L2 is weather dependent, these results are providing an unprecedented sub-ns consistency between two independently calibrated microwave and optical satellite time transfer techniques.

  13. Sub-ns time transfer consistency: a direct comparison between GPS CV and T2L2

    NASA Astrophysics Data System (ADS)

    Exertier, P.; Samain, E.; Courde, C.; Aimar, M.; Torre, J. M.; Rovera, G. D.; Abgrall, M.; Uhrich, P.; Sherwood, R.; Herold, G.; Schreiber, U.; Guillemot, P.

    2016-12-01

    This paper presents a direct comparison between two satellite time transfer techniques: common-view (CV) of satellites from the global positioning system (GPS) constellation, and time transfer by laser link (T2L2) through the low orbiting satellite Jason-2. We describe briefly both techniques, together with two independent relative calibration campaigns of the links involving four European laboratories. Between the same remote time scale reference points, the mean values of the calibrated differences between GPS CV and T2L2 are below 240 ps, with standard deviations below 500 ps, mostly due to GPS CV. Almost all sample deviations from 0 ns are within the combined uncertainty estimates. Despite the relatively small number of common points obtained, due to the fact that T2L2 is weather dependent, these results provide an unprecedented sub-ns consistency between two independently calibrated microwave and optical satellite time transfer techniques.

  14. Specificity of psychological treatments for bulimia nervosa and binge eating disorder? A meta-analysis of direct comparisons.

    PubMed

    Spielmans, Glen I; Benish, Steven G; Marin, Catherine; Bowman, Wesley M; Menster, Maria; Wheeler, Anthony J

    2013-04-01

    Treatment guidelines state that cognitive-behavioral therapy (CBT) and interpersonal therapy are the best-supported psychotherapies for bulimia nervosa (BN) and that CBT is the preferred psychological treatment for binge eating disorder (BED). However, no meta-analysis which both examined direct comparisons between psychological treatments for BN and BED and considered the role of moderating variables, such as the degree to which psychotherapy was bona fide, has previously been conducted Thus, such an analysis was undertaken. We included 77 comparisons reported in 53 studies. The results indicated that: (a) bona fide therapies outperformed non-bona fide treatments, (b) bona fide CBT outperformed bona fide non-CBT interventions by a statistically significant margin (only approaching statistical significance for BN and BED when examined individually), but many of these trials had confounds which limited their internal validity, (c) full CBT treatments offered no benefit over their components, and (d) the distribution of effect size differences between bona fide CBT treatments was homogeneously distributed around zero. These findings provide little support for treatment specificity in psychotherapy for BN and BED.

  15. Direct Numerical Simulation of Fracture Behaviour for Random Short Wood Fibres Reinforced Composites, Comparison with Digital Image Correlation Experiments

    NASA Astrophysics Data System (ADS)

    Shen, M.; Touchard, F.; Bezine, G.; Brillaud, J.

    2010-06-01

    The work is to predict fracture behaviour of bio-composites from the tensile properties of its components. In this work, we have realized a direct numerical simulation of fracture behaviour for random short spruce fibers reinforced composites. For calculations, wood fibers have been considered as linear elastic bodies, polypropylene matrix as an elastic-plastic material. Then, numerical results have been compared with experimental results that have been obtained by digital image correlation. This comparison indicates that random fiber FE model of random short spruce fibers reinforced composites can be able to fairly reflect the influence of random fibers microstructure in the composite on its fracture behavior. The calculation of both random fiber and homogeneous FE model and their comparison with experiments show that the average values of J-integral in a region in the front of the crack tip from both numerical FE models are in good agreement with the average J value of DIC experiment in the same region when the numerical and experimental CT specimens of the short spruce fiber reinforced composite are subjected to the same extension at their loading point.

  16. Comparisons of treatment optimization directly incorporating random patient setup uncertainty with a margin-based approach.

    PubMed

    Moore, Joseph A; Gordon, John J; Anscher, Mitchell S; Siebers, Jeffrey V

    2009-09-01

    The purpose of this study is to incorporate the dosimetric effect of random patient positioning uncertainties directly into a commercial treatment planning system's IMRT plan optimization algorithm through probabilistic treatment planning (PTP) and compare coverage of this method with margin-based planning. In this work, PTP eliminates explicit margins and optimizes directly on the estimated integral treatment dose to determine optimal patient dose in the presence of setup uncertainties. Twenty-eight prostate patient plans adhering to the RTOG-0126 criteria are optimized using both margin-based and PTP methods. Only random errors are considered. For margin-based plans, the planning target volume is created by expanding the clinical target volume (CTV) by 2.1 mm to accommodate the simulated 3 mm random setup uncertainty. Random setup uncertainties are incorporated into IMRT dose evaluation by convolving each beam's incident fluence with a sigma = 3 mm Gaussian prior to dose calculation. PTP optimization uses the convolved fluence to estimate dose to ensure CTV coverage during plan optimization. PTP-based plans are compared to margin-based plans with equal CTV coverage in the presence of setup errors based on dose-volume metrics. The sensitivity of the optimized plans to patient-specific setup uncertainty variations is assessed by evaluating dose metrics for dose distributions corresponding to halving and doubling of the random setup uncertainty used in the optimization. Margin-based and PTP-based plans show similar target coverage. A physician review shows that PTP is preferred for 21 patients, margin-based plans are preferred in 2 patients, no preference is expressed for 1 patient, and both autogenerated plans are rejected for 4 patients. For the PTP-based plans, the average CTV receiving the prescription dose decreases by 0.5%, while the mean dose to the CTV increases by 0.7%. The CTV tumor control probability (TCP) is the same for both methods with the exception

  17. Direct power comparisons between simple LOD scores and NPL scores for linkage analysis in complex diseases.

    PubMed

    Abreu, P C; Greenberg, D A; Hodge, S E

    1999-09-01

    Several methods have been proposed for linkage analysis of complex traits with unknown mode of inheritance. These methods include the LOD score maximized over disease models (MMLS) and the "nonparametric" linkage (NPL) statistic. In previous work, we evaluated the increase of type I error when maximizing over two or more genetic models, and we compared the power of MMLS to detect linkage, in a number of complex modes of inheritance, with analysis assuming the true model. In the present study, we compare MMLS and NPL directly. We simulated 100 data sets with 20 families each, using 26 generating models: (1) 4 intermediate models (penetrance of heterozygote between that of the two homozygotes); (2) 6 two-locus additive models; and (3) 16 two-locus heterogeneity models (admixture alpha = 1.0,.7,.5, and.3; alpha = 1.0 replicates simple Mendelian models). For LOD scores, we assumed dominant and recessive inheritance with 50% penetrance. We took the higher of the two maximum LOD scores and subtracted 0.3 to correct for multiple tests (MMLS-C). We compared expected maximum LOD scores and power, using MMLS-C and NPL as well as the true model. Since NPL uses only the affected family members, we also performed an affecteds-only analysis using MMLS-C. The MMLS-C was both uniformly more powerful than NPL for most cases we examined, except when linkage information was low, and close to the results for the true model under locus heterogeneity. We still found better power for the MMLS-C compared with NPL in affecteds-only analysis. The results show that use of two simple modes of inheritance at a fixed penetrance can have more power than NPL when the trait mode of inheritance is complex and when there is heterogeneity in the data set.

  18. Comparison of fine particle measurements from a direct-reading instrument and a gravimetric sampling method.

    PubMed

    Kim, Jee Young; Magari, Shannon R; Herrick, Robert F; Smith, Thomas J; Christiani, David C

    2004-11-01

    Particulate air pollution, specifically the fine particle fraction (PM2.5), has been associated with increased cardiopulmonary morbidity and mortality in general population studies. Occupational exposure to fine particulate matter can exceed ambient levels by a large factor. Due to increased interest in the health effects of particulate matter, many particle sampling methods have been developed In this study, two such measurement methods were used simultaneously and compared. PM2.5 was sampled using a filter-based gravimetric sampling method and a direct-reading instrument, the TSI Inc. model 8520 DUSTTRAK aerosol monitor. Both sampling methods were used to determine the PM2.5 exposure in a group of boilermakers exposed to welding fumes and residual fuel oil ash. The geometric mean PM2.5 concentration was 0.30 mg/m3 (GSD 3.25) and 0.31 mg/m3 (GSD 2.90)from the DUSTTRAK and gravimetric method, respectively. The Spearman rank correlation coefficient for the gravimetric and DUSTTRAK PM2.5 concentrations was 0.68. Linear regression models indicated that log, DUSTTRAK PM2.5 concentrations significantly predicted loge gravimetric PM2.5 concentrations (p < 0.01). The association between log(e) DUSTTRAK and log, gravimetric PM2.5 concentrations was found to be modified by surrogate measures for seasonal variation and type of aerosol. PM2.5 measurements from the DUSTTRAK are well correlated and highly predictive of measurements from the gravimetric sampling method for the aerosols in these work environments. However, results from this study suggest that aerosol particle characteristics may affect the relationship between the gravimetric and DUSTTRAK PM2.5 measurements. Recalibration of the DUSTTRAK for the specific aerosol, as recommended by the manufacturer, may be necessary to produce valid measures of airborne particulate matter.

  19. Fossomatic cell-counting on ewe milk: comparison with direct microscopy and study of variation factors.

    PubMed

    Gonzalo, C; Martínez, J R; Carrledo, J A; San Primitivo, F

    2003-01-01

    Using the Fossomatic method (FSCC) a total of 23,003 analytical SCC observations were carried out on 6400 aliquots taken from 80 individual ewe milk samples with the objective of studying the influence of 4 preservation procedures (without preservation, potassium dichromate, azidiol, and bronopol), 2 storage temperatures (ambient and refrigeration), 10 milk ages (3,6,12, and 24h, and 2,3,4,5,7, and 9d postcollection), and two analytical temperatures (40 and 60 degrees C). In addition, each sample was analyzed with direct microscopic method (DMSCC), using 3 different stainings for each sample: methylene blue (MB), May-Grünwald-Giemsa (MGG) and Pyronin Y-methyl green (PGM). This allowed DMSCC and FSCC (at 24 h of age) to be compared. The reference DMSCC from MB staining was a reliable method in ewe milk, though more specific stainings such as MGG and PMG slightly improve the residual standard deviation for repeated SCC. Between DMSCC and FSCC, the highest coefficients of correlation (0.972 to 0.996) corresponded to preserved and refrigerated milk, and the lowest (0.708 to 0.919) to unpreserved and ambient stored aliquots. Except for the unpreserved and ambient stored aliquots, SCC values were similar in all aliquots. Under FSCC, preservation, storage and analytical temperature, milk age, and most of the interactions showed a significant effect on SCC variation. In preserved samples, logSCC values ranged between 5.67 (bronopol) and 5.62 (azidiol). The higest values (5.72) were for unpreserved milk, which showed false overestimation of SCC due to bacterial proliferation. LogSCC was higher at 60 degrees C (5.68) than at 40 degrees C (5.65). The interaction between age, preservation and storage temperature showed no cell degeneration in properly handled samples over the 9 d of study.

  20. Evaluation of iodovinyl antibody conjugates: Comparison with a p-iodobenzoyl conjugate and direct radioiodination

    SciTech Connect

    Hadley, S.W.; Wilbur, D.S. )

    1990-03-01

    The preparations and conjugations of 2,3,5,6-tetrafluorophenyl 5-(125I/131I)iodo-4-pentenoate (7a) and 2,3,5,6-tetrafluorophenyl 3,3-dimethyl-5-(125I/131I)iodo-4-pentenoate (7b) to monoclonal antibodies are reported. Reagents 7a and 7b were prepared in high radiochemical yield by iododestannylation of their corresponding 5-tri-n-butylstannyl precursors. Radioiodinated antibody conjugates were prepared by reaction of 7a or 7b with the protein at basic pH. Evaluation of these conjugates by several in vitro procedures demonstrated that the radiolabel was attached to the antibody in a stable manner and that the conjugates maintained immunoreactivity. Comparative dual-isotope biodistribution studies of a monoclonal antibody Fab fragment conjugate of 7a and 7b with the same Fab fragment labeled with N-succinimidyl p-(131I)iodobenzoate (PIB, p-iodobenzoate, 2) or directly radioiodinated have been carried out in tumor-bearing nude mice. Coinjection of the Fab conjugate of 7a with the Fab conjugate of 2 demonstrated that the biodistributions were similar in most organs, except the neck tissue (thyroid-containing) and the stomach, which contained substantially increased levels of the 7a label. Coinjection of the Fab conjugate of 7a with the Fab fragment radioiodinated by using the chloramine-T method demonstrated that the biodistributions were remarkably similar, suggesting roughly equivalent in vivo deiodination of these labeled antibody fragments. Coinjection of the Fab conjugate of 7a with the Fab conjugate of 7b indicated that there was {approximately} a 2-fold reduction in the amount of in vivo deiodination of the 7b conjugate as compared to the 7a conjugate.

  1. Study and comparison of the maximum stress directions and main fault orientations in some active zones in Iran

    NASA Astrophysics Data System (ADS)

    Forouhid, Khatereh; Faraji, Atefeh; Ghorashi, Manouchehr

    2010-05-01

    Study and comparison of the maximum stress directions and main fault orientations in some active zones in Iran Khatereh Forouhid, Manouchehr Ghorashi, Atefeh Faraji Institute of Geophysics, Tehran University, Tehran, Iran kforouhid@yahoo.com Farajiatefeh@yahoo.com The Iranian plateau is the widest active zone in Alpine-Himalayan collision system that is located between two stable platforms, the Arabia in southwest and Eurasia in northeast. The convergence of these two platforms towards each other is the main reason for seismicity and different styles of deformation observed in Iran. In this study, the Iranian plateau is divided into 7 regions based on their seismotectonic characteristics. These regions are; Zagros, Makran, East Iran, Alborz, Kopeh Dagh, Central Iran and Azarbayejan (northwest of Iran). In each region, focal mechanism solutions of early and modern instrumental earthquakes (the only source of information suitable to use for stress distribution study in Iran) with magnitudes more than 5.0 and their relations to active faults are considered. By studying each maximum stress direction based on a group of earthquake focal mechanisms and considering main fault orientations, each region is studied individually. According to these data, some of these regions are divided into smaller parts. These sub-divided parts have some characters that make them different from their neighbors in the same region. In this regard, Zagros is studied in detail based on seismotectonic characteristics and divided into three parts, with N-S maximum stress direction (compressional) in one part and two different kind of NE-SW direction in two other. We use this information to investigate the style and distribution of active faulting in the Zagros and the relationships of this activity with shortening of the Arabia-Eurasia collision. It is worth to mention that as the fault slip will almost occur in the direction of maximum resolved shear stress on the fault plane, probably strain

  2. Comparison of four phenotypic methods for detection of metallo-β-lactamase-producing Gram-negative bacteria in rural teaching hospital

    PubMed Central

    Panchal, Chinjal A.; Oza, Sweta Sunil; Mehta, Sanjay J.

    2017-01-01

    CONTEXT: Metallo-β-lactamase (MBL)-producing bacteria lead to resistance to carbapenem an antibiotic that used as the last resort for treatment of multidrug-resistant bacteria, extended spectrum beta-lactamases, and AmpC β-lactamase-producing Gram-negative bacteria (GNB). The emergence of MBL-producing GNB is challenge to microbiology laboratories because there are no standardized guidelines available to detect them. The aim of this study was to compare four phenotypic methods to detect MBL production in GNB and to determine antibiotic sensitivity of MBL-producing isolates. MATERIALS AND METHODS: A total of 107 clinical isolates of GNB were tested for MBL production. Imipenem (IPM)-resistant GNB were taken as positive for MBL screening. MBL detection was done using ethylene diamine tetra acetic acid (EDTA) as MBL inhibitor. Four phenotypic methods were evaluated: (1) Combined disk synergy test (CDST) with 0.5M EDTA (CDST-0.5 M EDTA), (2) CDST with 0.1 M EDTA (CDST-0.1 M EDTA), (3) double-disk synergy test (DDST) with 0.5M EDTA (DDST-0.5 M EDTA), and (4) DDST with 0.1 M EDTA (DDST-0.1 M EDTA). RESULTS: Out of 107 GNB, 30 were resistant to IPM considered as screening positive. Out of 30, 21 (70%) isolates were MBL positive by CDST-0.1 M EDTA, 19 (63.33%) by CDST-0.5M EDTA, 17 (56.67%) by DDST-0.1 M EDTA, and 16 (53.33%) by DDST-0.5M EDTA. All MBL-producing Gram-negative Bacilli were resistant to ampicillin/sulbactam. Polymyxin B was found to be the most sensitive drug. CONCLUSION: CDST-0.1 M EDTA is the most sensitive method MBL detection. The detection of MBL-producing GNB is very important to control spread of the resistance. PMID:28367020

  3. Direct Comparison of Brookhaven Reflectivity Measurements with Free-Electron Theory

    SciTech Connect

    Bane, Karl L.F.

    2010-12-13

    The reflectivity at normal incidence of copper and aluminum samples was recently measured over a large frequency range at Brookhaven by one of us (JT). Then using the Kramers-Kroning integrals, and assuming the free-electron model of conductivity, the dependence of conductivity on frequency was obtained. The results seemed to suggest, for example, that the dc conductivities of the copper and evaporated aluminum samples are a factor of 3 lower than expected. We propose in this report, instead, directly fitting the free-electron model to the low frequency end of the reflectivity data. This fitting does not depend on the higher frequency results and on Kramers-Kronig integrations, but it does assume that the data at the low frequency end is sufficiently accurate. Note that for our LCLS wakefield studies, it is only over these (relatively) low frequencies that we need to know the electrical properties of the metals. The equations that relate reflectivity R with the free electron parameters dc conductivity {sigma} and relaxation time {tau} are: (1) {tilde {sigma}} = {sigma}/1-ikc{tau}; (2) {tilde n} = {radical} {tilde {epsilon}} = {radical}(1+4{pi}i{tilde k}c/{omega}); and (3) R = |{tilde n}-1/{tilde n} + 1|{sup 2}. The parameters are ac conductivity {tilde {sigma}}, index of refraction {tilde n}, dielectric constant {tilde {epsilon}}, and wave number k = {omega}/c, with {omega} frequency and c the speed of light. In Fig. 1 we show the ideal behavior of R for a reasonably good conducting metal, where {sigma} = 0.12 x 10{sup 17}/s and {tau} = 0.55 x 10{sup -14} s (solid line); these parameters are, respectively, 2% ({sigma}) and 20% ({tau}) of the nominal values for copper. The parameters were chosen so that the important features of R(k) could be seen easily in one plot. We see 3 distinct regions: (1) for low frequencies, k {approx}< 1/c{tau}, R continually decreases, with positive curvature, and with a low frequency asymptote of (1 - {radical}2kc/{pi}{sigma}); (2) for

  4. Complementation of sugary-1 Phenotype in Rice Endosperm with the Wheat Isoamylase1 Gene Supports a Direct Role for Isoamylase1 in Amylopectin Biosynthesis

    PubMed Central

    Kubo, Akiko; Rahman, Sadequr; Utsumi, Yoshinori; Li, Zhongyi; Mukai, Yasuhiko; Yamamoto, Maki; Ugaki, Masashi; Harada, Kyuya; Satoh, Hikaru; Konik-Rose, Christine; Morell, Matthew; Nakamura, Yasunori

    2005-01-01

    To examine the role of isoamylase1 (ISA1) in amylopectin biosynthesis in plants, a genomic DNA fragment from Aegilops tauschii was introduced into the ISA1-deficient rice (Oryza sativa) sugary-1 mutant line EM914, in which endosperm starch is completely replaced by phytoglycogen. A. tauschii is the D genome donor of wheat (Triticum aestivum), and the introduced fragment effectively included the gene for ISA1 for wheat (TaISA1) that was encoded on the D genome. In TaISA1-expressing rice endosperm, phytoglycogen synthesis was substantially replaced by starch synthesis, leaving only residual levels of phytoglycogen. The levels of residual phytoglycogen present were inversely proportional to the expression level of the TaISA1 protein, although the level of pullulanase that had been reduced in EM914 was restored to the same level as that in the wild type. Small but significant differences were found in the amylopectin chain-length distribution, gelatinization temperatures, and A-type x-ray diffraction patterns of the starches from lines expressing TaISA1 when compared with wild-type rice starch, although in the first two parameters, the effect was proportional to the expression level of TaISA. The impact of expression levels of ISA1 on starch structure and properties provides support for the view that ISA1 is directly involved in the synthesis of amylopectin. PMID:15618430

  5. Detailed comparison of the geodetic and direct glaciological mass balances on an annual time scale at Hintereisferner, Austria

    NASA Astrophysics Data System (ADS)

    Klug, Christoph; Bollmann, Erik; Galos, Stephan; Kaser, Georg; Prinz, Rainer; Rieg, Lorenzo; Sailer, Rudolf

    2016-04-01

    The quantification of glacier mass changes is fundamental for glacier monitoring and provides important information for climate change assessments, hydrological applications and sea-level changes. On Alpine glaciers two methods of measuring glacier mass changes are widely applied: the direct glaciological method and the geodetic method. Over the last decades several studies compared the mass balance estimates obtained by both methods to identify and correct stochastic and systematic errors. In almost all of these studies, the time span for comparison between the two methods is about one decade or longer. On Hintereisferner (HEF; Ötztal Alps, Austria) mass balance measurements were initiated in the glaciological year 1952/53, resulting in a consistent mass balance data set with an estimated accuracy of ±0.2 m w.e. a-1. Furthermore, 11 airborne laser scanning (ALS) campaigns were conducted between 2001 and 2011 at HEF, all consistent in accuracy as well as in precision (± 0.04 to 0.10 m for slopes ≤ 50°). This is a world-wide unique ALS dataset of a glacierized alpine catchment. Flight campaigns were performed close to the end of the hydrological year (30th September). Resulting data provide high quality topographic information to derive glacier mass changes by applying the geodetic method. On sub-decadal time-scales such method comparisons are rare, or reveal unexplainable large discrepancies between both mass balance methods. In this study we estimate stochastic and systematic uncertainties of the ALS data for processing volume changes, and quantify methodological differences, such as density assumptions, unequal measurement dates, crevasses and glacier dynamics. Hence, we present a method to compare direct glaciological and geodetic mass balances on an annual basis. In a first step, we calculate the annual geodetic mass balance of HEF between 2001 and 2011, resulting in a thickness change map of the glacier. In a second step, the snow cover, which has

  6. A directional Secular Variation Curve for Greece for the last 4500 years: Comparison with regional and global geomagnetic field models

    NASA Astrophysics Data System (ADS)

    de Marco, E.; Tema, E.; Lanos, P.; Kondopoulou, D.

    2009-12-01

    A total of 64 Greek archaeomagnetic directional data have been used for the establishment of the variation of the Earth’s magnetic field in Greece over the past 4500 years. Most of the data come from archaeological material but some data from Santorini lava flows are also included. The data ages range from Minoan times (~2500 BC) up to the last century with a gap around 10th to 6th century BC. All data have been relocated to Athens (37.97° N, 23.72° E) using the virtual geomagnetic pole method. Data coming from direct measurements available in Greece for the last four centuries have been also added. The secular variation (SV) curves for declination and inclination have been obtained using hierarchical Bayesian modelling. For comparison, the dataset has been also analysed using the bi-variate moving average window technique with 150 years time window shifted by 75 years. The obtained smoothed curves accompanied by a 95 % confidence envelope are compared with archaeomagnetic data from Mediterranean area and with SV curves from nearby countries. The Greek curves have also been compared with the predictions of the SCHA.DIF.3K regional and the CALS7K and ARCH3K global geomagnetic field models. Despite the differences recognised between these models, the Greek archaeomagnetic SV curve is in reasonably good agreement with their basic trends. The proposed directional SV curve can contribute, together with the intensity SV curve previously published for Greece, to the reliable archaeomagnetic dating of Greek artefacts based on the full description of the Earth’s magnetic field (declination, inclination, intensity). It is clear that the continuous update of the dataset with new results from well-dated archaeological material will increase the precision of the SV curve, especially for the time periods poorly covered by data.

  7. Seten: A tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles.

    PubMed

    Budak, Gungor; Srivastava, Rajneesh; Janga, Sarath Chandra

    2017-03-23

    RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single nucleotide resolution in a cell, currently there are very few tools which can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps. Here, we present Seten, a web-based and a command line tool, which can identify and compare processes, phenotypes and diseases associated with RBPs from condition-specific CLIP-seq profiles. Seten uses BED files resulting from most peak calling algorithms which include scores reflecting the extent of binding of an RBP on the target transcript, to provide both traditional functional enrichment as well as gene set enrichment results for a number of gene set collections including BioCarta, KEGG, Reactome, Gene Ontology (GO), Human Phenotype Ontology (HPO) and MalaCards Disease Ontology for several organisms including fruit fly, human, mouse, rat, worm, and yeast. It also provides an option to dynamically compare the associated gene sets across datasets as bubble charts, to facilitate comparative analysis. Benchmarking of Seten using eCLIP data for IGF2BP1, SRSF7 and PTBP1 against their corresponding CRISPR RNA-seq in K562 cells as well as randomized negative controls, demonstrated that its gene set enrichment method outperforms functional enrichment, with scores significantly contributing to the discovery of true annotations. Comparative performance analysis using these CRISPR control datasets revealed significantly higher precision and comparable recall to that observed using ChIP-Enrich. Seten's web interface currently provides precomputed results for about 200 CLIP-seq datasets and both command line as well as web interfaces can be used to analyze CLIP

  8. Identifying Mutations of the Tetratricopeptide Repeat Domain 37 (TTC37) Gene in Infants With Intractable Diarrhea and a Comparison of Asian and Non-Asian Phenotype and Genotype

    PubMed Central

    Lee, Wen-I; Huang, Jing-Long; Chen, Chien-Chang; Lin, Ju-Li; Wu, Ren-Chin; Jaing, Tang-Her; Ou, Liang-Shiou

    2016-01-01

    Abstract Syndromic diarrhea/tricho-hepato-enteric syndrome (SD/THE) is a rare, autosomal recessive and severe bowel disorder mainly caused by mutations in the tetratricopeptide repeat domain 37 (TTC37) gene which act as heterotetrameric cofactors to enhance aberrant mRNAs decay. The phenotype and immune profiles of SD/THE overlap those of primary immunodeficiency diseases (PIDs). Neonates with intractable diarrhea underwent immunologic assessments including immunoglobulin levels, lymphocyte subsets, lymphocyte proliferation, superoxide production, and IL-10 signaling function. Candidate genes for PIDs predisposing to inflammatory bowel disease were sequencing in this study. Two neonates, born to nonconsanguineous parents, suffered from intractable diarrhea, recurrent infections, and massive hematemesis from esopharyngeal varices due to liver cirrhosis or accompanying Trichorrhexis nodosa that developed with age and thus guided the diagnosis of SD/THE compatible to TTC37 mutations (homozygous DelK1155H, Fs∗2; heterozygous Y1169Ter and InsA1143, Fs∗3). Their immunologic evaluation showed normal mitogen-stimulated lymphocyte proliferation, superoxide production, and IL-10 signaling, but low IgG levels, undetectable antibody to hepatitis B surface antigen and decreased antigen-stimulated lymphocyte proliferation. A PubMed search for bi-allelic TTC37 mutations and phenotypes were recorded in 14 Asian and 12 non-Asian cases. They had similar presentations of infantile onset refractory diarrhea, facial dysmorphism, hair anomalies, low IgG, low birth weight, and consanguinity. A higher incidence of heart anomalies (8/14 vs 2/12; P = 0.0344, Chi-square), nonsense mutations (19 in 28 alleles), and hot-spot mutations (W936Ter, 2779-2G>A, and Y1169Ter) were found in the Asian compared with the non-Asian patients. Despite immunoglobulin therapy in 20 of the patients, 4 died from liver cirrhosis and 1 died from sepsis. Patients of all ethnicities with SD/THE with the

  9. A Korean family with KBG syndrome identified by ANKRD11 mutation, and phenotypic comparison of ANKRD11 mutation and 16q24.3 microdeletion.

    PubMed

    Kim, Hyo Jeong; Cho, Eunhae; Park, Jong Bum; Im, Woo Young; Kim, Hyon J

    2015-02-01

    KBG syndrome is a rare disease characterized by intellectual disability, typical craniofacial dysmorphism, macrodontia of the upper central incisors, short stature, and skeletal anomalies. Recently, ANKRD11 was identified as a gene that is responsible for the disease. In addition, microdeletion of 16q24.3, including ANKRD11, has been reported to result in the KBG syndrome phenotype. Herein, we discuss a Korean family with KBG syndrome, as identified by ANKRD11 gene mutation. The patients included a nine-month-old boy and his 21-month-old sister who failed to thrive and have delayed development. Chromosomal microarray was performed to identify the underlying genetic cause, but the results showed no abnormalities. However, the mother of the children was found to have features similar to her children. Therefore, we strongly suspected an autosomal-dominant inherited disease and performed whole exome sequencing. A mutation of ANKRD11 gene was found in all patients, and the frameshift variant c.2395-2398delAAAG was confirmed. Clinical manifestations of the patients were consistent with KBG syndrome. We reviewed all reported cases with confirmed ANKRD11 mutation or 16q24.3 microdeletion including ANKRD11. As a result, we conclude that severe short stature, intellectual disability, and macrodontia are the main characteristics in KBG syndrome related to ANKRD11 mutation.

  10. Bacterial communities associated with Brassica napus L. grown on trace element-contaminated and non-contaminated fields: a genotypic and phenotypic comparison

    PubMed Central

    Croes, S; Weyens, N; Janssen, J; Vercampt, H; Colpaert, JV; Carleer, R; Vangronsveld, J

    2013-01-01

    Summary Cultivable bacterial strains associated with field-grown Brassica napus L. (soil, rhizosphere and roots) from a trace elements (Cd, Zn and Pb) contaminated field and a non-contaminated control field were characterized genotypically and phenotypically. Correspondence analysis of the genotypic data revealed a correlation between soil and rhizosphere communities isolated from the same field, indicating that local conditions play a more important role in influencing the composition of (rhizosphere) soil bacterial communities than root exudates. In contrast, endophytic communities of roots showed a correlation between fields, suggesting that plants on the two fields contain similar obligate endophytes derived from a common seed endophytic community and/or can select bacteria from the rhizosphere. The latter seemed not very likely since, despite the presence of several potential endophytic taxa in the rhizosphere, no significant correlation was found between root and rhizosphere communities. The majority of Cd/Zn tolerant strains capable of phosphorus solubilization, nitrogen fixation, indole-3-acetic acid production and showing 1-aminocyclopropane-1-carboxylate deaminase capacity were found in the rhizosphere and roots of plants growing on the contaminated field. PMID:23594409

  11. Direct comparison of flow-FISH and qPCR as diagnostic tests for telomere length measurement in humans.

    PubMed

    Gutierrez-Rodrigues, Fernanda; Santana-Lemos, Bárbara A; Scheucher, Priscila S; Alves-Paiva, Raquel M; Calado, Rodrigo T

    2014-01-01

    Telomere length measurement is an essential test for the diagnosis of telomeropathies, which are caused by excessive telomere erosion. Commonly used methods are terminal restriction fragment (TRF) analysis by Southern blot, fluorescence in situ hybridization coupled with flow cytometry (flow-FISH), and quantitative PCR (qPCR). Although these methods have been used in the clinic, they have not been comprehensively compared. Here, we directly compared the performance of flow-FISH and qPCR to measure leukocytes' telomere length of healthy individuals and patients evaluated for telomeropathies, using TRF as standard. TRF and flow-FISH showed good agreement and correlation in the analysis of healthy subjects (R(2) = 0.60; p<0.0001) and patients (R(2) = 0.51; p<0.0001). In contrast, the comparison between TRF and qPCR yielded modest correlation for the analysis of samples of healthy individuals (R(2) = 0.35; p<0.0001) and low correlation for patients (R(2) = 0.20; p = 0.001); Bland-Altman analysis showed poor agreement between the two methods for both patients and controls. Quantitative PCR and flow-FISH modestly correlated in the analysis of healthy individuals (R(2) = 0.33; p<0.0001) and did not correlate in the comparison of patients' samples (R(2) = 0.1, p = 0.08). Intra-assay coefficient of variation (CV) was similar for flow-FISH (10.8 ± 7.1%) and qPCR (9.5 ± 7.4%; p = 0.35), but the inter-assay CV was lower for flow-FISH (9.6 ± 7.6% vs. 16 ± 19.5%; p = 0.02). Bland-Altman analysis indicated that flow-FISH was more precise and reproducible than qPCR. Flow-FISH and qPCR were sensitive (both 100%) and specific (93% and 89%, respectively) to distinguish very short telomeres. However, qPCR sensitivity (40%) and specificity (63%) to detect telomeres below the tenth percentile were lower compared to flow-FISH (80% sensitivity and 85% specificity). In the clinical setting, flow-FISH was more accurate, reproducible, sensitive, and specific in the measurement of human

  12. Direct Comparison of Flow-FISH and qPCR as Diagnostic Tests for Telomere Length Measurement in Humans

    PubMed Central

    Gutierrez-Rodrigues, Fernanda; Santana-Lemos, Bárbara A.; Scheucher, Priscila S.; Alves-Paiva, Raquel M.; Calado, Rodrigo T.

    2014-01-01

    Telomere length measurement is an essential test for the diagnosis of telomeropathies, which are caused by excessive telomere erosion. Commonly used methods are terminal restriction fragment (TRF) analysis by Southern blot, fluorescence in situ hybridization coupled with flow cytometry (flow-FISH), and quantitative PCR (qPCR). Although these methods have been used in the clinic, they have not been comprehensively compared. Here, we directly compared the performance of flow-FISH and qPCR to measure leukocytes' telomere length of healthy individuals and patients evaluated for telomeropathies, using TRF as standard. TRF and flow-FISH showed good agreement and correlation in the analysis of healthy subjects (R2 = 0.60; p<0.0001) and patients (R2 = 0.51; p<0.0001). In contrast, the comparison between TRF and qPCR yielded modest correlation for the analysis of samples of healthy individuals (R2 = 0.35; p<0.0001) and low correlation for patients (R2 = 0.20; p = 0.001); Bland-Altman analysis showed poor agreement between the two methods for both patients and controls. Quantitative PCR and flow-FISH modestly correlated in the analysis of healthy individuals (R2 = 0.33; p<0.0001) and did not correlate in the comparison of patients' samples (R2 = 0.1, p = 0.08). Intra-assay coefficient of variation (CV) was similar for flow-FISH (10.8±7.1%) and qPCR (9.5±7.4%; p = 0.35), but the inter-assay CV was lower for flow-FISH (9.6±7.6% vs. 16±19.5%; p = 0.02). Bland-Altman analysis indicated that flow-FISH was more precise and reproducible than qPCR. Flow-FISH and qPCR were sensitive (both 100%) and specific (93% and 89%, respectively) to distinguish very short telomeres. However, qPCR sensitivity (40%) and specificity (63%) to detect telomeres below the tenth percentile were lower compared to flow-FISH (80% sensitivity and 85% specificity). In the clinical setting, flow-FISH was more accurate, reproducible, sensitive, and specific in the

  13. A Multicenter Study on Genotype-Phenotype Correlations in the Fragile X Syndrome, Using Direct Diagnosis with Probe StB12.3: The First 2,253 Cases

    PubMed Central

    Rousseau, F.; Heitz, D.; Tarleton, J.; MacPherson, J.; Malmgren, H.; Dahl, N.; Barnicoat, A.; Mathew, C.; Mornet, E.; Tejada, I.; Maddalena, A.; Spiegel, R.; Schinzel, A.; Marcos, J. A. G.; Schorderet, D. F.; Schaap, T.; Maccioni, L.; Russo, S.; Jacobs, P. A.; Schwartz, C.; Mandel, J. L.

    1994-01-01

    We report the results of a 14-center collaborative study of genotype-phenotype correlations in 318 fragile X families; these families comprised 2,253 individuals, 1,344 of whom carried a fragile X mutation and 693 of whom had a typical full fragile X mutation. This study demonstrates that direct DNA diagnosis establishes the genotype at the FRAXA-FMR-1 locus. There was a significantly higher prevalence of “mosaic” cases among males who carry a full mutation (12%) than among females who carry a full mutation (6%); the mosaic males had a larger expansion than did the mosaic females. Mental status of premutated individuals did not differ from that of those with a normal genotype. Both the abnormal methylation of the FMR-1–EagI site and the size of the expansion were highly correlated with cytogenetics, facial dysmorphism, macroorchidism, and mental retardation (MR). Among female carriers of a full mutation, those with MR had significantly larger expansion than did those without MR. Among 164 independent couples, 3 unrelated husbands carried a premutation that suggests that the prevalence of fragile X premutations in the general population is ∼0.9% of the X chromosomes. Our data validate the use of direct DNA testing for fragile X diagnosis as well as for carrier identification and support and complete the established relationships among the DNA results and the cytogenetic, physical, and psychological aspects of the disease. PMID:8037202

  14. A multicenter study on genotype-phenotype correlations in the fragile X syndrome, using direct diagnosis with probe StB12. 3: The first 2,253 cases

    SciTech Connect

    Rousseau, F. ); Heitz, D. ); Tarleton, J. ); MacPherson, J. ); Malmgren, H.; Dahl, N.; Barnicoat, A.; Mathew, C.; Mornet, E.; Tejada, I.

    1994-08-01

    The authors report the results of a 14-center collaborative study of genotype-phenotype correlations in 318 fragile X families; these families comprised 2,253 individuals, 1,344 of whom carried a fragile X mutation and 693 of whom had a typical full fragile X mutation. This study demonstrates that direct DNA diagnosis establishes the genotype at the FRAXA-FMR-1 locus. There was a significantly higher prevalence of [open quotes]mosaic[close quotes] cases among males who carry a full mutation (12%) than among females who carry a full mutation (6%); the mosaic males had a larger expansion than did the mosaic females. Mental status of premutated individuals did not differ from that of those with a normal genotype. Both the abnormal methylation of the FMR-1-EagI site and the size of the expansion were highly correlated with cytogenetics, facial dysmorphism, macroorchidism, and mental retardation (MR). Among female carriers of a full mutation, those with MR had significantly larger expansion than did those without MR. Among 164 independent couples, 3 unrelated husbands carried a premutation that suggests that the prevalence of fragile X premutations in the general population is [approximately] 0.9% of the X chromosomes. The data validate the use of direct DNA testing for fragile X diagnosis as well as for carrier identification and support and complete the established relationships among the DNA results and the cytogenetic, physical, and psychological aspects of the disease. 38 refs., 1 fig., 9 tabs.

  15. Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

    SciTech Connect

    Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; Opper, Kathleen L.; Wagener, Kenneth B.; Stevens, Mark J.; Frischknecht, Amalie Lucile; Winey, Karen I.

    2015-02-09

    Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. In these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average

  16. Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

    DOE PAGES

    Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; ...

    2015-02-09

    Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the

  17. The influence of carbon sources on recombinant-human- growth-hormone production by Pichia pastoris is dependent on phenotype: a comparison of Muts and Mut+ strains.

    PubMed

    Orman, Mehmet Ali; Calik, Pinar; Ozdamar, Tunçer H

    2009-03-01

    The influence of carbon sources on rhGH (recombinant human growth hormone) production by two Pichia pastoris strains having different methanol utilization phenotypes (P. pastoris-hGH-Mut(+) and P. pastoris-hGH-Mut(s)) was investigated using batch bioreactors. The effect of methanol concentration (C(MeOH)) in defined and complex media, and further glycerol/methanol mixed defined media, was analysed systematically over a wide range. With methanol as the sole carbon source, strain Mut(s) grew only slightly, whereas with Mut(+), a cell concentration (C(X)) of 6.0 g of dry cells/dm(3) was obtained and an rhGH concentration (C(rhGH)) of 0.032 g/dm(3) was produced. In complex medium without glycerol at a C(MeOH) of 2% (v/v), a C(rhGH) of 0.16 g of rhGH/dm(3) was produced by Mut(s), a value 3-fold higher than that produced by Mut(+), despite the fact that the C(X) of Mut(+) (6.1 g/dm(3)) was 2-fold higher than that of Mut(s) (3.0 g/dm(3)). In a glycerol/methanol mixed defined medium, methanol consumption began when glycerol was totally depleted, indicating that glycerol is a repressor of the AOX1 (alcohol oxidase-1 gene) promoter. With strain Mut(s) at a glycerol concentration (C(Gly)) of 30 g/dm(3) and a C(MeOH) of 1% (v/v), the C(rhGH) produced was 0.11 g/dm(3), whereas, with the Mut(+) strain, a C(rhGH) of 0.06 g/dm(3) was obtained at a C(Gly) of 30 g/dm(3) and a C(MeOH) of 4%. As methanol is not consumed by Mut(s) strain effectively and the presence of methanol in the fermentation broth triggers induction of the AOX1 promoter, our results encourage the use of the Mut(s) strain for rhGH production. In addition to rhGH production, the specific cell growth rates, specific methanol and/or glycerol utilization rates and maintenance coefficients in methanol- and glycerol-based defined media were determined. With a methanol-based defined medium and using the Mut(+) strain, a higher specific growth rate (mu) of approx. 0.14 h(-1) was observed during the exponential cell growth

  18. Rapid identification of ascomycetous yeasts from clinical specimens by a molecular method based on flow cytometry and comparison with identifications from phenotypic assays.

    PubMed

    Page, Brent T; Shields, Christine E; Merz, William G; Kurtzman, Cletus P

    2006-09-01

    This study was designed to compare the identification of ascomycetous yeasts recovered from clinical specimens by using phenotypic assays (PA) and a molecular flow cytometric (FC) method. Large-subunit rRNA domains 1 and 2 (D1/D2) gene sequence analysis was also performed and served as the reference for correct strain identification. A panel of 88 clinical isolates was tested that included representatives of nine commonly encountered species and six infrequently encountered species. The PA included germ tube production, fermentation of seven carbohydrates, morphology on corn meal agar, urease and phenoloxidase activities, and carbohydrate assimilation tests when needed. The FC method (Luminex) employed species-specific oligonucleotides attached to polystyrene beads, which were hybridized with D1/D2 amplicons from the unidentified isolates. The PA identified 81 of 88 strains correctly but misidentified 4 of Candida dubliniensis, 1 of C. bovina, 1 of C. palmioleophila, and 1 of C. bracarensis. The FC method correctly identified 79 of 88 strains and did not misidentify any isolate but did not identify nine isolates because oligonucleotide probes were not available in the current library. The FC assay takes approximately 5 h, whereas the PA takes from 2 h to 5 days for identification. In conclusion, PA did well with the commonly encountered species, was not accurate for uncommon species, and takes significantly longer than the FC method. These data strongly support the potential of FC technology for rapid and accurate identification of medically important yeasts. With the introduction of new antifungals, rapid, accurate identification of pathogenic yeasts is more important than ever for guiding antifungal chemotherapy.

  19. Prevalence of microdeletion 22q11 in patients with hypernasal speech due to velopharyngeal insufficiency: Expanded phenotype and clinical comparison to nondeletion

    SciTech Connect

    Siegel-Bartelt, J.; Cytrynbaum, C.; Witzel, M.A.; Teshima, I.E.

    1994-09-01

    Microdeletion 22q11.2 has been reported as a frequent ethiology of both velocardiofacial (VCF) and DiGeorge syndromes. We have studied the prevalence of microdeletion 22q11 in a group of patients ascertained through a Speech and Language clinic presenting with (1) velopharyngeal insufficiency (VPI) and (2) difficultly in school. Growth parameters were measured, and facies were scored for features of VCF. Microdeletions were detected at locus D22S75 by FISH with probe N25 (Oncor), and at 22q11.2 with high resolution banding analysis (HRB). One child with typical VCF facies was considered to have a deletion at 22q11 with HRB, but is not deleted with N25, indicating that N25 may not detect all deletion patients. An additional 8/30 children tested to date were deleted with the N25 probe. Heart defects were present in only 2/8 deletion patients: VSD/ASD and PS/AS. One N25 deletion patient was atypica; he has a tall, lanky habitus (height = 90%), and facies not characteristic of CVF. As expected, there is a trend to lower head size, smaller ear size, and more typical facies in deletion patients; however, four of the nondeletion patients also had a clinical diagnosis of VCF. Medially displaced carotid arteries were present in both groups, which is therefore not a diagnostic feature of microdeletion 22q11. Our findings indicate that the microdeletion 22q11 is frequent (26% in this series) in a population with VPI, even when not selected for typical facies. We believe this series supports the view that microdeletion 22q11 has a broader clinical phenotype than previously recognized.

  20. Comparison of the Accuracy of Two Conventional Phenotypic Methods and Two MALDI-TOF MS Systems with That of DNA Sequencing Analysis for Correctly Identifying Clinically Encountered Yeasts

    PubMed Central

    Chao, Qiao-Ting; Lee, Tai-Fen; Teng, Shih-Hua; Peng, Li-Yun; Chen, Ping-Hung; Teng, Lee-Jene; Hsueh, Po-Ren

    2014-01-01

    We assessed the accuracy of species-level identification of two commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Bruker Biotyper and Vitek MS) and two conventional phenotypic methods (Phoenix 100 YBC and Vitek 2 Yeast ID) with that of rDNA gene sequencing analysis among 200 clinical isolates of commonly encountered yeasts. The correct identification rates of the 200 yeast isolates to species or complex (Candida parapsilosis complex, C. guilliermondii complex and C. rugosa complex) levels by the Bruker Biotyper, Vitek MS (using in vitro devices [IVD] database), Phoenix 100 YBC and Vitek 2 Yeast ID (Sabouraud's dextrose agar) systems were 92.5%, 79.5%, 89%, and 74%, respectively. An additional 72 isolates of C. parapsilosis complex and 18 from the above 200 isolates (30 in each of C. parapsilosis, C. metapsilosis, and C. orthopsilosis) were also evaluated separately. Bruker Biotyper system could accurately identify all C. parapsilosis complex to species level. Using Vitek 2 MS (IVD) system, all C. parapsilosis but none of C. metapsilosis, or C. orthopsilosis could be accurately identified. Among the 89 yeasts misidentified by the Vitek 2 MS (IVD) system, 39 (43.8%), including 27 C. orthopsilosis isolates, could be correctly identified Using the Vitek MS Plus SARAMIS database for research use only. This resulted in an increase in the rate of correct identification of all yeast isolates (87.5%) by Vitek 2 MS. The two species in C. guilliermondii complex (C. guilliermondii and C. fermentati) isolates were correctly identified by cluster analysis of spectra generated by the Bruker Biotyper system. Based on the results obtained in the current study, MALDI-TOF MS systems present a promising alternative for the routine identification of yeast species, including clinically commonly and rarely encountered yeast species and several species belonging to C. parapsilosis complex, C. guilliermondii complex

  1. Direct comparison of repeated soil inventory and carbon flux budget to detect soil carbon stock changes in grassland

    NASA Astrophysics Data System (ADS)

    Ammann, C.; Leifeld, J.; Neftel, A.; Fuhrer, J.

    2012-04-01

    Experimental assessment of soil carbon (C) stock changes over time is typically based on the application of either one of two methods, namely (i) repeated soil inventory and (ii) determination of the ecosystem C budget or net biome productivity (NBP) by continuous measurement of CO2 exchange in combination with quantification of other C imports and exports. However, there exist hardly any published study hitherto that directly compared the results of both methods. Here, we applied both methods in parallel to determine C stock changes of two temperate grassland fields previously converted from long-term cropland. The grasslands differed in management intensity with either intensive management (high fertilization, frequent cutting) or extensive management (no fertilization, less frequent cutting). Soil organic C stocks (0-45 cm depth) were quantified at the beginning (2001) and the end (2006) of a 5 year observational period using the equivalent soil mass approach. For the same period and in both fields, NBP was quantified from net CO2 fluxes monitored using eddy covariance systems, and measured C import by organic fertilizer and C export by harvest. Both NBP and repeated soil inventories revealed a consistent and significant difference between management systems of 170 ± 48 and 253 ± 182 g C m-2 a-1, respectively. For both fields, the inventory method showed a tendency towards higher C loss/smaller C gain than NBP. In the extensive field, a significant C loss was observed by the inventory but not by the NBP approach. Thus both, flux measurements and repeated soil sampling, seem to be adequate and equally suited for detecting relative management effects. However, the suitability for tracking absolute changes in SOC could not be proven for neither of the two methods. Overall, our findings stress the need for more direct comparisons to evaluate whether the observed difference in the outcome of the two approaches reflects a general methodological bias, which would

  2. Quantification of Microbial Phenotypes

    PubMed Central

    Martínez, Verónica S.; Krömer, Jens O.

    2016-01-01

    Metabolite profiling technologies have improved to generate close to quantitative metabolomics data, which can be employed to quantitatively describe the metabolic phenotype of an organism. Here, we review the current technologies available for quantitative metabolomics, present their advantages and drawbacks, and the current challenges to generate fully quantitative metabolomics data. Metabolomics data can be integrated into metabolic networks using thermodynamic principles to constrain the directionality of reactions. Here we explain how to estimate Gibbs energy under physiological conditions, including examples of the estimations, and the different methods for thermodynamics-based network analysis. The fundamentals of the methods and how to perform the analyses are described. Finally, an example applying quantitative metabolomics to a yeast model by 13C fluxomics and thermodynamics-based network analysis is presented. The example shows that (1) these two methods are complementary to each other; and (2) there is a need to take into account Gibbs energy errors. Better estimations of metabolic phenotypes will be obtained when further constraints are included in the analysis. PMID:27941694

  3. Evaluation of [123I]isopropyliodoamphetamine as a tracer for local cerebral blood flow using direct autoradiographic comparison.

    PubMed

    Lear, J L; Ackermann, R F; Kameyama, M; Kuhl, D E

    1982-01-01

    We investigated [123I]isopropyliodoamphetamine (IMP) for potential use in the autoradiographic determination of local cerebral blood flow (LCBF) in animals. The technique of direct autoradiographic comparison, derived from double radionuclide autoradiography, was used to compare the simultaneous uptakes of IMP and [14C]iodoantipyrine (IAP), a reference tracer, in awake and anesthetized rats. This new technique offers several advantages over the previously developed methods of comparing tracers, brain uptake index and first pass extraction ratio. These include the avoidance of disrupting normal cerebral blood-brain tracer exchange and the ability to compare uptakes at substructural levels, whereas the other methods are limited to larger areas. Mean values of LCBF obtained with IMP agreed closely with those using IAP, from 20 to 300 ml/100 g/min. Because IMP was found to have an extremely high effective brain:blood partition coefficient, approximately 25:1, a linear uptake tracer model could be used for IMP yielding more precise values than could IAP for LCBF values above 150. IMP was found to measure choroid plexus flows much more accurately than IAP, values being greater than 500 for IMP compared to approximately 200 for IAP. Because the mechanism of the extremely high partition coefficient of IMP is not yet defined, however, care must be used in measuring LCBF with IMP where the trapping mechanisms of normal vessels may be disrupted.

  4. Evaluation of (/sup 123/I)isopropyliodoamphetamine as a tracer for local cerebral blood flow using direct autoradiographic comparison

    SciTech Connect

    Lear, J.L.; Ackermann, R.F.; Kameyama, M.; Kuhl, D.E.

    1982-01-01

    We investigated (/sup 123/I)isopropyliodoamphetamine (IMP) for potential use in the autoradiographic determination of local cerebral blood flow (LCBF) in animals. The technique of direct autoradiographic comparison, derived from double radionuclide autoradiography, was used to compare the simultaneous uptakes of IMP and (/sup 14/C)iodoantipyrine (IAP), a reference tracer, in awake and anesthetized rats. This new technique offers several advantages over the previously developed methods of comparing tracers, brain uptake index and first pass extraction ratio. These include the avoidance of disrupting normal cerebral blood-brain tracer exchange and the ability to compare uptakes at substructural levels, whereas the other methods are limited to larger areas. Mean values of LCBF obtained with IMP agreed closely with those using IAP, from 20 to 300 ml/100 g/min. Because IMP was found to have an extremely high effective brain:blood partition coefficient, approximately 25:1, a linear uptake tracer model could be used for IMP yielding more precise values than could IAP for LCBF values above 150. IMP was found to measure choroid plexus flows much more accurately than IAP, values being greater than 500 for IMP compared to approximately 200 for IAP. Because the mechanism of the extremely high partition coefficient of IMP is not yet defined, however, care must be used in measuring LCBF with IMP where the trapping mechanisms of normal vessels may be disrupted.

  5. A direct comparison of methods used to measure oxidized glutathione in biological samples: 2-vinylpyridine and N-ethylmaleimide.

    PubMed

    Mcgill, Mitchell R; Jaeschke, Hartmut

    2015-01-01

    The ratio of glutathione disulfide (GSSG) to reduced glutathione (GSH) in biological samples is a frequently used parameter of oxidative stress. As a result, many methods are developed to measure GSSG. The most popular and convenient of these relies on enzymatic cycling following the chemical masking of GSH in the sample using 2-vinylpyridine (2VP). However, 2VP is a slow reactant and its use may result in artificially high GSSG values due to oxidation of the sample over time. Fast-reacting reagents such as N-ethylmaleimide (NEM) may provide more accurate results. We performed a direct comparison of methods using 2VP and NEM. With 2VP, the percentage of total glutathione (GSH+GSSG) in the oxidized form was significantly higher in all tested tissues (kidney, lung and liver) compared to the same procedure performed using NEM. We conclude that NEM, when coupled with a simple solid-phase extraction procedure, is more accurate for the determination of GSSG. We also tested the effects of various handling and storage conditions on GSSG. A detailed description and a discussion of other methods are also included.

  6. A direct comparison of methods used to measure oxidized glutathione in biological samples: 2-vinylpyridine and N-ethylmaleimide

    PubMed Central

    McGill, Mitchell R.; Jaeschke, Hartmut

    2016-01-01

    The ratio of glutathione disulfide (GSSG) to reduced glutathione (GSH) in biological samples is a frequently used parameter of oxidative stress. As a result, many methods have been developed to measure GSSG. The most popular and convenient of these relies on enzymatic cycling following the chemical masking of GSH in the sample using 2-vinylpyridine (2VP). However, 2VP is a slow reactant and its use may result in artificially high GSSG values due to oxidation of the sample over time. Faster-reacting reagents like N-ethylmaleimide (NEM) may provide more accurate results. We have performed a direct comparison of methods using 2VP and NEM. With 2VP, the percentage of total glutathione (GSH+GSSG) in the oxidized form was significantly higher in all tested tissues (kidney, lung, and liver) compared to the same procedure performed using NEM. We conclude that NEM, when coupled with a simple solid phase extraction procedure, is more accurate for determination of GSSG. We also tested the effects of various handling and storage conditions on GSSG. A detailed description and a discussion of other methods are also included. PMID:26461121

  7. Revisiting AI-2 quorum sensing inhibitors: direct comparison of alkyl-DPD analogues and a natural product fimbrolide.

    PubMed

    Lowery, Colin A; Abe, Takumi; Park, Junguk; Eubanks, Lisa M; Sawada, Daisuke; Kaufmann, Gunnar F; Janda, Kim D

    2009-11-04

    Quorum sensing (QS) systems have been discovered in a wide variety of bacteria, and mediate both intra- and interspecies communication. The AI-2-based QS system represents the most studied of these proposed interspecies systems and has been shown to regulate diverse functions such as bioluminescence, expression of virulence factors, and biofilm formation. As such, the development of modulatory compounds, both agonists and antagonists, is of great interest for the study of unknown AI-2-based QS systems and the potential treatment of bacterial infections. The fimbrolide class of natural products has exhibited excellent inhibitory activity against AI-2-based QS and as such may be considered the "gold standard" of AI-2 inhibitors. Thus, we sought to include a fimbrolide as a control compound for our recently developed alkyl-DPD panel of AI-2 modulators. Herein, we present a revised synthesis of a commonly studied fimbrolide as well as a direct comparison between the fimbrolide and alkyl-DPD analogues. We demonstrate that our alkyl-DPD analogues are more potent inhibitors of QS in both Vibrio harveyi and Salmonella typhimurium, the two organisms with defined AI-2 QS systems, and in doing so call into question the widely accepted use of fimbrolide-derived compounds as the "gold standard" of AI-2 inhibition.

  8. Gas exchange dependency on diffusion coefficient: direct /sup 222/Rn and /sup 3/He comparisons in a small lake

    SciTech Connect

    Torgersen, T.; Mathieu, G.; Hesslein, R.H.; Broecker, W.S.

    1982-01-20

    A direct field comparison was conducted to determine the dependency of gas exchange coefficient (k/sub x/) on the diffusion coefficient (D/sub x/). The study also sought to confirm the enhanced vertical exchange properties of limnocorrals and similar enclosures. Gas exchange coefficients for /sup 222/Rn and /sup 3/He were determined in a small northern Ontario lake, using a /sup 226/Ra and /sup 3/H spike to gain the necessary precision. The results indicate that the gas exchange coefficient is functionally dependent on the diffusion coefficient raised to the 1.22/sub -35//sup + > 12/ power (k/sub x/ = f(D/sub x//sup 1.22)), clearly supporting the stagnant film model of gas exchange. Limnocorrals were found to have gas exchange rates up to 1.7 times higher than the whole lake in spite of the observation of more calm surface conditions in the corral than in the open lake. 33 references, 6 figures, 8 tables.

  9. A Bioequivalence Test by the Direct Comparison of Concentration-versus-Time Curves Using Local Polynomial Smoothers

    PubMed Central

    Chang, Howard H.; Orange, Dana

    2016-01-01

    In order to test if two chemically or pharmaceutically equivalent products have the same efficacy and/or toxicity, a bioequivalence (BE) study is conducted. The 80%/125% rule is the most commonly used criteria for BE and states that BE cannot be claimed unless the 90% CIs for the ratio of selected pharmacokinetics (PK) parameters of the tested to the reference drug are within 0.8 to 1.25. Considering that estimates of these PK parameters are derived from the concentration-versus-time curves, a direct comparison between these curves motivates an alternative and more flexible approach to test BE. Here, we propose to frame the BE test in terms of an equivalence of concentration-versus-time curves which are constructed using local polynomial smoother (LPS). A metric is presented to quantify the distance between the curves and its 90% CIs are calculated via bootstrapping. Then, we applied the proposed procedures to data from an animal study and found that BE between a generic drug and its brand name cannot be concluded, which was consistent with the results by applying the 80%/125% rule. However, the proposed procedure has the advantage of testing only on a single metric, instead of all PK parameters. PMID:28050196

  10. Component processes in contour integration: a direct comparison between snakes and ladders in a detection and a shape discrimination task.

    PubMed

    Vancleef, Kathleen; Wagemans, Johan

    2013-11-01

    In contour integration, a relevant question is whether snakes and ladders are processed similarly. Higher presentation time thresholds for ladders in detection tasks indicate this is not the case. However, in a detection task only processing differences at the level of element linking and possibly contour localization might be picked up, while differences at the shape encoding level cannot be noticed. In this study, we make a direct comparison of detection and shape discrimination tasks to investigate if processing differences in the visual system between snakes and ladders are limited to contour detection or extend to higher level contour processing, like shape encoding. Stimuli consisted of elements that were oriented collinearly (snakes) or orthogonally (ladders) to the contour path and were surrounded by randomly oriented background elements. In two tasks, six experienced subjects either detected the contour when presented with a contour and a completely random stimulus or performed a shape discrimination task when presented with two contours with different curvature. Presentation time was varied in 9 steps between 8 and 492 ms. By applying a generalized linear mixed model we found that differences in snake and ladder processing are not limited to a detection stage but are also apparent at a shape encoding stage.

  11. Direct simulation of electron transfer using ring polymer molecular dynamics: comparison with semiclassical instanton theory and exact quantum methods.

    PubMed

    Menzeleev, Artur R; Ananth, Nandini; Miller, Thomas F

    2011-08-21

    The use of ring polymer molecular dynamics (RPMD) for the direct simulation of electron transfer (ET) reaction dynamics is analyzed in the context of Marcus theory, semiclassical instanton theory, and exact quantum dynamics approaches. For both fully atomistic and system-bath representations of condensed-phase ET, we demonstrate that RPMD accurately predicts both ET reaction rates and mechanisms throughout the normal and activationless regimes of the thermodynamic driving force. Analysis of the ensemble of reactive RPMD trajectories reveals the solvent reorganization mechanism for ET that is anticipated in the Marcus rate theory, and the accuracy of the RPMD rate calculation is understood in terms of its exact description of statistical fluctuations and its formal connection to semiclassical instanton theory for deep-tunneling processes. In the inverted regime of the thermodynamic driving force, neither RPMD nor a related formulation of semiclassical instanton theory capture the characteristic turnover in the reaction rate; comparison with exact quantum dynamics simulations reveals that these methods provide inadequate quantization of the real-time electronic-state dynamics in the inverted regime.

  12. Kinetic simulation of direct-drive capsule implosions and its comparison with experiments and radiation hydrodynamic simulation

    NASA Astrophysics Data System (ADS)

    Kwan, Thomas; Le, Ari; Schmitt, Mark; Herrmann, Hans; Batha, Steve

    2015-11-01

    We have carried out simulations of direct-drive capsule implosion experiments conducted on Omega laser facility at the Laboratory of Laser energetics of the University of Rochester. The capsules had a glass shell (SiO2) with D, T, He-3 fills at various proportions. One-dimensional radiation hydrodynamic calculations and kinetic particle/hybrid simulations with LSP were carried out for the post-shot analysis to compare neutron yield, yield ratio, and shell convergence in assessing the effects of plasma kinetic effects. The LSP simulations were initiated with the output from the rad-hydro simulations at the end of the laser-drive. The electrons are treated as a fluid while all the ion species by the kinetic PIC technique. Our LSP simulations clearly showed species separation between the deuterons, tritons and He-3 during the implosion but significantly less after the compression. The neutron yield, gamma bang-time and -width from the LSP simulations compared favorably with experiments. Detail comparison among the kinetic simulations, rad-hydro simulations, and experimental results will be presented. Work performed under the auspices of the US Department of Energy by Los Alamos National Laboratory under Contract No. W-7405-ENG-36.

  13. Mass spectrometry of planetary exospheres at high relative velocity: direct comparison of open- and closed source measurements

    NASA Astrophysics Data System (ADS)

    Meyer, Stefan; Tulej, Marek; Wurz, Peter

    2016-04-01

    The exploration of habitable worlds around the gas giants in the Solar System is of major interest in upcoming planetary missions. Exactly this theme is addressed by the Jupiter Icy Moons Explorer (JUICE) mission of ESA, which will characterise Ganymede, Europa and Callisto as planetary objects and potential habitats [1], [2]. We developed a prototype of the Neutral gas and Ion Mass spectrometer (NIM) of the Particle Environment Package (PEP) for the JUICE mission intended for composition measurements of neutral gas and thermal plasma. NIM/PEP will be used to measure the chemical composition of the exospheres of the icy Jovian moons. Besides direct ion measurement, the NIM instrument is able to measure the inflowing neutral gas in two different modes: in neutral mode the gas enters directly the ion source (open source) and in thermal mode, the gas gets thermally accommodated to wall temperature by several collisions inside an equilibrium sphere before entering the ion source (closed source). We performed measurements with the prototype NIM using a neutral gas beam of 1 up to 5 km/s velocity in the neutral and thermal mode. The current trajectory of JUICE foresees a flyby velocity of 4 km/s at Europa, other flybys are in the range of 1 up to 7 km/s and velocity in Ganymede orbits is around 2 km/s. Different species are used for gas beam, such as noble gases Ne, Ar, Kr as well as molecules like H2, Methane, Ethane, Propane and more complex ones. We will present the results of these measurements with respect to fragmentation and density enhancements in the closed source mode. Furthermore, we will give a direct comparison between open and closed source mode measurements. References: [1] ESA, "JUICE assessment study report (Yellow Book)", ESA/SRE(2011)18, 2012. [2] O. Grasset, M.K. Dougherty, A. Coustenis, E.J. Bunce, C. Erd, D. Titov, M. Blanc, A. Coates, P. Drossart, L.N. Fletcher, H. Hussmann, R. Jaumann, N. Krupp, J.-P. Lebreton, O. Prieto-Ballesteros, P. Tortora, F

  14. A database of Caenorhabditis elegans behavioral phenotypes.

    PubMed

    Yemini, Eviatar; Jucikas, Tadas; Grundy, Laura J; Brown, André E X; Schafer, William R

    2013-09-01

    Using low-cost automated tracking microscopes, we have generated a behavioral database for 305 Caenorhabditis elegans strains, including 76 mutants with no previously described phenotype. The growing database currently consists of 9,203 short videos segmented to extract behavior and morphology features, and these videos and feature data are available online for further analysis. The database also includes summary statistics for 702 measures with statistical comparisons to wild-type controls so that phenotypes can be identified and understood by users.

  15. Unguided clinical and actuarial assessment of re-offending risk: a direct comparison with sex offenders in Denmark.

    PubMed

    Bengtson, Susanne; Långström, Niklas

    2007-06-01

    Meta-analyses suggest that actuarial risk assessments outperform unguided clinical judgment for prediction of recidivism in criminal offenders. However, there is a lack of direct comparisons of the predictive accuracy of clinical judgment and actuarial risk scales for sexual offenders. We followed up 121 male sex offenders (> or =18 years) subjected to pre-trial forensic psychiatric assessment in Denmark in 1978-1992 (mean post-detainment time = 16.4 years) to compare the predictive validity of unstructured clinical judgment of recidivism risk with that of the well-established Static-99 (Hanson and Thornton, Law and Human Behavior 24:119-136, 2000) and an extension of the Static-99, the Static-2002 (Hanson and Thornton, Notes on the development of Static-2002 (Rep. No. 2003-01), Public Safety and Emergency Preparedness Canada, Ottawa, Canada, 2003). The predictive accuracy of unguided judgment did not exceed chance for any sexual, severe sexual or any violent (sexual or non-sexual) reconviction (AUCs of the ROC curve = 0.52, 95%CI = 0.41-0.63; 0.50, 95%CI = 0.34-0.67; and 0.57, 95%CI = 0.40-0.73, respectively). In contrast, all three outcomes were predicted significantly better than chance by the Static-99 (AUC = 0.62, 95%CI = 0.52-0.72; 0.72, 95%CI = 0.59-0.84; and 0.71, 95%CI = 0.56-0.86) and the Static-2002 (AUC = 0.67, 95%CI = 0.57-0.77; 0.69, 95%CI = 0.56-0.83; and 0.70, 95%CI = 0.55-0.86). Static-99 outperformed clinical judgment for sexual recidivision (chi(2) = 5.11, df = 1, p < .05). The Static-2002 was significantly more accurate for the prediction of any sexual recidivism as compared to unguided clinical judgment but its advantage fell just short of statistical significance for severe sexual recidivism (chi(2) = 3.56, df = 1, p = 0.06). When tested for recidivism within 2 years, none of the three prediction methods yielded results significantly better than chance for any outcome. This direct trial of the unguided clinical method argues against its

  16. [Sweat chloride measurement using direct potentiometry: Spotchem(®) (Elitech-Arkray) evaluation and comparison with coulometry and conductivity].

    PubMed

    Nguyen-Khoa, Thao; Borgard, Jean-Pierre; Miled, Ryad; Rota, Michèle

    2013-01-01

    Sweat chloride (Cl(-)) measurement is a key step for the diagnosis of cystic fibrosis. The coulometric technique is validated in this context by international guidelines. The aim of our study was to evaluate the assay for sweat Cl(-) ions using direct potentiometry on disposable cassette (Spotchem™ SE EL-1520, Elitech-Arkray) by comparing results to those obtained on the same sample, by coulometry (Chloride analyser Sherwood 926S, Dutscher). To complete our table of correspondence between the results of Cl(-) ions and sweat conductivity (Sweat Check™ 3100), conductivity has been also achieved for 99 of the 139 sweat samples studied. Linearity of each technique performed extends from 10 to 120 mmol/L. The coefficients of variation within and between runs are < 5%. Comparison of 139 results (Passing - Bablock regression) shows a significant difference (p < 0.001): [Spotchem] = 1.026 [Chloride analyser] + 1.8, r = 0.996. After correction with regression factors, only 6 pairs of values (4.6%) had a difference greater than ± 5 mmol/L). The results of conductivity measurement is strongly correlated with those of Cl(-) ions (r = 0.959 for Chloride analyser and 0.965 for Spotchem; p = 0.576) with a linear relationship between the decision thresholds from 30 to 60 mmol/L Cl(-). Sweat Cl(-) determinations using Spotchem™ analyser meet the criteria required by analytical recommendations. The technique is standardized, easy to perform and fast. Its good practicability makes the sweat test independent to operator and allows point-of care use.

  17. Direct comparison of progenitor cells derived from adipose, muscle, and bone marrow from wild-type or craniosynostotic rabbits

    PubMed Central

    GM, Cooper; EL, Lensie; JJ, Cray; MR, Bykowski; GE, DeCesare; MA, Smalley; MP, Mooney; PG, Campbell; JE, Losee

    2010-01-01

    Background Reports have identified cells capable of osteogenic differentiation in bone marrow, muscle, and adipose tissues, but there are few direct comparisons of these different cell-types. Also, few have investigated the potential connection between a tissue-specific pathology and cells derived from seemingly unrelated tissues. Here, we compare cells isolated from wild-type rabbits or rabbits with nonsyndromic craniosynostosis, defined as the premature fusion of one or more of the cranial sutures. Methods Cells were derived from bone marrow, adipose, and muscle of 10 day-old wild-type rabbits (WT; n=17) or from age-matched rabbits with familial nonsyndromic craniosynostosis (CS; n=18). Cells were stimulated with bone morphogenetic protein 4 (BMP4) and alkaline phosphatase expression and cell proliferation were assessed. Results In WT rabbits, cells derived from muscle had more alkaline phosphatase activity than cells derived from either adipose or bone marrow. The cells derived from CS rabbit bone marrow and muscle were significantly more osteogenic than WT. Adipose-derived cells demonstrated no significant differences. While muscle-derived cells were most osteogenic in WT rabbits, bone marrow-derived cells were most osteogenic in CS rabbits. Conclusions Results suggest that cells from different tissues have different potentials for differentiation. Furthermore, cells derived from rabbits with craniosynostosis were different from wild-type derived cells. Interestingly, cells derived from the craniosynostotic rabbits were not uniformly more responsive compared with wild-type cells, suggesting that specific tissue-derived cells may react differently in individuals with craniosynostosis. PMID:20871482

  18. Endothelial Dysfunction of Bypass Graft: Direct Comparison of In Vitro and In Vivo Models of Ischemia-Reperfusion Injury

    PubMed Central

    Veres, Gábor; Hegedűs, Péter; Barnucz, Enikő; Zöller, Raphael; Klein, Stephanie; Schmidt, Harald; Radovits, Tamás; Korkmaz, Sevil; Karck, Matthias; Szabó, Gábor

    2015-01-01

    Background Although, ischemia/reperfusion induced vascular dysfunction has been widely described, no comparative study of in vivo- and in vitro-models exist. In this study, we provide a direct comparison between models (A) ischemic storage and in-vitro reoxygenation (B) ischemic storage and in vitro reperfusion (C) ischemic storage and in-vivo reperfusion. Methods and Results Aortic arches from rats were stored for 2 hours in saline. Arches were then (A) in vitro reoxygenated (B) in vitro incubated in hypochlorite for 30 minutes (C) in vivo reperfused after heterotransplantation (2, 24 hours and 7 days reperfusion). Endothelium-dependent and independent vasorelaxations were assessed in organ bath. DNA strand breaks were assessed by TUNEL-method, mRNA expressions (caspase-3, bax, bcl-2, eNOS) by quantitative real-time PCR, proteins by Western blot analysis and the expression of CD-31 by immunochemistry. Endothelium-dependent maximal relaxation was drastically reduced in the in-vivo models compared to ischemic storage and in-vitro reperfusion group, and no difference showed between ischemic storage and control group. CD31-staining showed significantly lower endothelium surface ratio in-vivo, which correlated with TUNEL-positive ratio. Increased mRNA and protein levels of pro- and anti-apoptotic gens indicated a significantly higher damage in the in-vivo models. Conclusion Even short-period of ischemia induces severe endothelial damage (in-vivo reperfusion model). In-vitro models of ischemia-reperfusion injury can be limitedly suited for reliable investigations. Time course of endothelial stunning is also described. PMID:25875813

  19. First Directly Retrieved Global Distribution of Tropospheric Column Ozone from GOME: Comparison with the GEOS-CHEM Model

    NASA Technical Reports Server (NTRS)

    Liu, Xiong; Chance, Kelly; Sioris, Christopher E.; Kurosu, Thomas P.; Spurr, Robert J. D.; Martin, Randall V.; Fu, Tzung-May; Logan, Jennifer A.; Jacob, Daniel J.; Palmer, Paul I.; Newchurch, Michael J.; Megretskaia, Inna A.; Chatfield, Robert B.

    2006-01-01

    We present the first directly retrieved global distribution of tropospheric column ozone from Global Ozone Monitoring Experiment (GOME) ultraviolet measurements during December 1996 to November 1997. The retrievals clearly show signals due to convection, biomass burning, stratospheric influence, pollution, and transport. They are capable of capturing the spatiotemporal evolution of tropospheric column ozone in response to regional or short time-scale events such as the 1997-1998 El Nino event and a 10-20 DU change within a few days. The global distribution of tropospheric column ozone displays the well-known wave-1 pattern in the tropics, nearly zonal bands of enhanced tropospheric column ozone of 36-48 DU at 20degS-30degS during the austral spring and at 25degN-45degN during the boreal spring and summer, low tropospheric column ozone of <30 DU uniformly distributed south of 35 S during all seasons, and relatively high tropospheric column ozone of >33 DU at some northern high-latitudes during the spring. Simulation from a chemical transport model corroborates most of the above structures, with small biases of <+/-5 DU and consistent seasonal cycles in most regions, especially in the southern hemisphere. However, significant positive biases of 5-20 DU occur in some northern tropical and subtropical regions such as the Middle East during summer. Comparison of GOME with monthly-averaged Measurement of Ozone and Water Vapor by Airbus in-service Aircraft (MOZAIC) tropospheric column ozone for these regions usually shows good consistency within 1 a standard deviations and retrieval uncertainties. Some biases can be accounted for by inadequate sensitivity to lower tropospheric ozone, the different spatiotemporal sampling and the spatiotemporal variations in tropospheric column ozone.

  20. The role of predation in variation in body shape in guppies Poecilia reticulata: a comparison of field and common garden phenotypes.

    PubMed

    Burns, J G; Di Nardo, P; Rodd, F H

    2009-10-01

    The body shapes of both wild-caught and laboratory-reared male and female Trinidadian guppies Poecilia reticulata from two low-predation and two high-predation populations were studied, but predation regime did not seem to be the most important factor affecting body shape. Instead, complicated patterns of plasticity in body shape among populations and the sexes were found. In particular, populations differed in the depth of the caudal peduncle, which is the muscular region just anterior to the tail fin rays and from which most swimming power is generated. Strikingly, the direction of population differences in caudal peduncle depth observed in wild-caught individuals was reversed when P. reticulata were raised in a common laboratory environment.

  1. In vivo comparison of CXA-101 (FR264205) with and without tazobactam versus piperacillin-tazobactam using human simulated exposures against phenotypically diverse gram-negative organisms.

    PubMed

    Bulik, Catharine C; Tessier, Pamela R; Keel, Rebecca A; Sutherland, Christina A; Nicolau, David P

    2012-01-01

    CXA-101 is a novel antipseudomonal cephalosporin with enhanced activity against Gram-negative organisms displaying various resistance mechanisms. This study evaluates the efficacy of exposures approximating human percent free time above the MIC (%fT > MIC) of CXA-101 with or without tazobactam and piperacillin-tazobactam (TZP) against target Gram-negative organisms, including those expressing extended-spectrum β-lactamases (ESBLs). Sixteen clinical Gram-negative isolates (6 Pseudomonas aeruginosa isolates [piperacillin-tazobactam MIC range, 8 to 64 μg/ml], 4 Escherichia coli isolates (2 ESBL and 2 non-ESBL expressing), and 4 Klebsiella pneumoniae isolates (3 ESBL and 1 non-ESBL expressing) were used in an immunocompetent murine thigh infection model. After infection, groups of mice were administered doses of CXA-101 with or without tazobactam (2:1) designed to approximate the %fT > MIC observed in humans given 1 g of CXA-101 with or without tazobactam every 8 h as a 1-h infusion. As a comparison, groups of mice were administered piperacillin-tazobactam doses designed to approximate the %fT > MIC observed in humans given 4.5 g piperacillin-tazobactam every 6 h as a 30-min infusion. Predicted piperacillin-tazobactam %fT > MIC exposures of greater than 40% resulted in static to >1 log decreases in CFU in non-ESBL-expressing organisms with MICs of ≤32 μg/ml after 24 h of therapy. Predicted CXA-101 with or without tazobactam %fT > MIC exposures of ≥37.5% resulted in 1- to 3-log-unit decreases in CFU in non-ESBL-expressing organisms, with MICs of ≤16 μg/ml after 24 h of therapy. With regard to the ESBL-expressing organisms, the inhibitor combinations showed enhanced CFU decreases versus CXA-101 alone. Due to enhanced in vitro potency and resultant increased in vivo exposure, CXA-101 produced statistically significant reductions in CFU in 9 isolates compared with piperacillin-tazobactam. The addition of tazobactam to CXA-101 produced significant reductions in

  2. Comparison of direct numerical simulation of lean premixed methane-air flames with strained laminar flame calculations.

    SciTech Connect

    Chen, Jacqueline H.; Hawkes, Evatt R.

    2004-08-01

    Direct numerical simulation (DNS) with complex chemistry was used to study statistics of displacement and consumption speeds in turbulent lean premixed methane-air flames. The main focus of the study is an evaluation of the extent to which a turbulent flame in the thin reaction zones regime can be described by an ensemble of strained laminar flames. Conditional averages with respect to strain for displacement and consumption speeds are presented over a wide range of strain typically encountered in a turbulent flame, compared with previous studies that either made local pointwise comparisons or conditioned the data on small strain and curvature. The conditional averages for positive strains are compared with calculated data from two different canonical strained laminar configurations to determine which is the optimal representation of a laminar flame structure embedded in a turbulent flame: the reactant-to-product (R-to-P) configuration or the symmetric twin flame configuration. Displacement speed statistics are compared for the progress-variable isosurface of maximum reaction rate and an isosurface toward the fresh gases, which are relevant for both modeling and interpretation of experiment results. Displacement speeds in the inner reaction layer are found to agree very well with the laminar R-to-P calculations over a wide range of strain for higher Damkhler number conditions, well beyond the regime in which agreement was expected. For lower Damkhler numbers, a reduced response to strain is observed, consistent with previous studies and theoretical expectations. Compared with the inner layer, broader and shifted probability density functions (PDFs) of displacement speed were observed in the fresh gases, and the agreement with the R-to-P calculations deteriorated. Consumption speeds show a poorer agreement with strained laminar calculations, which is attributed to multidimensional effects and a more attenuated unsteady response to strain fluctuations; however, they

  3. Comparison of direct numerical simulation of lean premixed methane-air flames with strained laminar flame calculations

    SciTech Connect

    Hawkes, Evatt R.; Chen, Jacqueline H.

    2006-01-01

    Direct numerical simulation (DNS) with complex chemistry was used to study statistics of displacement and consumption speeds in turbulent lean premixed methane-air flames. The main focus of the study is an evaluation of the extent to which a turbulent flame in the thin reaction zones regime can be described by an ensemble of strained laminar flames. Conditional averages with respect to strain for displacement and consumption speeds are presented over a wide range of strain typically encountered in a turbulent flame, compared with previous studies that either made local pointwise comparisons or conditioned the data on small strain and curvature. The conditional averages for positive strains are compared with calculated data from two different canonical strained laminar configurations to determine which is the optimal representation of a laminar flame structure embedded in a turbulent flame: the reactant-to-product (R-to-P) configuration or the symmetric twin flame configuration. Displacement speed statistics are compared for the progress-variable isosurface of maximum reaction rate and an isosurface toward the fresh gases, which are relevant for both modeling and interpretation of experiment results. Displacement speeds in the inner reaction layer are found to agree very well with the laminar R-to-P calculations over a wide range of strain for higher Damkohler number conditions, well beyond the regime in which agreement was expected. For lower Damkohler numbers, a reduced response to strain is observed, consistent with previous studies and theoretical expectations. Compared with the inner layer, broader and shifted probability density functions (PDFs) of displacement speed were observed in the fresh gases, and the agreement with the R-to-P calculations deteriorated. Consumption speeds show a poorer agreement with strained laminar calculations, which is attributed to multidimensional effects and a more attenuated unsteady response to strain fluctuations; however

  4. Generalizability and Dependability of Behavior Assessment Methods to Estimate Academic Engagement: A Comparison of Systematic Direct Observation and Direct Behavior Rating

    ERIC Educational Resources Information Center

    Briesch, Amy M.; Chafouleas, Sandra M.; Riley-Tillman, T. Chris

    2010-01-01

    Although substantial attention has been directed toward building the psychometric evidence base for academic assessment methods (e.g., state mastery tests, curriculum-based measurement), similar examination of behavior assessment methods has been comparatively limited, particularly with regard to assessment purposes most desirable within…

  5. Wind directions predicted from global circulation models and wind directions determined from eolian sandstones of the western United States-A comparison

    USGS Publications Warehouse

    Parrish, Judith T.; Peterson, F.

    1988-01-01

    Wind directions for Middle Pennsylvanian through Jurassic time are predicted from global circulation models for the western United States. These predictions are compared with paleowind directions interpreted from eolian sandstones of Middle Pennsylvanian through Jurassic age. Predicted regional wind directions correspond with at least three-quarters of the paleowind data from the sandstones; the rest of the data may indicate problems with correlation, local effects of paleogeography on winds, and lack of resolution of the circulation models. The data and predictions suggest the following paleoclimatic developments through the time interval studied: predominance of winter subtropical high-pressure circulation in the Late Pennsylvanian; predominance of summer subtropical high-pressure circulation in the Permian; predominance of summer monsoonal circulation in the Triassic and earliest Jurassic; and, during the remainder of the Jurassic, influence of both summer subtropical and summer monsoonal circulation, with the boundary between the two systems over the western United States. This sequence of climatic changes is largely owing to paleogeographic changes, which influenced the buildup and breakdown of the monsoonal circulation, and possibly owing partly to a decrease in the global temperature gradient, which might have lessened the influence of the subtropical high-pressure circulation. The atypical humidity of Triassic time probably resulted from the monsoonal circulation created by the geography of Pangaea. This circulation is predicted to have been at a maximum in the Triassic and was likely to have been powerful enough to draw moisture along the equator from the ocean to the west. ?? 1988.

  6. Comparison of the direct antiglobulin rosetting reaction (DARR) and direct immunofluorescence (DIF) for demonstration of sIg-bearing lymphocytes in pigs, sheep and cattle.

    PubMed Central

    Binns, R M; Licence, S T; Symons, D B; Gurner, B W; Coombs, R R; Walters, D E

    1979-01-01

    Tests with untreated and trypsin-treated red cells (rbc) from a variety of species showed that anti-Ig-coupled pig RBC are good indicator cells for the study of ruminant blood sIg + lymphocytes by the DARR test; coupled donkey and rabbit RBC are suitable for investigating pig lymphocytes. The different species showed the following percentages of sIg + lymphocytes (M +/- SE) by direct immunofluorescence (DIF) and the direct antiglobulin rosetting reaction (DARR) respectively:pigs 9.2 +/- 0.7% and 16.3 +/- 1.2%; sheep 20.2 +/- 1.2% and 33.1 +/- 1.6%; Cattle 13.5 +/- 1.4% and 28.9 +/- 3.5%. The mean ratio of sIg + lymphocytes shown by the two tests (DARR/DIF) for each species was 1.80 +/- 0.08 for pigs, 1.73 +/- 0.7 for sheep and 2.15 +/- 0.18 for cattle. Preincubation of pig and sheep lymphocytes at 37 degrees for 1 h did not alter the proportion of sIg + lymphocytes detected by either test. Thus the DARR test reveals a further population of sIg + lymphocytes in addition to that detected by immunofluorescence, whose number is proportional to the B population as measured by DIF and whose sIg is intimately associated with the membrane. PMID:374254

  7. Phenotype definition in epilepsy.

    PubMed

    Winawer, Melodie R

    2006-05-01

    Phenotype definition consists of the use of epidemiologic, biological, molecular, or computational methods to systematically select features of a disorder that might result from distinct genetic influences. By carefully defining the target phenotype, or dividing the sample by phenotypic characteristics, we can hope to narrow the range of genes that influence risk for the trait in the study population, thereby increasing the likelihood of finding them. In this article, fundamental issues that arise in phenotyping in epilepsy and other disorders are reviewed, and factors complicating genotype-phenotype correlation are discussed. Methods of data collection, analysis, and interpretation are addressed, focusing on epidemiologic studies. With this foundation in place, the epilepsy subtypes and clinical features that appear to have a genetic basis are described, and the epidemiologic studies that have provided evidence for the heritability of these phenotypic characteristics, supporting their use in future genetic investigations, are reviewed. Finally, several molecular approaches to phenotype definition are discussed, in which the molecular defect, rather than the clinical phenotype, is used as a starting point.

  8. Membrane fouling of forward osmosis (FO) membrane for municipal wastewater treatment: A comparison between direct FO and OMBR.

    PubMed

    Sun, Yan; Tian, Jiayu; Zhao, Zhiwei; Shi, Wenxin; Liu, Dongmei; Cui, Fuyi

    2016-11-01

    In this work, membrane fouling behavior in a direct forward osmosis (FO) and an osmotic membrane bioreactor (OMBR) for municipal wastewater treatment was systematically investigated and compared. During the long-term operation, much severer flux decline was observed for the direct FO than that for the OMBR. The cake layer was found to be much thicker, together with large amounts of microorganisms growing on the membrane surface in direct FO. Interestingly, no obvious attachment of microorganisms on the membrane surface was observed in the OMBR. The fourier transform infrared spectroscopy (FTIR) and excitation emission matrices (EEM) analyses showed the polysaccharides and proteins were the dominant organic foulants in the fouling layer, and the quantity of the organic substances was also higher in direct FO than that in OMBR. Energy-dispersive X-ray (EDX) results indicated the main inorganic elements in the fouling layer were Ca, Mg, Fe and P, all of which exhibited higher relative percentages in direct FO than that in OMBR. The occurrence of higher contents of microorganisms, organic foulants and inorganic elements in the cake layer caused a higher filtration resistance for the FO membrane in the direct FO. Although more severe membrane fouling was identified in direct FO, the hydraulic and chemical cleaning was more effective on recovering the water permeability of the membrane in direct FO than that in OMBR.

  9. A direct comparison of local-global integration in autism and other developmental disorders: implications for the central coherence hypothesis.

    PubMed

    Bernardino, Inês; Mouga, Susana; Almeida, Joana; van Asselen, Marieke; Oliveira, Guiomar; Castelo-Branco, Miguel

    2012-01-01

    The weak central coherence hypothesis represents one of the current explanatory models in Autism Spectrum Disorders (ASD). Several experimental paradigms based on hierarchical figures have been used to test this controversial account. We addressed this hypothesis by testing central coherence in ASD (n = 19 with intellectual disability and n = 20 without intellectual disability), Williams syndrome (WS, n = 18), matched controls with intellectual disability (n = 20) and chronological age-matched controls (n = 20). We predicted that central coherence should be most impaired in ASD for the weak central coherence account to hold true. An alternative account includes dorsal stream dysfunction which dominates in WS. Central coherence was first measured by requiring subjects to perform local/global preference judgments using hierarchical figures under 6 different experimental settings (memory and perception tasks with 3 distinct geometries with and without local/global manipulations). We replicated these experiments under 4 additional conditions (memory/perception*local/global) in which subjects reported the correct local or global configurations. Finally, we used a visuoconstructive task to measure local/global perceptual interference. WS participants were the most impaired in central coherence whereas ASD participants showed a pattern of coherence loss found in other studies only in four task conditions favoring local analysis but it tended to disappear when matching for intellectual disability. We conclude that abnormal central coherence does not provide a comprehensive explanation of ASD deficits and is more prominent in populations, namely WS, characterized by strongly impaired dorsal stream functioning and other phenotypic traits that contrast with the autistic phenotype. Taken together these findings suggest that other mechanisms such as dorsal stream deficits (largest in WS) may underlie impaired central coherence.

  10. Direct comparison between X-ray nanotomography and scanning electron microscopy for the microstructure characterization of a solid oxide fuel cell anode

    SciTech Connect

    Quey, R.; Suhonen, H.; Laurencin, J.; Cloetens, P.; Bleuet, P.

    2013-04-15

    X-ray computed nanotomography (nano-CT) and scanning electron microscopy (SEM) have been applied to characterize the microstructure of a Solid Oxide Fuel Cell (SOFC) anode. A direct comparison between the results of both methods is conducted on the same region of the microstructure to assess the spatial resolution of the nano-CT microstructure, SEM being taken as a reference. A registration procedure is proposed to find out the position of the SEM image within the nano-CT volume. It involves a second SEM observation, which is taken along an orthogonal direction and gives an estimate reference SEM image position, which is then refined by an automated optimization procedure. This enables an unbiased comparison between the cell porosity morphologies provided by both methods. In the present experiment, nano-CT is shown to underestimate the number of pores smaller than 1 μm and overestimate the size of the pores larger than 1.5 μm. - Highlights: ► X-ray computed nanotomography (nano-CT) and SEM are used to characterize an SOFC anode. ► A methodology is proposed to compare the nano-CT and SEM data on the same region. ► The spatial resolution of the nano-CT data is assessed from that comparison.

  11. Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms

    PubMed Central

    Rokyta, Darin R.; Margres, Mark J.; Calvin, Kate

    2015-01-01

    Protein expression is a major link in the genotype–phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms. PMID:26358130

  12. Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms.

    PubMed

    Rokyta, Darin R; Margres, Mark J; Calvin, Kate

    2015-09-09

    Protein expression is a major link in the genotype-phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms.

  13. The overshoot and phenotypic equilibrium in characterizing cancer dynamics of reversible phenotypic plasticity.

    PubMed

    Chen, Xiufang; Wang, Yue; Feng, Tianquan; Yi, Ming; Zhang, Xingan; Zhou, Da

    2016-02-07

    The paradigm of phenotypic plasticity indicates reversible relations of different cancer cell phenotypes, which extends the cellular hierarchy proposed by the classical cancer stem cell (CSC) theory. Since it is still questionable if the phenotypic plasticity is a crucial improvement to the hierarchical model or just a minor extension to it, it is worthwhile to explore the dynamic behavior characterizing the reversible phenotypic plasticity. In this study we compare the hierarchical model and the reversible model in predicting the cell-state dynamics observed in biological experiments. Our results show that the hierarchical model shows significant disadvantages over the reversible model in describing both long-term stability (phenotypic equilibrium) and short-term transient dynamics (overshoot) in cancer cell populations. In a very specific case in which the total growth of population due to each cell type is identical, the hierarchical model predicts neither phenotypic equilibrium nor overshoot, whereas the reversible model succeeds in predicting both of them. Even though the performance of the hierarchical model can be improved by relaxing the specific assumption, its prediction to the phenotypic equilibrium strongly depends on a precondition that may be unrealistic in biological experiments. Moreover, it still does not show as rich dynamics as the reversible model in capturing the overshoots of both CSCs and non-CSCs. By comparison, it is more likely for the reversible model to correctly predict the stability of the phenotypic mixture and various types of overshoot behavior.

  14. Comparison and relation of indirect and direct dynamic indexes of cardiac pumping capacity in chronic heart failure.

    PubMed

    Williams, Simon G; Tzeng, Bing-H; Barker, Diane; Tan, Lip-Bun

    2005-10-15

    Cardiac power output (CPO), the product of cardiac output (CO) and mean arterial pressure (MAP), is a direct measure of cardiac pumping capability and is strongly indicative of prognosis and exercise ability in patients with chronic heart failure (CHF). However, it is not as easily measured as indirect indicators of cardiac function, such as peak oxygen consumption (VO(2)) or peak "circulatory power" (CircP), the product of VO(2) and MAP. The relation between direct and indirect indexes of cardiac pumping capacity was evaluated in 219 ambulatory patients with CHF. CircP was found to have a direct and consistent relation with CPO, overall (R = 0.93, p <0.0001) and at peak exercise (R = 0.84, p < 0.0001). The results suggest CircP to be an adequate measure of cardiac pumping capacity when the more directly measured CPO is not available.

  15. Direct Comparison of the Performance of a Bio-inspired Synthetic Nickel Catalyst and a [NiFe]-Hydrogenase, Both Covalently Attached to Electrodes

    SciTech Connect

    Rodriguez-Macia, Patricia; Dutta, Arnab; Lubitz, Wolfgang; Shaw, Wendy J.; Rudiger, Olaf

    2015-10-12

    The active site of hydrogenases has been a source of inspiration for the development of molecular catalysts. However, direct comparisons between molecular catalysts and enzymes have not been possible because different techniques are used to evaluate both types of catalysts, minimizing our ability to determine how far we’ve come in mimicking the impressive enzymatic performance. Here we directly compare the catalytic properties of the [Ni(PCy2NGly2)2]2+ complex with the [NiFe]-hydrogenase from Desulfobivrio vulgaris Miyazaki F (DvMF) immobilized to a functionalized electrode under identical conditions. At pH=7, the enzyme has higher performance in both activity and overpotential, and is more stable, while at low pH, the molecular catalyst outperforms the enzyme in all respects. The Ni complex also has increased tolerance to CO. This is the first direct comparison of enzymes and molecular complexes, enabling a unique understanding of the benefits and detriments of both systems, and advancing our understanding of the utilization of these bioinspired complexes in fuel cells. AD and WJS acknowledge the Office of Science Early Career Research Program through the US Department of Energy (US DOE), Office of Science, Office of Basic Energy Sciences (BES), and Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the US DOE.

  16. A new method to infer causal phenotype networks using QTL and phenotypic information.

    PubMed

    Wang, Huange; van Eeuwijk, Fred A

    2014-01-01

    In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs) to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO) algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG) algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request.

  17. [Comparison between the official indirect method and the direct method of control of vaccines against sheep enterotoxemia].

    PubMed

    Dufrene, M; Poul, J; Gayot, G

    1976-01-01

    The official methods of control of vaccines against sheep enterotoxemia are indirect in two ways : on the one hand they are carried out on animals for which the vaccine is not intended, and on the other hand they test only an immunological serum reaction. Another method consisting of direct testing by intravenous injection of toxin has been carried out on mice previously vaccinated with different doses. It has been shown that it is possible to obtain a certain level of protection giving a good dose-effect relation. However, immunity provided by this direct method is weak although the vaccine utilized is considered very efficacious with regard to the official norms of the direct test. These results, which are both encouraging and disappointing, will be the subject of a more intensive study of the different parameters in question.

  18. Simulation of Channel Segregation During Directional Solidification of In—75 wt pct Ga. Qualitative Comparison with In Situ Observations

    NASA Astrophysics Data System (ADS)

    Saad, Ali; Gandin, Charles-André; Bellet, Michel; Shevchenko, Natalia; Eckert, Sven

    2015-11-01

    Freckles are common defects in industrial casting. They result from thermosolutal convection due to buoyancy forces generated from density variations in the liquid. The present paper proposes a numerical analysis for the formation of channel segregation using the three-dimensional (3D) cellular automaton (CA)—finite element (FE) model. The model integrates kinetics laws for the nucleation and growth of a microstructure with the solution of the conservation equations for the casting, while introducing an intermediate modeling scale for a direct representation of the envelope of the dendritic grains. Directional solidification of a cuboid cell is studied. Its geometry, the alloy chosen as well as the process parameters are inspired from experimental observations recently reported in the literature. Snapshots of the convective pattern, the solute distribution, and the morphology of the growth front are qualitatively compared. Similitudes are found when considering the coupled 3D CAFE simulations. Limitations of the model to reach direct simulation of the experiments are discussed.

  19. Comparison of IPDA lidar receiver sensitivity for coherent detection and for direct detection using sine-wave and pulsed modulation.

    PubMed

    Sun, Xiaoli; Abshire, James B

    2012-09-10

    We use theoretical models to compare the receiver signal to noise ratio (SNR) vs. average rate of detected signal photons for an integrated path differential absorption (IPDA) lidar using coherent detection with continuous wave (CW) lasers and direct detection with sine-wave and pulse modulations. The results show the coherent IPDA lidar has high receiver gain and narrow bandwidth to overcome the effects of detector circuit noise and background light, but the actual receiver performance can be limited by the coherent mixing efficiency, speckle and other factors. For direct detection, using sine-wave modulation allows the use of a low peak power laser transmitter and synchronous detection. The pulse modulation technique requires higher laser peak powers but is more efficient than sine-wave modulation in terms of average detected signal photon rate required to achieve a given receiver SNR. We also conducted experiments for the direct detection cases and the results agreed well with theory.

  20. Comparisons of jitter, shimmer, and signal-to-noise ratio from directly digitized versus taped voice samples.

    PubMed

    Gelfer, M P; Fendel, D M

    1995-12-01

    The purpose of this study was to compare jitter, shimmer, and signal-to-noise ratio (SNR) measures obtained from tape-recorded samples with the same measures made on directly digitized voice samples, with use of the CSpeech acoustic analysis program. Subjects included 30 young women who phonated the vowel /a/ at a comfortable pitch and loudness level. Voice samples were simultaneously recorded and digitized, and the resulting perturbation measures for the two conditions were compared. Results indicated that there were small but statistically significant differences between percent jitter, percent shimmer, and SNR calculated from taped samples compared with the same measures calculated from directly digitized samples. It was concluded that direct digitization for clinical measures of vocal perturbation was most desirable, but that taped samples could be used, if necessary, with some caution.

  1. A comparison of EGFR mutation testing methods in lung carcinoma: direct sequencing, real-time PCR and immunohistochemistry.

    PubMed

    Angulo, Bárbara; Conde, Esther; Suárez-Gauthier, Ana; Plaza, Carlos; Martínez, Rebeca; Redondo, Pilar; Izquierdo, Elisa; Rubio-Viqueira, Belén; Paz-Ares, Luis; Hidalgo, Manuel; López-Ríos, Fernando

    2012-01-01

    The objective of this study is to compare two EGFR testing methodologies (a commercial real-time PCR kit and a specific EGFR mutant immunohistochemistry), with direct sequencing and to investigate the limit of detection (LOD) of both PCR-based methods. We identified EGFR mutations in 21 (16%) of the 136 tumours analyzed by direct sequencing. Interestingly, the Therascreen EGFR Mutation Test kit was able to characterize as wild-type one tumour that could not be analyzed by direct sequencing of the PCR product. We then compared the LOD of the kit and that of direct sequencing using the available mutant tumours. The kit was able to detect the presence of a mutation in a 1% dilution of the total DNA in nine of the 18 tumours (50%), which tested positive with the real-time quantitative PCR method. In all cases, EGFR mutation was identified at a dilution of 5%. Where the mutant DNA represented 30% of the total DNA, sequencing was able to detect mutations in 12 out of 19 cases (63%). Additional experiments with genetically defined standards (EGFR ΔE746-A750/+ and EGFR L858R/+) yielded similar results. Immunohistochemistry (IHC) staining with exon 19-specific antibody was seen in eight out of nine cases with E746-A750del detected by direct sequencing. Neither of the two tumours with complex deletions were positive. Of the five L858R-mutated tumours detected by the PCR methods, only two were positive for the exon 21-specific antibody. The specificity was 100% for both antibodies. The LOD of the real-time PCR method was lower than that of direct sequencing. The mutation specific IHC produced excellent specificity.

  2. A Comparison of EGFR Mutation Testing Methods in Lung Carcinoma: Direct Sequencing, Real-time PCR and Immunohistochemistry

    PubMed Central

    Angulo, Bárbara; Conde, Esther; Suárez-Gauthier, Ana; Plaza, Carlos; Martínez, Rebeca; Redondo, Pilar; Izquierdo, Elisa; Rubio-Viqueira, Belén; Paz-Ares, Luis; Hidalgo, Manuel; López-Ríos, Fernando

    2012-01-01

    The objective of this study is to compare two EGFR testing methodologies (a commercial real-time PCR kit and a specific EGFR mutant immunohistochemistry), with direct sequencing and to investigate the limit of detection (LOD) of both PCR-based methods. We identified EGFR mutations in 21 (16%) of the 136 tumours analyzed by direct sequencing. Interestingly, the Therascreen EGFR Mutation Test kit was able to characterize as wild-type one tumour that could not be analyzed by direct sequencing of the PCR product. We then compared the LOD of the kit and that of direct sequencing using the available mutant tumours. The kit was able to detect the presence of a mutation in a 1% dilution of the total DNA in nine of the 18 tumours (50%), which tested positive with the real-time quantitative PCR method. In all cases, EGFR mutation was identified at a dilution of 5%. Where the mutant DNA represented 30% of the total DNA, sequencing was able to detect mutations in 12 out of 19 cases (63%). Additional experiments with genetically defined standards (EGFR ΔE746-A750/+ and EGFR L858R/+) yielded similar results. Immunohistochemistry (IHC) staining with exon 19-specific antibody was seen in eight out of nine cases with E746-A750del detected by direct sequencing. Neither of the two tumours with complex deletions were positive. Of the five L858R-mutated tumours detected by the PCR methods, only two were positive for the exon 21-specific antibody. The specificity was 100% for both antibodies. The LOD of the real-time PCR method was lower than that of direct sequencing. The mutation specific IHC produced excellent specificity. PMID:22952784

  3. COMPARISON OF HIGH-DEFINITION OSCILLOMETRIC AND DIRECT ARTERIAL BLOOD PRESSURE MEASUREMENT IN ANESTHETIZED CHEETAHS (ACINONYX JUBATUS).

    PubMed

    Sant Cassia, Emma V; Boswood, Adrian; Tordiffe, Adrian S W

    2015-09-01

    Blood pressure measurement reveals important insights into the health of conscious and anesthetized individuals. This is of particular interest in cheetahs (Acinonyx jubatus), which in captivity are known to suffer from chronic diseases that may be associated with hypertension and which often require immobilization for transport or veterinary treatment. Invasive testing methods are considered the gold standard but are not practical in many settings. Consequently, it is important to evaluate the use of noninvasive methods in this species. Measurements for systolic, diastolic, and mean arterial pressure obtained using high-definition oscillometry (HDO) at the coccygeal artery were compared to simultaneous direct measurements obtained via catheterization of the femoral or dorsal pedal artery in eight anesthetized captive cheetahs during nine anesthetic events. Overall, HDO and direct measurements agreed most closely for mean arterial pressure, and the poorest agreement was observed for systolic pressure. There was a tendency for low diastolic pressures to be underestimated and for high diastolic pressures to be overestimated. Across all three parameters, HDO measurements from the tail overestimated directly measured pressures in the femoral artery and underestimated those in the dorsal pedal artery. HDO agreed most closely with directly measured dorsal pedal pressures. Mean arterial pressure showed the greatest precision (standard deviation of 10.2 mm Hg) and lowest bias (-1.2 mm Hg), with 75.9% of readings within 10 mm Hg of the direct dorsal pedal pressure. Agreement with systolic pressure was hindered by a high bias (-10.4 mm Hg), but if a correction factor of +10 mm Hg was applied to all systolic measurements, agreement was improved and 65.7% of readings were within 10 mm Hg of the direct pressure. When compared to criteria defined by the American College of Veterinary Internal Medicine for validation of blood pressure devices, results were favorable, but a

  4. Properties of fujicalin, a new modified anhydrous dibasic calcium phosphate for direct compression: comparison with dicalcium phosphate dihydrate.

    PubMed

    Schlack, H; Bauer-Brandl, A; Schubert, R; Becker, D

    2001-09-01

    The novel, commercially available, free-flowing spherically granulated dicalcium phosphate anhydrous (SGDCPA) Fujicalin for direct tableting was compared with directly compressible dicalcium phosphate dihYdrate (DCPD), the properties of which are well known. The two excipients were investigated and compared with regard to their physical and powder properties, compressibility, and compactibility. As a consequence of the spherical shape of its particles, SGDCPA shows the same good flowability and even better compactibility. In contrast to DCPD, SGDCPA shows significant uptake of moisture when exposed to relative humidities (RHs) exceeding 70%. For both excipients, the main deformation mechanism is fragmentation, with SGDCPA yielding significantly stronger tablets.

  5. Macrophage phenotypes in atherosclerosis.

    PubMed

    Colin, Sophie; Chinetti-Gbaguidi, Giulia; Staels, Bart

    2014-11-01

    Initiation and progression of atherosclerosis depend on local inflammation and accumulation of lipids in the vascular wall. Although many cells are involved in the development and progression of atherosclerosis, macrophages are fundamental contributors. For nearly a decade, the phenotypic heterogeneity and plasticity of macrophages has been studied. In atherosclerotic lesions, macrophages are submitted to a large variety of micro-environmental signals, such as oxidized lipids and cytokines, which influence the phenotypic polarization and activation of macrophages resulting in a dynamic plasticity. The macrophage phenotype spectrum is characterized, at the extremes, by the classical M1 macrophages induced by T-helper 1 (Th-1) cytokines and by the alternative M2 macrophages induced by Th-2 cytokines. M2 macrophages can be further classified into M2a, M2b, M2c, and M2d subtypes. More recently, additional plaque-specific macrophage phenotypes have been identified, termed as Mox, Mhem, and M4. Understanding the mechanisms and functional consequences of the phenotypic heterogeneity of macrophages will contribute to determine their potential role in lesion development and plaque stability. Furthermore, research on macrophage plasticity could lead to novel therapeutic approaches to counteract cardiovascular diseases such as atherosclerosis. The present review summarizes our current knowledge on macrophage subsets in atherosclerotic plaques and mechanism behind the modulation of the macrophage phenotype.

  6. Automatic Direction of Spatial Attention to Male Versus Female Stimuli: A Comparison of Heterosexual Men and Women.

    PubMed

    Snowden, Robert J; Curl, Catriona; Jobbins, Katherine; Lavington, Chloe; Gray, Nicola S

    2016-05-01

    Abundant research has shown that men's sexual attractions are more category-specific in relation to gender than women's are. We tested whether the early automatic allocation of spatial attention reflects these sexual attractions. The dot-probe task was used to assess whether spatial attention was attracted to images of either male or female models that were naked or partially clothed. In Experiment 1, men were faster if the target appeared after the female stimulus, whereas women were equally quick to respond to targets after male or female stimuli. In Experiment 2, neutral cues were introduced. Men were again faster to female images in comparison to male or neutral images, but showed no bias on the male versus neutral test. Women were faster to both male and female pictures in comparison to neutral pictures. However, in this experiment they were also faster to female pictures than to male pictures. The results suggest that early attentional processes reveal category-specific interest to the preferred sexual category for heterosexual men, and suggest that heterosexual women do not have category-specific guidance of attentional mechanisms. The technique may have promise in measuring sexual interest in other situations where participants may not be able, or may not be willing, to report upon their sexual interests (e.g., assessment of paedophilic interest).

  7. Estimation of Bi induced changes in the direct E0 band gap of III-V-Bi alloys and comparison with experimental data

    NASA Astrophysics Data System (ADS)

    Samajdar, D. P.; Dhar, S.

    2016-03-01

    Quantum dielectric Theory (QDT) is used to explain the band gap bowing effect observed in III-V-Bismides such as InSb1-xBix, InAs1-xBix, InP1-xBix, GaSb1-xBix, GaAs1-xBix and GaP1-xBix. The dependence of the direct E0 band gap for these alloys on Bi mole fraction is calculated using QDT which requires the evaluation of the bowing parameter c. The bowing parameter gives the deviation of the direct E0 band gap from the linear relationship of E0 with Bi mole fraction. The band gap reduction values obtained using QDT are compared with those calculated using Virtual Crystal approximation (VCA) and Valence Band Anticrossing (VBAC) model as well as with the reported experimental data and the results of the comparison shows excellent agreement.

  8. Comparison of measured direct normal irradiance data to values calculated using the DISC model for Texas Panhandle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Direct normal irradiance (DNI) is required in the performance estimation of concentrating solar energy systems. The objective of this paper is to compare measured and modeled DNI data for a site in the Texas Panhandle (Bushland, Texas) to determine the accuracy of the model and where improvements mi...

  9. Direct measurement of single and multiple passband intelligibilities: Comparison with estimates based upon the Speech Intelligibility Index

    NASA Astrophysics Data System (ADS)

    Warren, Richard M.; Bashford, James A.; Lenz, Peter W.

    2004-05-01

    The intelligibility of individual bands spanning the speech spectrum is of interest for theoretical and practical reasons, and has been the subject of considerable experimental investigation. Direct measurement of passband intelligibility can be confounded with contributions from filter slopes, but by employing sufficiently high orders of FIR filtering, the present study has removed all slope contributions and measured directly intelligibilities of 1-octave and 1/3-octave passbands. Stimuli employed were based upon the same commercial recording of monosyllabic words and the same frequency bands used for the Speech Intelligibility Index (SII) [American National Standards Institute, S3.5, 1997]. SII employs an indirect procedure for estimating intelligibility: lists of band ``importance'' values are derived from intelligibility scores for high-pass and low-pass speech having incrementally varied cutoff frequencies. These importance values are correlated with intelligibility, and were transformed into intelligibility estimates using the published transfer function. Directly measured intelligibilities differ for some, but not all, SII-based intelligibility estimates for bands heard singly and in combination. Direct determination of intelligibilities of individual and multiple passbands is suggested as a simple and accurate alternative to the methods based upon SII and other indirect procedures for estimating the intelligibility of frequency-limited speech. [Work supported by NIH.

  10. Interactions of Tollmien-Schlichting waves and Dean vortices. Comparison of direct numerical simulation and a weakly nonlinear theory

    NASA Technical Reports Server (NTRS)

    Singer, Bart A.; Zang, Thomas A.

    1989-01-01

    Direct numerical simulation is used to evaluate a weakly nonlinear theory describing the interaction of Tollmien-Schlichting waves with Dean vortices in curved channel flow. The theory and the simulation agree for certain combinations of parameters, but the two approaches give conflicting results for other combinations. Some possibilities for these discrepancies are discussed.

  11. Using Direct Behavior Rating (DBR) to Screen for School Social Risk: A Preliminary Comparison of Methods in a Kindergarten Sample

    ERIC Educational Resources Information Center

    Chafouleas, Sandra M.; Kilgus, Stephen P.; Hernandez, Paul

    2009-01-01

    In this study, preliminary evidence of the potential for Direct Behavior Rating (DBR) in screening assessment of school social behavior is provided through evaluation of the concurrent validity of DBR with a commonly used criterion measure. The teacher-completed form of the "Social Skills Rating System" (SSRS) was selected as the…

  12. Model-measurement comparison of ammonia bi-directional air-surface exchange fluxes over agricultural fields

    EPA Science Inventory

    Modeling of the bi-directional fluxes (BDFs) of ammonia (NH3) over fertilized soybean and corn canopies was evaluated for three intensive sampling periods: the first, during the summer of 2002 in Warsaw, North Carolina (NC), USA; and the second and third during the summer of 2007...

  13. Comparison of Direct Instruction and Problem Solving Approach in Teaching Social Skills to Children with Mental Retardation

    ERIC Educational Resources Information Center

    Dagseven Emecen, Deniz

    2011-01-01

    This study was aimed at comparing the effectiveness and efficiency of direct instruction and problem solving approaches in teaching social skills to children with mental retardation. The design was adapted alternating treatment design. The subjects of the study consist of a girl and a boy between the ages of 11 and 13 who are mentally retarded. In…

  14. A Comparison Study of the Paper-and-Pencil, Personal Computer, and Internet Versions of Holland's Self-Directed Search

    ERIC Educational Resources Information Center

    Lumsden, Jill A.; Sampson, James P., Jr.; Reardon, Robert C.; Lenz, Janet G.; Peterson, Gary W.

    2004-01-01

    The authors examined the extent to which the Realistic, Investigative, Artistic, Social, Enterprising, and Conventional scales and 3-point codes of the Self-Directed Search may be considered statistically and practically equivalent across 3 different modes of administration: paper-and-pencil, personal computer, and Internet. Student preferences…

  15. A comparison of systolic blood pressure measurement obtained using a pulse oximeter, and direct systolic pressure measurement in anesthetized sows.

    PubMed Central

    Caulkett, N A; Duke, T; Bailey, J V

    1994-01-01

    Systolic blood pressure measurement obtained with a pulse oximeter has been compared to values obtained by other indirect methods in man. Direct pressure measurement is subject to less error than indirect techniques. This study was designed to compare systolic pressure values obtained using a pulse oximeter, with values obtained by direct arterial pressure measurement. The pulse oximeter waveform was used as an indication of perfusion. A blood pressure cuff was applied proximal to the pulse oximeter probe. The cuff was inflated until the oximeter waveform disappeared, this value was recorded as the systolic pressure at the disappearance of the waveform (SPD). The cuff was inflated to a pressure > 200 mmHg, then gradually deflated until the waveform reappeared, this value was recorded as the systolic pressure at reappearance of the waveform (SPR). The average of the two values, SPD and SPR, was calculated and recorded as SPA. The study was performed in sows (n = 21) undergoing cesarean section under epidural anesthesia and IV sedation. A total of 280 measurements were made of SPD, SPR and SPA. Regression analysis of SPA and direct measurement revealed a correlation coefficient (r) of 0.81. Calculation of mean difference (bias) and standard deviation of the bias (precision) for direct pressure--SPA revealed a value of 1.3 +/- 12.1. When compared with direct measurement, the correlation of this technique was similar to that recorded for other indirect techniques used in small animals. This indicates that this technique would be useful for following systolic pressure trends.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8004540

  16. Comparison of direct (X-ray diffraction and infrared spectrophotometry) and indirect (infrared spectrophotometry) methods for the analysis of alpha-quartz in airborne dusts.

    PubMed

    Kauffer, E; Masson, A; Moulut, J C; Lecaque, T; Protois, J C

    2005-11-01

    In this study, the alpha-quartz contents measured by different analytical techniques (X-ray diffraction, direct method; and infrared spectrophotometry, direct and indirect methods) were compared. The analyses were carried out on filters sampled in an industrial setting by means of a Dorr-Oliver cyclone. To verify the methodology used, filters loaded with pure alpha-quartz were also analysed. By and large, the agreement between the two direct methods was close on average, but on the basis of a comparison of the individual results, considerable differences exist. In absolute value, the mean relative deviation between the two techniques was <25% in only 47.8% of the cases. The results obtained by the indirect method (infrared) were on average 13% lower than the results obtained by the two direct methods with a more important difference (23%) for samples where calcite was identified by X-ray diffraction in comparison with those where it was not (8%). This underestimation, which was not owing to dust losses during preparation, is probably explained by the elimination of organic compounds during dust calcinations or by the transformation of mineral compounds. The indirect method introduces additional sample handling operations with more risk of material loss. When the quantity of calcined material was <0.4 mg, the weighing operations necessary to correct any losses of material resulted in considerable variability. In terms of overall uncertainty, it would be better in this case not to carry out correction and to employ an operating mode favouring the recovery of a maximum of material while accepting a bias of about 5-7%.

  17. Identifying effective connectivity parameters in simulated fMRI: a direct comparison of switching linear dynamic system, stochastic dynamic causal, and multivariate autoregressive models

    PubMed Central

    Smith, Jason F.; Chen, Kewei; Pillai, Ajay S.; Horwitz, Barry

    2013-01-01

    The number and variety of connectivity estimation methods is likely to continue to grow over the coming decade. Comparisons between methods are necessary to prune this growth to only the most accurate and robust methods. However, the nature of connectivity is elusive with different methods potentially attempting to identify different aspects of connectivity. Commonalities of connectivity definitions across methods upon which base direct comparisons can be difficult to derive. Here, we explicitly define “effective connectivity” using a common set of observation and state equations that are appropriate for three connectivity methods: dynamic causal modeling (DCM), multivariate autoregressive modeling (MAR), and switching linear dynamic systems for fMRI (sLDSf). In addition while deriving this set, we show how many other popular functional and effective connectivity methods are actually simplifications of these equations. We discuss implications of these connections for the practice of using one method to simulate data for another method. After mathematically connecting the three effective connectivity methods, simulated fMRI data with varying numbers of regions and task conditions is generated from the common equation. This simulated data explicitly contains the type of the connectivity that the three models were intended to identify. Each method is applied to the simulated data sets and the accuracy of parameter identification is analyzed. All methods perform above chance levels at identifying correct connectivity parameters. The sLDSf method was superior in parameter estimation accuracy to both DCM and MAR for all types of comparisons. PMID:23717258

  18. Direct dynamics simulations of the product channels and atomistic mechanisms for the OH(-) + CH3I reaction. Comparison with experiment.

    PubMed

    Xie, Jing; Sun, Rui; Siebert, Matthew R; Otto, Rico; Wester, Roland; Hase, William L

    2013-08-15

    Electronic structure and direct dynamics calculations were used to study the potential energy surface and atomic-level dynamics for the OH(-) + CH3I reactions. The results are compared with crossed molecular beam, ion imaging experiments. The DFT/B97-1/ECP/d level of theory gives reaction energetics in good agreement with experiment and higher level calculations, and it was used for the direct dynamics simulations that were performed for reactant collision energies of 2.0, 1.0, 0.5, and 0.05 eV. Five different pathways are observed in the simulations, forming CH3OH + I(-), CH2I(-) + H2O, CH2 + I(-) + H2O, IOH(-) + CH3, and [CH3--I--OH](-). The SN2 first pathway and the proton-transfer second pathway dominate the reaction dynamics. Though the reaction energetics favor the SN2 pathway, the proton-transfer pathway is more important except for the lowest collision energy. The relative ion yield determined from the simulations is in overall good agreement with experiment. Both the SN2 and proton-transfer pathways occur via direct rebound, direct stripping, and indirect mechanisms. Except for the highest collision energy, 70-90% of the indirect reaction for the SN2 pathway occurs via formation of the hydrogen-bonded OH(-)---HCH2I prereaction complex. For the proton-transfer pathway the indirect reaction is more complex with the roundabout mechanism and formation of the OH(-)---HCH2I and CH2I(-)---HOH complexes contributing to the reaction. The majority of the SN2 reaction is direct at 2.0, 1.0, and 0.5 eV, dominated by stripping. At 0.05 eV the two direct mechanisms and the indirect mechanisms have nearly equal contributions. The majority of the proton-transfer pathway is direct stripping at 2.0, 1.0, and 0.5 eV, but the majority of the reaction is indirect at 0.05 eV. The product relative translational energy distributions are in good agreement with experiment for both the SN2 and proton-transfer pathways. For both, direct reaction preferentially transfers the product

  19. A direct comparison amongst different technologies (aerobic granular sludge, SBR and MBR) for the treatment of wastewater contaminated by 4-chlorophenol.

    PubMed

    Carucci, Alessandra; Milia, Stefano; Cappai, Giovanna; Muntoni, Aldo

    2010-05-15

    Environmental concern on chlorinated phenols is rising due to their extreme toxicity even at low concentrations and their persistency in water and soils. Since the high amount of published data often lacks in terms of uniformity, direct comparisons amongst different treatment technologies are very difficult, or even impossible. In this study, granular sludge developed in an acetate-fed Granular sludge Sequencing Batch Reactor (GSBR) was used for the aerobic degradation of low chlorinated 4-chlorophenol (4CP), with readily biodegradable sodium acetate (NaAc) as growth substrate. A conventional Sequencing Batch Reactor (SBR) and a Membrane BioReactor (MBR) were operated in parallel under the same 4CP influent concentrations and/or 4CP volumetric organic loading rates as the GSBR, in order to carry out a direct comparison in terms of 4CP removal efficiencies and specific removal rates, effluent quality, waste sludge production, system simplicity, land area requirement, start-up times, NaAc dosage as growth substrate and maximum applied 4CP volumetric organic loading rate. A decision matrix was built to define the best technology to suit different scenarios: the GSBR was proved to be the most suitable technology when system simplicity, low land area requirement and short start-up times were considered as critical parameters for decision making.

  20. Comparison of residual stresses in Inconel 718 simple parts made by electron beam melting and direct laser metal sintering

    DOE PAGES

    Kolbus, Lindsay M.; Payzant, E. Andrew; Cornwell, Paris A.; ...

    2015-01-10

    Residual stress profiles were mapped using neutron diffraction in two simple prism builds of Inconel 718: one fabricated with electron beam melting and the other with direct laser sintering. Spatially indexed stress-free cubes were obtained by EDM sectioning equivalent prisms of similar shape. The (311) interplanar spacing examined for the EDM sectioned sample was compared to the interplanar spacings calculated to fulfill force and moment balance. We have shown that Applying force and moment balance is a necessary supplement to the measurements for the stress-free cubes with respect to accurate stress calculations in additively manufactured components. Furthermore, our work hasmore » shown that residual stresses in electron beam melting parts are much smaller than that of direct laser metal sintering parts.« less

  1. Comparison of residual stresses in Inconel 718 simple parts made by electron beam melting and direct laser metal sintering

    SciTech Connect

    Kolbus, Lindsay M.; Payzant, E. Andrew; Cornwell, Paris A.; Watkins, Thomas R.; Babu, Sudarsanam Suresh; Dehoff, Ryan R.; Duty, Chad E.; Lorenz, M.; Ovchinnikova, O. S.

    2015-01-10

    Residual stress profiles were mapped using neutron diffraction in two simple prism builds of Inconel 718: one fabricated with electron beam melting and the other with direct laser sintering. Spatially indexed stress-free cubes were obtained by EDM sectioning equivalent prisms of similar shape. The (311) interplanar spacing examined for the EDM sectioned sample was compared to the interplanar spacings calculated to fulfill force and moment balance. We have shown that Applying force and moment balance is a necessary supplement to the measurements for the stress-free cubes with respect to accurate stress calculations in additively manufactured components. Furthermore, our work has shown that residual stresses in electron beam melting parts are much smaller than that of direct laser metal sintering parts.

  2. Comparison of Residual Stresses in Inconel 718 Simple Parts Made by Electron Beam Melting and Direct Laser Metal Sintering

    NASA Astrophysics Data System (ADS)

    Sochalski-Kolbus, L. M.; Payzant, E. A.; Cornwell, P. A.; Watkins, T. R.; Babu, S. S.; Dehoff, R. R.; Lorenz, M.; Ovchinnikova, O.; Duty, C.

    2015-03-01

    Residual stress profiles were mapped using neutron diffraction in two simple prism builds of Inconel 718: one fabricated with electron beam melting (EBM) and the other with direct laser metal sintering. Spatially indexed stress-free cubes were obtained by electrical discharge machining (EDM) equivalent prisms of similar shape. The (311) interplanar spacings from the EDM sectioned sample were compared to the interplanar spacings calculated to fulfill stress and moment balance. We have shown that applying stress and moment balance is a necessary supplement to the measurements for the stress-free cubes with respect to accurate stress calculations in additively manufactured components. In addition, our work has shown that residual stresses in electron beam melted parts are much smaller than that of direct laser metal sintered parts most likely due to the powder preheating step in the EBM process.

  3. A Modeled Comparison of Direct and Food Web-Mediated Impacts of Common Pesticides on Pacific Salmon

    PubMed Central

    Macneale, Kate H.; Spromberg, Julann A.; Baldwin, David H.; Scholz, Nathaniel L.

    2014-01-01

    In the western United States, pesticides used in agricultural and urban areas are often detected in streams and rivers that support threatened and endangered Pacific salmon. Although concentrations are rarely high enough to cause direct salmon mortality, they can reach levels sufficient to impair juvenile feeding behavior and limit macroinvertebrate prey abundance. This raises the possibility of direct adverse effects on juvenile salmon health in tandem with indirect effects on salmon growth as a consequence of reduced prey abundance. We modeled the growth of ocean-type Chinook salmon (Oncorhynchus tshawytscha) at the individual and population scales, investigating insecticides that differ in how long they impair salmon feeding behavior and in how toxic they are to salmon compared to macroinvertebrates. The relative importance of these direct vs. indirect effects depends both on how quickly salmon can recover and on the relative toxicity of an insecticide to salmon and their prey. Model simulations indicate that when exposed to a long-acting organophosphate insecticide that is highly toxic to salmon and invertebrates (e.g., chlorpyrifos), the long-lasting effect on salmon feeding behavior drives the reduction in salmon population growth with reductions in prey abundance having little additional impact. When exposed to short-acting carbamate insecticides at concentrations that salmon recover from quickly but are lethal to invertebrates (e.g., carbaryl), the impacts on salmon populations are due primarily to reductions in their prey. For pesticides like carbaryl, prey sensitivity and how quickly the prey community can recover are particularly important in determining the magnitude of impact on their predators. In considering both indirect and direct effects, we develop a better understanding of potential impacts of a chemical stressor on an endangered species and identify data gaps (e.g., prey recovery rates) that contribute uncertainty to these assessments. PMID

  4. Comparison of broth enhancement to direct plating for screening of rectal cultures for ciprofloxacin-resistant Escherichia coli.

    PubMed

    Liss, Michael A; Nakamura, Kristen K; Peterson, Ellena M

    2013-01-01

    A transrectal prostate biopsy is the most common procedure used to establish the diagnosis of prostate cancer. Prior to biopsy, patients are commonly given ciprofloxacin for prophylaxis. However, a complication of the procedure is infection with ciprofloxacin-resistant organisms, in particular resistant Escherichia coli. In order to identify patients carrying ciprofloxacin-resistant E. coli, so as to tailor their antibiotic prophylaxis, rectal swabs are screened using selective broth and/or solid medium. In our evaluation, we compared broth enrichment and direct plating techniques by using brain heart infusion broth and MacConkey agar containing 1 μg/ml or 10 μg/ml of ciprofloxacin. Of the 100 patients included in the study, 20 were colonized with ciprofloxacin-resistant organisms, 19 of which were E. coli. There was no significant difference (P > 0.1) between the culture methods or the ciprofloxacin concentrations in the medium when identifying patients with ciprofloxacin-resistant E. coli; however, broth enrichment using 1 μg/ml ciprofloxacin was the most sensitive at 100%, but it was the least specific. Direct plating of rectal swabs onto MacConkey agar containing 10 μg/ml of ciprofloxacin was 100% specific and missed only 1 positive specimen, with a sensitivity of 94.7%; this method was the most cost-effective. Therefore, direct plating of rectal swabs onto selective medium proved to be a sensitive and cost-effective approach in identifying patients colonized with ciprofloxacin-resistant E. coli.

  5. [Blood flow measurement in arteriovenous fistula. Comparison of 2 ultrasonic methods, direct and indirect by compression of the fistula].

    PubMed

    Deklunder, G; Goullard, L; Lecroart, J L; Foulard, M; Houdas, Y

    1990-05-19

    Measuring blood flow in arteriovenous fistulae in patients under chronic dialysis is of interest to evaluate the repercussions of the fistula on the heart. The apparently simplest method is direct measurement of the mean blood flow velocity by the pulsed doppler technique and ot the cross-section area by ultrasonography, the product of these two values being the blood flow rate. Another method has been proposed, which consists of measuring the cardiac output before and after compression of the fistula, the difference between the two values being supposed to represent the blood flow rate in the fistula. A comparative study of these two methods was conducted in 17 patients aged from 2 to 21 years (mean: 14 years). The direct method gave a figure of 475 ml.min-1.m-2 (SD = 240), while the figure obtained with the indirect method was 471 ml.min-1.m-2 (SD = 227); the difference was statistically not significant. In terms of concept, however, the indirect method is open to much more severe criticism than the direct method, and whenever possible the latter should be preferred when measuring blood flow in arteriovenous fistulae.

  6. Degree versus direction: a comparison of four handedness classification schemes through the investigation of lateralised semantic priming.

    PubMed

    Kaploun, Kristen A; Abeare, Christopher A

    2010-09-01

    Four classification systems were examined using lateralised semantic priming in order to investigate whether degree or direction of handedness better captures the pattern of lateralised semantic priming. A total of 85 participants completed a lateralised semantic priming task and three handedness questionnaires. The classification systems tested were: (1) the traditional right- vs left-handed (RHs vs LHs); (2) a four-factor model of strong and weak right- and left-handers (SRHs, WRHs, SLHs, WLHs); (3) strong- vs mixed-handed (SHs vs MHs); and (4) a three-factor model of consistent left- (CLHs), inconsistent left- (ILHs), and consistent right-handers (CRHs). Mixed-factorial ANOVAs demonstrated significant visual field (VF) by handedness interactions for all but the third model. Results show that LHs, SLHs, CLHs, and ILHs responded faster to LVF targets, whereas RHs, SRHs, and CRHs responded faster to RVF targets; no significant VF by handedness interaction was found between SHs and MHs. The three-factor model better captures handedness group divergence on lateralised semantic priming by incorporating the direction of handedness as well as the degree. These findings help explain some of the variance in language lateralisation, demonstrating that direction of handedness is as important as degree. The need for greater consideration of handedness subgroups in laterality research is highlighted.

  7. Intubating condition, hemodynamic parameters and upper airway morbidity: A comparison of intubating laryngeal mask airway with standard direct laryngoscopy

    PubMed Central

    Kavitha, J.; Tripathy, Debendra Kumar; Mishra, Sandeep Kumar; Mishra, Gayatri; Chandrasekhar, L. J.; Ezhilarasu, P.

    2011-01-01

    Background: Intubating Laryngeal Mask Airway (ILMA) is a relatively new device designed to have better intubating characteristics than the standard Laryngeal Mask Airway. This study was designed to compare Intubating Laryngeal Mask with standard Direct Laryngoscopy (DLS), taking into account ease of intubation, time taken for intubation, success rate of intubation, hemodynamic responses and upper airway morbidity. Materials and Methods: Sixty patients, ASA I or II, of age between 20 and 60 years, were enrolled in this prospective and randomized study. They were randomly allocated to one of the two groups: group ILMA, Intubating Laryngeal Mask Airway; group DLS, Direct Laryngoscopy. The patients were intubated orally using either equipment after induction of general anesthesia. Results and Conclusions: DLS is comparatively a faster method to secure tracheal intubation than Intubating Laryngeal Mask. ILMA offers no advantage in attenuating the hemodynamic responses compared to direct laryngoscope. The success rate of intubation through Intubating Laryngeal Mask is comparable with that of DLS. The upper airway morbidity and mean oxygen saturation are comparable in both the groups. PMID:25885300

  8. A network-based phenotype mapping approach to identify genes that modulate drug response phenotypes

    PubMed Central

    Cairns, Junmei; Ung, Choong Yong; da Rocha, Edroaldo Lummertz; Zhang, Cheng; Correia, Cristina; Weinshilboum, Richard; Wang, Liewei; Li, Hu

    2016-01-01

    To better address the problem of drug resistance during cancer chemotherapy and explore the possibility of manipulating drug response phenotypes, we developed a network-based phenotype mapping approach (P-Map) to identify gene candidates that upon perturbed can alter sensitivity to drugs. We used basal transcriptomics data from a panel of human lymphoblastoid cell lines (LCL) to infer drug response networks (DRNs) that are responsible for conferring response phenotypes for anthracycline and taxane, two common anticancer agents use in clinics. We further tested selected gene candidates that interact with phenotypic differentially expressed genes (PDEGs), which are up-regulated genes in LCL for a given class of drug response phenotype in triple-negative breast cancer (TNBC) cells. Our results indicate that it is possible to manipulate a drug response phenotype, from resistant to sensitive or vice versa, by perturbing gene candidates in DRNs and suggest plausible mechanisms regulating directionality of drug response sensitivity. More important, the current work highlights a new way to formulate systems-based therapeutic design: supplementing therapeutics that aim to target disease culprits with phenotypic modulators capable of altering DRN properties with the goal to re-sensitize resistant phenotypes. PMID:27841317

  9. Diet or exercise interventions vs combined behavioral weight management programs: a systematic review and meta-analysis of direct comparisons.

    PubMed

    Johns, David J; Hartmann-Boyce, Jamie; Jebb, Susan A; Aveyard, Paul

    2014-10-01

    Weight loss can reduce the health risks associated with being overweight or obese. However, the most effective method of weight loss remains unclear. Some programs emphasize physical activity, others diet, but existing evidence is mixed as to whether these are more effective individually or in combination. We aimed to examine the clinical effectiveness of combined behavioral weight management programs (BWMPs) targeting weight loss in comparison to single component programs, using within study comparisons. We included randomized controlled trials of combined BWMPs compared with diet-only or physical activity-only programs with at least 12 months of follow-up, conducted in overweight and obese adults (body mass index ≥25). Systematic searches of nine databases were run and two reviewers extracted data independently. Random effects meta-analyses were conducted for mean difference in weight change at 3 to 6 months and 12 to 18 months using a baseline observation carried forward approach for combined BWMPs vs diet-only BWMPs and combined BWMPs vs physical activity-only BWMPs. In total, eight studies were included, representing 1,022 participants, the majority of whom were women. Six studies met the inclusion criteria for combined BWMP vs diet-only. Pooled results showed no significant difference in weight loss from baseline or at 3 to 6 months between the BWMPs and diet-only arms (-0.62 kg; 95% CI -1.67 to 0.44). However, at 12 months, a significantly greater weight-loss was detected in the combined BWMPs (-1.72 kg; 95% CI -2.80 to -0.64). Five studies met the inclusion criteria for combined BWMP vs physical activity-only. Pooled results showed significantly greater weight loss in the combined BWMPs at 3 to 6 months (-5.33 kg; 95% CI -7.61 to -3.04) and 12 to 18 months (-6.29 kg; 95% CI -7.33 to -5.25). Weight loss is similar in the short-term for diet-only and combined BWMPs but in the longer-term weight loss is increased when diet and physical activity are combined

  10. Comparison of theoretically predicted lateral-directional aerodynamic characteristics with full-scale wind tunnel data on the ATLIT airplane

    NASA Technical Reports Server (NTRS)

    Griswold, M.; Roskam, J.

    1980-01-01

    An analytical method is presented for predicting lateral-directional aerodynamic characteristics of light twin engine propeller-driven airplanes. This method is applied to the Advanced Technology Light Twin Engine airplane. The calculated characteristics are correlated against full-scale wind tunnel data. The method predicts the sideslip derivatives fairly well, although angle of attack variations are not well predicted. Spoiler performance was predicted somewhat high but was still reasonable. The rudder derivatives were not well predicted, in particular the effect of angle of attack. The predicted dynamic derivatives could not be correlated due to lack of experimental data.

  11. Comparison of remote video and diver's direct observations to quantify reef fishes feeding on benthos in coral and rocky reefs.

    PubMed

    Longo, G O; Floeter, S R

    2012-10-01

    This study compared remote underwater video and traditional direct diver observations to assess reef fish feeding impact on benthos across multiple functional groups within different trophic categories (e.g. herbivores, zoobenthivores and omnivores) and in two distinct reef systems: a subtropical rocky reef and a tropical coral reef. The two techniques were roughly equivalent, both detecting the species with higher feeding impact and recording similar bite rates, suggesting that reef fish feeding behaviour at the study areas are not strongly affected by the diver's presence.

  12. Direct comparison of gluco-oligosaccharide oxidase variants and glucose oxidase: substrate range and H2O2 stability

    PubMed Central

    Vuong, Thu V.; Foumani, Maryam; MacCormick, Benjamin; Kwan, Rachel; Master, Emma R.

    2016-01-01

    Glucose oxidase (GO) activity is generally restricted to glucose and is susceptible to inactivation by H2O2. By comparison, the Y300A variant of gluco-oligosaccharide oxidase (GOOX) from Sarocladium strictum showed broader substrate range and higher H2O2 stability. Specifically, Y300A exhibited up to 40 times higher activity on all tested sugars except glucose, compared to GO. Moreover, fusion of the Y300A variant to a family 22 carbohydrate binding module from Clostridium thermocellum (CtCBM22A) nearly doubled its catalytic efficiency on glucose, while retaining significant activity on oligosaccharides. In the presence of 200 mM of H2O2, the recombinant CtCBM22A_Y300A retained 80% of activity on glucose and 100% of activity on cellobiose, the preferred substrate for this enzyme. By contrast, a commercial glucose oxidase reported to contain ≤0.1 units catalase/ mg protein, retained 60% activity on glucose under the same conditions. GOOX variants appear to undergo a different mechanism of inactivation, as a loss of histidine instead of methionine was observed after H2O2 incubation. The addition of CtCBM22A also promoted functional binding of the fusion enzyme to xylan, facilitating its simultaneous purification and immobilization using edible oat spelt xylan, which might benefit the usage of this enzyme preparation in food and baking applications. PMID:27869125

  13. Direct comparison of gluco-oligosaccharide oxidase variants and glucose oxidase: substrate range and H2O2 stability.

    PubMed

    Vuong, Thu V; Foumani, Maryam; MacCormick, Benjamin; Kwan, Rachel; Master, Emma R

    2016-11-21

    Glucose oxidase (GO) activity is generally restricted to glucose and is susceptible to inactivation by H2O2. By comparison, the Y300A variant of gluco-oligosaccharide oxidase (GOOX) from Sarocladium strictum showed broader substrate range and higher H2O2 stability. Specifically, Y300A exhibited up to 40 times higher activity on all tested sugars except glucose, compared to GO. Moreover, fusion of the Y300A variant to a family 22 carbohydrate binding module from Clostridium thermocellum (CtCBM22A) nearly doubled its catalytic efficiency on glucose, while retaining significant activity on oligosaccharides. In the presence of 200 mM of H2O2, the recombinant CtCBM22A_Y300A retained 80% of activity on glucose and 100% of activity on cellobiose, the preferred substrate for this enzyme. By contrast, a commercial glucose oxidase reported to contain ≤0.1 units catalase/ mg protein, retained 60% activity on glucose under the same conditions. GOOX variants appear to undergo a different mechanism of inactivation, as a loss of histidine instead of methionine was observed after H2O2 incubation. The addition of CtCBM22A also promoted functional binding of the fusion enzyme to xylan, facilitating its simultaneous purification and immobilization using edible oat spelt xylan, which might benefit the usage of this enzyme preparation in food and baking applications.

  14. Direct Comparison of the Safety and Efficacy of Ferric Carboxymaltose versus Iron Dextran in Patients with Iron Deficiency Anemia.

    PubMed

    Hussain, Iftikhar; Bhoyroo, Jessica; Butcher, Angelia; Koch, Todd A; He, Andy; Bregman, David B

    2013-01-01

    Several intravenous iron complexes are available for the treatment of iron deficiency anemia (IDA). Iron dextran (DEX) is associated with an elevated risk of potentially serious anaphylactic reactions, whereas others must be administered in several small infusions to avoid labile iron reactions. Ferric carboxymaltose (FCM) is a nondextran intravenous iron which can be administered in high single doses. A randomized, open label, and multicenter comparison of FCM to DEX in adults with IDA and baseline hemoglobin of ≤11.0 g/dL was conducted. A total of 160 patients were in the safety population (FCM n = 82; DEX n = 78). Adverse events, including immune system disorders (0% in FCM versus 10.3% in DEX, P = 0.003) and skin disorders (7.3% in FCM versus 24.4% in DEX, P = 0.004), were less frequently observed in the FCM group. A greater portion of patients in the FCM group experienced a transient, asymptomatic decrease in phosphate compared to patients in the DEX group (8.5% in FCM versus 0% in DEX, P = 0.014). In the FCM arm, the change in hemoglobin from baseline to the highest observed level was 2.8 g/dL, whereas the DEX arm displayed a change of 2.4 g/dL (P = 0.20). Treatment of IDA with FCM resulted in fewer hypersensitivity-related reactions than DEX.

  15. Comparison of Five Diagnostic Modalities for Direct Detection of Borrelia burgdorferi in Patients with Early Lyme Disease

    PubMed Central

    Liveris, Dionysios; Schwartz, Ira; McKenna, Donna; Nowakowski, John; Nadelman, Robert; DeMarco, Joseph; Iyer, Radha; Bittker, Susan; Cooper, Denise; Holmgren, Diane; Wormser, Gary P.

    2012-01-01

    Lyme disease, the most commonly reported tick-borne infection in North America, is caused by infection with the spirochete Borrelia burgdorferi. Although an accurate clinical diagnosis can often be made based on the presence of erythema migrans, in research studies microbiologic or molecular microbiologic confirmation of the diagnosis may be required. In this study, we evaluated the sensitivity of five direct diagnostic methods (culture and nested PCR of a 2 mm skin biopsy specimen, nested PCR and quantitative PCR (qPCR) performed on the same 1 mL aliquot of plasma and a novel qPCR-blood culture method) in 66 untreated adult patients with erythema migrans. One or more these tests were positive in 93.9% of the patients. Culture was more sensitive than PCR for both skin and blood, but the difference was only statistically significant for blood samples (p< 0.005). Blood culture was significantly more likely to be positive in patients with multiple erythema migrans skin lesions compared to those with a single lesion (p=0.001). Positive test results among the 48 patients for whom all five assays were performed invariably included either a positive blood or skin culture. The results of this study demonstrate that direct detection methods such as PCR and culture are highly sensitive in untreated adult patients with erythema migrans. This enabled microbiologic or molecular microbiologic confirmation of the diagnosis of B. burgdorferi infection in all but four (6.1%) of the 66 patients evaluated. PMID:22571973

  16. A COMPARISON OF MODEL BASED AND DIRECT OPTIMIZATION BASED FILTERING ALGORITHMS FOR SHEARWAVE VELOCITY RECONSTRUCTION FOR ELECTRODE VIBRATION ELASTOGRAPHY.

    PubMed

    Ingle, Atul; Varghese, Tomy

    2013-04-01

    Tissue stiffness estimation plays an important role in cancer detection and treatment. The presence of stiffer regions in healthy tissue can be used as an indicator for the possibility of pathological changes. Electrode vibration elastography involves tracking of a mechanical shear wave in tissue using radio-frequency ultrasound echoes. Based on appropriate assumptions on tissue elasticity, this approach provides a direct way of measuring tissue stiffness from shear wave velocity, and enabling visualization in the form of tissue stiffness maps. In this study, two algorithms for shear wave velocity reconstruction in an electrode vibration setup are presented. The first method models the wave arrival time data using a hidden Markov model whose hidden states are local wave velocities that are estimated using a particle filter implementation. This is compared to a direct optimization-based function fitting approach that uses sequential quadratic programming to estimate the unknown velocities and locations of interfaces. The mean shear wave velocities obtained using the two algorithms are within 10%of each other. Moreover, the Young's modulus estimates obtained from an incompressibility assumption are within 15 kPa of those obtained from the true stiffness data obtained from mechanical testing. Based on visual inspection of the two filtering algorithms, the particle filtering method produces smoother velocity maps.

  17. Phenotyping jasmonate regulation of root growth.

    PubMed

    Kellermeier, Fabian; Amtmann, Anna

    2013-01-01

    Root architecture is a complex and highly plastic feature of higher plants. Direct treatments with jasmonates and alterations in jasmonate signaling have been shown to elicit a range of root phenotypes. Here, we describe a fast, noninvasive, and semiautomatic method to monitor root architectural responses to environmental stimuli using plant tissue culture and the software tool EZ-RHIZO.

  18. Spectral comparison of directly imaged, young substellar companions using integral field spectroscopy - construction of an empiric log g sequence

    NASA Astrophysics Data System (ADS)

    Schmidt, T.; Neuhaüser, R.; Seifahrt, A.

    2010-10-01

    About 15 substellar companions with large separations (>∼50 AU) to their young primary stars and brown dwarfs are confirmed by both common proper motion and late-M / early-L type spectra. The origin and early evolution of these objects is still under debate. While often these substellar companions are regarded as brown dwarfs, they could possibly also be massive planets, the mass estimates are very uncertain so far. They are companions to primary stars or brown dwarfs in young associations and star forming regions like the TW Hya association, Upper Scorpius, Taurus, Beta Pic moving group, TucHor association, Lupus, Ophiuchus, and Chamaeleon, hence their ages and distances are well known, in contrast to free-floating brown dwarfs. An empirical classification is not possible, because a spectral sequence that is taking the lower gravity into account, is not existing. This problem leads to an apparent mismatch between spectra of old field type objects and young low-mass companions at the same effective temperature, hampering a determination of temperature and surface gravity independent from models. Now that about 15 such substellar candidates are found in associations of different ages, 1 - 35 Myrs, it is possible to study their spectra in comparison to each other using the advantage of light concentration by an adaptive optics system with their primary as guide star. Therefore we have begun the construction of an empirical log g sequence from beginning to observe all these substellar companions homogeneously using the AO-assisted integral field spectrograph SINFONI at VLT (ESO).

  19. Comparison of Direct Sequence Spread Spectrum Rake Receiver with a Maximum Ratio Combining Multicarrier Spread Spectrum Receiver

    SciTech Connect

    Daryl Leon Wasden; Hussein Moradi; Behrouz Farhang-Broujeny

    2014-06-01

    This paper presents a theoretical analysis of the performance of a filter bank-based multicarrier spread spectrum (FB-MC-SS) system. We consider an FB-MC-SS setup where each data symbol is spread across multiple subcarriers, but there is no spreading in time. The results are then compared with those of the well-known direct sequence spread spectrum (DS-SS) system with a rake receiver for its best performance. We compare the two systems when the channel noise is white. We prove that as the processing gains of the two systems tend to infinity both approach the same performance. However, numerical simulations show that, in practice, where processing gain is limited, FB-MC-SS outperforms DS-SS.

  20. An Improved K-Epsilon Model for Near-Wall Turbulence and Comparison with Direct Numerical Simulation

    NASA Technical Reports Server (NTRS)

    Shih, T. H.

    1990-01-01

    An improved k-epsilon model for low Reynolds number turbulence near a wall is presented. The near-wall asymptotic behavior of the eddy viscosity and the pressure transport term in the turbulent kinetic energy equation is analyzed. Based on this analysis, a modified eddy viscosity model, having correct near-wall behavior, is suggested, and a model for the pressure transport term in the k-equation is proposed. In addition, a modeled dissipation rate equation is reformulated. Fully developed channel flows were used for model testing. The calculations using various k-epsilon models are compared with direct numerical simulations. The results show that the present k-epsilon model performs well in predicting the behavior of near-wall turbulence. Significant improvement over previous k-epsilon models is obtained.

  1. Unsteady heat transfer and direct comparison to steady-state measurements in a rotor-wake experiment

    NASA Technical Reports Server (NTRS)

    Obrien, J. E.; Simoneau, R. J.; Lagraff, J. E.; Morehouse, K. A.

    1986-01-01

    Circumferentially local and time-resolved heat transfer measurements were obtained for a circular cylinder in crossflow located downstream of a rotating spoked wheel wake generator in a steady flow tunnel. The unsteady heat transfer effects were obtained by developing an extension of a thin film gauge technique employed to date exclusively in short-duration facilities. The time-average thin film results and conventional steady-state heat transfer measurements were compared. Time-averaged wake-induced stagnation heat transfer enhancement levels above the nowake case were about 10% for the four cylinder Reynolds numbers. This enhancement level was nearly independent of bar passing frequency and was related directly to the time integral of the heat transfer spikes observed at the bar passing frequency. It is observed that the wake-induced heat transfer spikes have peak magnitudes averaging 30 to 40% above the interwake heat transfer level.

  2. Blood perfusion values of laser speckle contrast imaging and laser Doppler flowmetry: is a direct comparison possible?

    PubMed

    Binzoni, Tiziano; Humeau-Heurtier, Anne; Abraham, Pierre; Mahe, Guillaume

    2013-05-01

    Laser Doppler flowmetry (LDF) and laser speckle contrast imaging (LSCI) allow the monitoring of microvascular blood perfusion. The relationship between the measurements obtained by these two techniques remains unclear. In the present contribution, we demonstrate, experimentally and theoretically, that skin blood flow measurements obtained by LDF and LSCI techniques cannot be compared directly even after "classical" normalization procedure. This technical problem is generated by the nonlinear relationship existing between LDF and LSCI flow data. The experiments have been performed on five healthy voluntary subjects (forearm) by using repeated ischemia/reperfusion cycles to induce the necessary skin blood flow changes. LDF and LSCI data were simultaneously acquired on the same region of interest. Considering the importance of this problem from the clinical point of view, it is concluded that the definition of new corrected algorithms for LSCI is probably a mandatory step that must be taken into account if LDF and LSCI blood flow have to be compared.

  3. C-directional compression of nano-graphite: a comparison between effects of uniform and non-uniform pressure

    NASA Astrophysics Data System (ADS)

    Zhu, Chunzhang; Guo, Wanlin

    2011-07-01

    The mechanism of phase transition and evolution in graphite under uniform compression and spherical nanoindentation along the c-direction is investigated through systematical molecular dynamics simulations. Under both the loading conditions, the soft graphite phase can sustain pressure up to 16-20 GPa, beyond which it transforms into a new phase characterized by a much higher stiffness. More and more interlayer bonds will be created in the new hard phase with the increase of the pressure until an unstable state is reached. The critical pressure to produce the quenchable hard phase with a permanent sp 3 bonding remaining after unloading is shown to be as high as ∼880 GPa under uniform compression, as opposed to only ∼75 GPa under nanoindentation. Therefore, application of non-uniform pressure is significantly more helpful for creating diamond-like sp 3 structures in graphite by cold-compressive technique.

  4. A Comparison of Expedition Medical Condition List Treatment Directives with Integrated Medical Model Simulation Data Presentation and Briefing Report

    NASA Technical Reports Server (NTRS)

    Lewis, Robert

    2013-01-01

    This aerospace medicine clerkship project is under the direction of Dr. Sharmila Watkins and is in cooperation with Dr. Eric Kerstman and Dr. Ronak Shah. The questions of the research project are: 1. What are the main drivers of evacuation and loss of crew life (LOCL) on three Design Reference Missions (DRMs): Near Earth Asteroid (NEA), Lunar Sortie and Lunar Outpost using an inexhaustible International Space Station medical kit 2. What are the treatment designations for these driving medical conditions as listed in Expedition Medical Condition List (EMCL) 3. Do the drivers make sense in the context of the given Design Reference Mission (DRM) 4. Do any EMCL treatment designations need re-assessing.

  5. Leg stiffness in human running: Comparison of estimates derived from previously published models to direct kinematic-kinetic measures.

    PubMed

    Coleman, David R; Cannavan, Dale; Horne, Sara; Blazevich, Anthony J

    2012-07-26

    It is not presently clear whether mathematical models used to estimate leg stiffness during human running are valid. Therefore, leg stiffness during the braking phase of ground contact of running was calculated directly using synchronous kinematic (high-speed motion analysis) and kinetic (force platform) analysis, and compared to stiffness calculated using four previously published kinetic models. Nineteen well-trained male middle distance runners (age=21.1±4.1yr; VO(2max)=69.5±7.5mlO(2)kg(-1)min(-1)) completed a series of runs of increasing speed from 2.5 to 6.5ms(-1). Leg stiffness was calculated directly from kinetic-kinematic analysis using both vertical and horizontal forces to obtain the resultant force in the line of leg compression (Model 1). Values were also estimated using four previously published mathematical models where only force platform derived and anthropometric measures were required (Models 2-5; Morin et al., 2005, Morin et al., 2011, Blum et al., 2009, Farley et al., 1993, respectively). The greatest statistical similarity between leg stiffness values occurred with Models 1 and 2. The poorest similarity occurred when values from Model 4 were compared with Model 1. Analyses suggest that the poor correlation between Model 1 other models may have resulted from errors in the estimation in change in leg length during the braking phase. Previously published mathematical models did not provide accurate leg stiffness estimates, although Model 2, used by Morin et al. (2005), provided reasonable estimates that could be further improved by the removal of systematic error using a correction factor (K=1.0496K(Model2)).

  6. Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae.

    PubMed

    Kranzfelder, Petra; Ekrem, Torbjørn; Stur, Elisabeth

    2016-01-01

    Insect skins (exuviae) are of extracellular origin and shed during moulting. The skins do not contain cells or DNA themselves, but epithelial cells and other cell-based structures might accidentally attach as they are shed. This source of trace DNA can be sufficient for PCR amplification and sequencing of target genes and aid in species identification through DNA barcoding or association of unknown life stages. Species identification is essential for biomonitoring programs, as species vary in sensitivities to environmental factors. However, it requires a DNA isolation protocol that optimizes the output of target DNA. Here, we compare the relative effectiveness of five different DNA extraction protocols and direct PCR in isolation of DNA from chironomid pupal exuviae. Chironomidae (Diptera) is a species-rich group of aquatic macroinvertebrates widely distributed in freshwater environments and considered a valuable bioindicator of water quality. Genomic DNA was extracted from 61.2% of 570 sampled pupal exuviae. There were significant differences in the methods with regard to cost, handling time, DNA quantity, PCR success, sequence success and the ability to sequence target taxa. The NucleoSpin(®) Tissue XS Kit, DNeasy(®) Blood and Tissue kit, and QuickExtract(™) DNA Extraction Solution provided the best results in isolating DNA from single pupal exuviae. Direct PCR and DTAB/CTAB methods gave poor results. While the observed differences in DNA isolation methods on trace DNA will be relevant to research that focuses on aquatic macroinvertebrate ecology, taxonomy and systematics, they should also be of interest for studies using environmental barcoding and metabarcoding of aquatic environments.

  7. Combined use of leaf size and economics traits allows direct comparison of hydrophyte and terrestrial herbaceous adaptive strategies

    PubMed Central

    Pierce, Simon; Brusa, Guido; Sartori, Matteo; Cerabolini, Bruno E. L.

    2012-01-01

    Background and Aims Hydrophytes generally exhibit highly acquisitive leaf economics. However, a range of growth forms is evident, from small, free-floating and rapidly growing Lemniden to large, broad-leaved Nymphaeiden, denoting variability in adaptive strategies. Traits used to classify adaptive strategies in terrestrial species, such as canopy height, are not applicable to hydrophytes. We hypothesize that hydrophyte leaf size traits and economics exhibit sufficient overlap with terrestrial species to allow a common classification of plant functional types, sensu Grime's CSR theory. Methods Leaf morpho-functional traits were measured for 61 species from 47 water bodies in lowland continental, sub-alpine and alpine bioclimatic zones in southern Europe and compared against the full leaf economics spectrum and leaf size range of terrestrial herbs, and between hydrophyte growth forms. Key Results Hydrophytes differed in the ranges and mean values of traits compared with herbs, but principal components analysis (PCA) demonstrated that both groups shared axes of trait variability: PCA1 encompassed size variation (area and mass), and PCA2 ranged from relatively dense, carbon-rich leaves to nitrogen-rich leaves of high specific leaf area (SLA). Most growth forms exhibited trait syndromes directly equivalent to herbs classified as R adapted, although Nymphaeiden ranged between C and SR adaptation. Conclusions Our findings support the hypothesis that hydrophyte adaptive strategy variation reflects fundamental trade-offs in economics and size that govern all plants, and that hydrophyte adaptive strategies can be directly compared with terrestrial species by combining leaf economics and size traits. PMID:22337079

  8. New system based on site-directed mutagenesis for highly accurate comparison of resistance levels conferred by SHV beta-lactamases.

    PubMed Central

    Nüesch-Inderbinen, M T; Hächler, H; Kayser, F H

    1995-01-01

    We developed a system based on site-directed mutagenesis that allows a precise comparison of SHV enzymes under isogenic conditions. In addition, the influences of two different, naturally occurring promoters were examined for each SHV derivative. The system comprised two separately cloned DNA fragments, each the size of 3.6 kb. Both fragments encoded an SHV gene originating from clinical isolates but with different promoters. The structural genes were made identical by site-directed mutagenesis. Other mutations were then introduced into both fragments by means of site-directed mutagenesis, resulting in the SHV derivatives SHV-1, SHV-2, SHV-2a, SHV-3, and SHV-5. The amino acid exchange of glutamic acid at position 235 for lysine in SHV-5 resulted in the highest resistance levels. SHV-3, differing from SHV-2 by the exchange of arginine at position 201 for leucine and previously described as indistinguishable from SHV-2, was shown to cause slightly higher resistance to ceftazidime and lower resistance to ceftriaxone, cefotaxime, and cefepime than SHV-2. The point mutation in SHV-2a, with the leucine-to-glutamine replacement at the unusual position 31, previously considered almost insignificant, proved to increase resistance to ceftazidime but reduced the MICs of all other cephalosporins tested when compared with those for SHV-2. For all clones harboring SHV derivatives, resistance was increased by a stronger promoter, in some cases masking the effect of the point mutation itself and demonstrating the importance of regulatory mechanisms of resistance. PMID:7486909

  9. Phenotypic plasticity and experimental evolution.

    PubMed

    Garland, Theodore; Kelly, Scott A

    2006-06-01

    Natural or artificial selection that favors higher values of a particular trait within a given population should engender an evolutionary response that increases the mean value of the trait. For this prediction to hold, the phenotypic variance of the trait must be caused in part by additive effects of alleles segregating in the population, and also the trait must not be too strongly genetically correlated with other traits that are under selection. Another prediction, rarely discussed in the literature, is that directional selection should favor alleles that increase phenotypic plasticity in the direction of selection, where phenotypic plasticity is defined as the ability of one genotype to produce more than one phenotype when exposed to different environments. This prediction has received relatively little empirical attention. Nonetheless, many laboratory experiments impose selection regimes that could allow for the evolution of enhanced plasticity (e.g. desiccation trials with Drosophila that last for several hours or days). We review one example that involved culturing of Drosophila on lemon for multiple generations and then tested for enhanced plasticity of detoxifying enzymes. We also review an example with vertebrates that involves selective breeding for high voluntary activity levels in house mice, targeting wheel-running behavior on days 5+6 of a 6-day wheel exposure. This selection regime allows for the possibility of wheel running itself or subordinate traits that support such running to increase in plasticity over days 1-4 of wheel access. Indeed, some traits, such as the concentration of the glucose transporter GLUT4 in gastrocnemius muscle, do show enhanced plasticity in the selected lines over a 5-6 day period. In several experiments we have housed mice from both the Selected (S) and Control (C) lines with or without wheel access for several weeks to test for differences in plasticity (training effects). A variety of patterns were observed, including

  10. Down Syndrome: Cognitive Phenotype

    ERIC Educational Resources Information Center

    Silverman, Wayne

    2007-01-01

    Down syndrome is the most prevalent cause of intellectual impairment associated with a genetic anomaly, in this case, trisomy of chromosome 21. It affects both physical and cognitive development and produces a characteristic phenotype, although affected individuals vary considerably with respect to severity of specific impairments. Studies…

  11. Mass spectrometry of planetary exospheres at high relative velocity: direct comparison of open- and closed-source measurements

    NASA Astrophysics Data System (ADS)

    Meyer, Stefan; Tulej, Marek; Wurz, Peter

    2017-01-01

    The exploration of habitable environments on or inside icy moons around the gas giants in the solar system is of major interest in upcoming planetary missions. Exactly this theme is addressed by the JUpiter ICy moons Explorer (JUICE) mission of ESA, which will characterise Ganymede, Europa and Callisto as planetary objects and potential habitats. We developed a prototype of the Neutral Gas and Ion Mass spectrometer (NIM) of the Particle Environment Package (PEP) for the JUICE mission intended for composition measurements of neutral gas and thermal plasma. NIM/PEP will be used to measure the chemical composition of the exospheres of the icy Jovian moons. Besides direct ion measurement, the NIM instrument is able to measure the inflowing neutral gas in two different modes: in neutral mode, where the gas enters directly the ion source (open source), and in thermal mode, where the gas gets thermally accommodated to the wall temperature by several collisions inside an equilibrium sphere, called antechamber, before entering the ion source (closed source). We performed measurements with the prototype NIM using a neutral gas beam of 1 up to 4.5 km s-1 velocity in the neutral and thermal mode. The current trajectory of JUICE foresees a flyby velocity of 4 km s-1 at Europa; other flybys are in the range of 1 up to 7 km s-1 and orbital velocity in Ganymede orbits is around 2 km s-1. Different species are used for the gas beam, such as noble gases Ne, Ar, Kr as well as molecules like H2, methane, ethane, propane and more complex ones. The NIM prototype was successfully tested under realistic JUICE mission conditions. In addition, we find that the antechamber (closed source) behaves as expected with predictable density enhancement over the specified mass range and within the JUICE mission phase velocities. Furthermore, with the open source and the closed source we measure almost the same composition for noble gases, as well as for molecules, indicating no additional

  12. Ionic liquid versus SiO2 gated a-IGZO thin film transistors: A direct comparison

    DOE PAGES

    Pudasaini, Pushpa Raj; Noh, Joo Hyon; Wong, Anthony T.; ...

    2015-08-12

    Here, ionic liquid gated field effect transistors have been extensively studied due to their low operation voltage, ease of processing and the realization of high electric fields at low bias voltages. Here, we report ionic liquid (IL) gated thin film transistors (TFTs) based on amorphous Indium Gallium Zinc Oxide (a-IGZO) active layers and directly compare the characteristics with a standard SiO2 gated device. The transport measurements of the top IL gated device revealed the n-channel property of the IGZO thin film with a current ON/OFF ratio ~105, a promising field effect mobility of 14.20 cm2V–1s–1, and a threshold voltage ofmore » 0.5 V. Comparable measurements on the bottom SiO2 gate insulator revealed a current ON/OFF ratio >108, a field effect mobility of 13.89 cm2V–1s–1 and a threshold voltage of 2.5 V. Furthermore, temperature-dependent measurements revealed that the ionic liquid electric double layer can be “frozen-in” by cooling below the glass transition temperature with an applied electrical bias. Positive and negative freezing bias locks-in the IGZO TFT “ON” and “OFF” state, respectively, which could lead to new switching and possibly non-volatile memory applications.« less

  13. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    PubMed Central

    Liu, Yang; Liu, Zhaoxia; Yang, Huaxin

    2016-01-01

    Quantitative nuclear magnetic resonance (qNMR) is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR) and only a few fluorine qNMR (19F qNMR) were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that 19F qNMR has similar precision and sensitivity to 1H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from 19F qNMR is that the analyte signal is with less or no interference from impurities. 19F qNMR is an excellent approach to quantify fluorine-containing analytes. PMID:27688925

  14. Dynamic Reaction Mechanisms of ClO(-) with CH3Cl: Comparison Between Direct Dynamics Trajectory Simulations and Experiment.

    PubMed

    Yu, Feng

    2016-03-24

    We have investigated the dynamic reaction mechanisms of *ClO¯ with CH3Cl (the asterisk is utilized to label a different Cl atom). Ab initio molecular dynamics simulations at the MP2/6-31+G(d,p) level of theory have been employed to compute the dynamic trajectories. On the basis of our simulations, the dynamic reaction pathways for the bimolecular nucleophilic substitution (SN2) reaction channel and SN2-induced elimination reaction channel are clearly illustrated. For the SN2 reaction channel, some trajectories directly dissociate to the final products of CH3O*Cl and Cl¯, whereas the others involve the dynamic Cl¯···CH3O*Cl intermediate complex. As to the SN2-induced elimination reaction channel, the trajectories lead to the final products of CH2O, HCl, and *Cl¯ through the dynamic Cl¯···CH3O*Cl intermediate complex. More significantly, the product branching ratios of Cl¯ and *Cl¯ predicted by our simulations are basically consistent with previous experimental results (Villano et al. J. Am. Chem. Soc. 2009, 131, 8227-8233).

  15. Big Sage (Artemisia tridentata var. wyomingensis): An initial comparison of seedling survival between direct seeding and planting containerized stock

    SciTech Connect

    Meikle, T.; Ballek, L.; Briggs, B.

    1995-09-01

    This study investigates the cost effectiveness of three separate reclamation methods utilized in the long-term establishment of Big Sage (Artemisia tridentata va. wyomingensis). Direct seeding and planting with four cubic inch and ten cubic inch containerized stock were compared using five 36 square meter plots per treatment within a fenced randomized block. Seed plots were hand broadcast at a rate of 2 kilograms per hectare and mulched with certified weed-free wheat straw. Containerized stock plots were planted at a density of one per square meter. Controls with no seeding or planting were established to differentiate actual plant production/reproduction from seed bank recruitment and migration from replaced topsoil and surrounding native areas. Stem density (stem/m{sup 2}), plant height (cm), and plant reproduction (seedlings/m{sup 2}) data will be gathered every spring and fall for three years (1994-1997). Final analysis of the data will relate establishment success to cost efficiency. This initial report on the study reviews only seedling establishment based on first year data.

  16. Ionic liquid versus SiO2 gated a-IGZO thin film transistors: A direct comparison

    SciTech Connect

    Pudasaini, Pushpa Raj; Noh, Joo Hyon; Wong, Anthony T.; Haglund, Amanda V.; Dai, Sheng; Ward, Thomas Zac; Mandrus, David; Rack, Philip D.

    2015-08-12

    Here, ionic liquid gated field effect transistors have been extensively studied due to their low operation voltage, ease of processing and the realization of high electric fields at low bias voltages. Here, we report ionic liquid (IL) gated thin film transistors (TFTs) based on amorphous Indium Gallium Zinc Oxide (a-IGZO) active layers and directly compare the characteristics with a standard SiO2 gated device. The transport measurements of the top IL gated device revealed the n-channel property of the IGZO thin film with a current ON/OFF ratio ~105, a promising field effect mobility of 14.20 cm2V–1s–1, and a threshold voltage of 0.5 V. Comparable measurements on the bottom SiO2 gate insulator revealed a current ON/OFF ratio >108, a field effect mobility of 13.89 cm2V–1s–1 and a threshold voltage of 2.5 V. Furthermore, temperature-dependent measurements revealed that the ionic liquid electric double layer can be “frozen-in” by cooling below the glass transition temperature with an applied electrical bias. Positive and negative freezing bias locks-in the IGZO TFT “ON” and “OFF” state, respectively, which could lead to new switching and possibly non-volatile memory applications.

  17. Comparison between direct-sequence and multicarrier spread-spectrum acoustic communications in time-varying channels.

    PubMed

    van Walree, P A

    2010-12-01

    Underwater communication experiments have been conducted in the Norwegian Oslofjord. Two modulation schemes are compared in a 7-kHz frequency band on a 14-kHz center frequency. The first scheme is direct-sequence spread spectrum (DSSS), using a 7-chip spreading code to achieve a raw data rate of 1000 bps on a single carrier. The second scheme is multicarrier spread spectrum (MCSS) and accomplishes spreading by using seven subbands. The DSSS receiver equalizes on the chips prior to explicit symbol despreading, whereas MCSS features joint multiband equalization and despreading. Four channels are examined, from nearly static to overspread. In slowly varying channels, MCSS offers the best performance. DSSS has the best tracking potential for rapidly varying channels, where the challenge is to obtain reliable chip decisions before symbol despreading. The tracking potential can be realized to some extent by hypothesis-feedback equalization. It is further shown that adaptive equalizers are capable of code conversion, i.e., the DSSS receiver can demodulate the MCSS waveform, and vice versa. Neither receiver requires knowledge of the spreading code in order to despread the data.

  18. Direct identification of bacteria in positive blood cultures: comparison of two rapid methods, FilmArray and mass spectrometry.

    PubMed

    Rand, Kenneth H; Delano, John P

    2014-07-01

    We evaluated the accuracy and performance of the FilmArray Direct from Positive Blood Culture system (BCID) (BioFire Diagnostics, Salt Lake City, UT, USA) and the VITEK Mass Spectrometry System (Vitek MS; bioMerieux, Durham, NC, USA) to identify bacterial isolates from 161 positive blood culture bottles. The BCID uses multiplex PCR to identify 90-95% of common isolates to the genus or species/complex level as well as mecA, Van A/B, and bla(KPC) genes in approximately 1 hour. Of 151 monomicrobic isolates, the FilmArray correctly identified 48/49 (98%) to the genus and 84/84 (100%) to the species/complex level, while 18/151 (12%) gave no identification, as expected from the database. Mass spectrometry correctly identified 142/151 (94%) monomicrobic cultures to the genus level, 137/151 (91%) to the species level, with only 8/151(5%) giving no identification. Although mass spectrometry has a much larger database, the filtration system was cumbersome in contrast to the 3-5 minutes hands-on-time for the BCID.

  19. Comparison of the scaling analysis of mixed-state magnetization data with direct measurements of the upper critical field for YBa2Cu3O7-x

    NASA Astrophysics Data System (ADS)

    Landau, I. L.

    2008-07-01

    By comparison of recent direct measurements of the temperature dependence of the upper critical field Hc2 of an YBa2Cu3O7-x high-Tc superconductor with the scaling analysis of magnetization data, collected in fields H \\ll H_{\\mathrm {c2}} , we demonstrate that the temperature dependence of the Ginzburg-Landau parameter κ is negligible. Another conclusion is that the normalized temperature dependence of Hc2 is independent of the orientation of the magnetic field with respect to the crystallographic axes of the sample. We also discuss the fact that isotropy of the temperature dependence of Hc2 straightforwardly follows from the Ginzburg-Landau theory if κ does not depend on the temperature.

  20. Naming times and standardized norms for the Italian PD/DPSS set of 266 pictures: direct comparisons with American, English, French, and Spanish published databases.

    PubMed

    Dell'Acqua, R; Lotto, L; Job, R

    2000-11-01

    The present study provides Italian normative measures for 266 line drawings belonging to the new set of pictures developed by Lotto, Dell'Acqua, and Job (in press). The pictures have been standardized on the following measures: number of letters, number of syllables, name frequency, within-category typically, familiarity, age of acquisition, name agreement, and naming time. In addition to providing the measures, the present study focuses on indirect and direct comparisons (i.e., correlations) of the present norms with databases provided by comparable studies in Italian (in which normative data were collected with Snodgrass & Vanderwart's set of pictures; Nisi, Longoni, & Snodgrass, 2000), in British English (Barry, Morrison, & Ellis, 1997), in American English (Snodgrass & Vanderwart, 1980; Snodgrass & Yuditsky, 1996), in French (Alario & Ferrand, 1999), and in Spanish (Sanfeliu & Fernandez, 1996).

  1. Validating NASA's Airborne Multikilohertz Microlaser Altimeter (Microaltimeter) by Direct Comparison of Data Taken Over Ocean City, Maryland Against an Existing Digital Elevation Model

    NASA Technical Reports Server (NTRS)

    Abel, Peter

    2003-01-01

    NASA's Airborne Multikilohertz Microlaser Altimeter (Microaltimeter) is a scanning, photon-counting laser altimeter, which uses a low energy (less than 10 microJuoles), high repetition rate (approximately 10 kHz) laser, transmitting at 532 nm. A 14 cm diameter telescope images the ground return onto a segmented anode photomultiplier, which provides up to 16 range returns for each fire. Multiple engineering flights were made during 2001 and 2002 over the Maryland and Virginia coastal area, all during daylight hours. Post-processing of the data to geolocate the laser footprint and determine the terrain height requires post- detection Poisson filtering techniques to extract the actual ground returns from the noise. Validation of the instrument's ability to produce accurate terrain heights will be accomplished by direct comparison of data taken over Ocean City, Maryland with a Digital Elevation Model (DEM) of the region produced at Ohio State University (OSU) from other laser altimeter and photographic sources. The techniques employed to produce terrain heights from the Microaltimeter ranges will be shown, along with some preliminary comparisons with the OSU DEM.

  2. Comparison between human awake, meditation and drowsiness EEG activities based on directed transfer function and MVDR coherence methods.

    PubMed

    Dissanayaka, Chamila; Ben-Simon, Eti; Gruberger, Michal; Maron-Katz, Adi; Sharon, Haggai; Hendler, Talma; Cvetkovic, Dean

    2015-07-01

    This study examined the electroencephalogram functional connectivity (coherence) and effective connectivity (flow of information) of selected brain regions during three different attentive states: awake, meditation and drowsiness. For the estimation of functional connectivity (coherence), Welch and minimum variance distortionless response (MVDR) methods were compared. The MVDR coherence was found to be more suitable since it is both data and frequency dependent and enables higher spectral resolution, while Welch's periodogram-based approach is both data and frequency independent. The directed transfer function (DTF) method was applied in order to estimate the effective connectivity or brain's flow of information between different regions during each state. DTF enables to identify the main brain areas that initiate EEG activity and the spatial distribution of these activities with time. Analysis was conducted using the EEG data of 30 subjects (ten awake, ten drowsy and ten meditating) focusing on six main electrodes (F3, F4, C3, C4, P3, P4, O1 and O2). For each subject, EEG data were recorded during 5-min baseline and 15 min of a specific condition (awake, meditation or drowsiness). Statistical analysis included the Kruskal-Wallis (KW) nonparametric analysis of variance followed by post hoc tests with Bonferroni alpha correction. The results reveal that both states of drowsiness and meditation states lead to a marked difference in the brain's flow of information (effective connectivity) as shown by DTF analyses. In specific, a significant increase in the flow of information in the delta frequency band was found only in the meditation condition and was further found to originate from frontal (F3, F4), parietal (P3, P4) and occipital (O1, O2) regions. Altogether, these results suggest that a change in attentiveness leads to significant changes in the spectral profile of the brain's information flow as well as in its functional connectivity and that these changes can

  3. Rapid Diagnosis of Diarrhea Caused by Shigella sonnei Using Dipsticks; Comparison of Rectal Swabs, Direct Stool and Stool Culture

    PubMed Central

    Duran, Claudia; Nato, Faridabano; Dartevelle, Sylvie; Thi Phuong, Lan Nguyen; Taneja, Neelam; Ungeheuer, Marie Noëlle; Soza, Guillermo; Anderson, Leslie; Benadof, Dona; Zamorano, Agustín; Diep, Tai The; Nguyen, Truong Quang; Nguyen, Vu Hoang; Ottone, Catherine; Bégaud, Evelyne; Pahil, Sapna; Prado, Valeria; Sansonetti, Philippe; Germani, Yves

    2013-01-01

    Background We evaluated a dipstick test for rapid detection of Shigella sonnei on bacterial colonies, directly on stools and from rectal swabs because in actual field situations, most pathologic specimens for diagnosis correspond to stool samples or rectal swabs. Methodology/Principal Findings The test is based on the detection of S. sonnei lipopolysaccharide (LPS) O-side chains using phase I-specific monoclonal antibodies coupled to gold particles, and displayed on a one-step immunochromatographic dipstick. A concentration as low as 5 ng/ml of LPS was detected in distilled water and in reconstituted stools in 6 minutes. This is the optimal time for lecture to avoid errors of interpretation. In distilled water and in reconstituted stools, an unequivocal positive reaction was obtained with 4 x 106 CFU/ml of S. sonnei. The specificity was 100% when tested with a battery of Shigella and different unrelated strains. When tested on 342 rectal swabs in Chile, specificity (281/295) was 95.3% (95% CI: 92.9% - 97.7%) and sensitivity (47/47) was 100%. Stool cultures and the immunochromatographic test showed concordant results in 95.5 % of cases (328/342) in comparative studies. Positive and negative predictive values were 77% (95% CI: 65% - 86.5%) and 100% respectively. When tested on 219 stools in Chile, Vietnam, India and France, specificity (190/198) was 96% (95% CI 92%–98%) and sensitivity (21/21) was 100%. Stool cultures and the immunochromatographic test showed concordant results in 96.3 % of cases (211/219) in comparative studies. Positive and negative predictive values were 72.4% (95% CI 56.1%–88.6%) and 100 %, respectively. Conclusion This one-step dipstick test performed well for diagnosis of S. sonnei both on stools and on rectal swabs. These data confirm a preliminary study done in Chile. PMID:24278267

  4. Young people's perceptions of tobacco packaging: a comparison of EU Tobacco Products Directive & Ireland's Standardisation of Tobacco Act

    PubMed Central

    Babineau, Kate; Clancy, Luke

    2015-01-01

    Objectives To measure young people's perceptions of tobacco packaging according to two current pieces of legislation: The EU Tobacco Products Directive (TPD) and Ireland's Public Health (Standardisation of Tobacco Products) Act. Design Within-subject experimental cross-sectional survey of a representative sample of secondary school students. School-based pen and paper survey. Setting 27 secondary schools across Ireland, randomly stratified for size, geographic location, gender, religious affiliation and school-level socioeconomic status. Data were collected between March and May 2014. Participants 1378 fifth year secondary school students aged 16–17 in Ireland. Main outcome measures Young people's perceptions of attractiveness, health risk and smoker characteristics of packs according to EU and Irish branding and packaging guidelines. Results Packs with more branding elements were thought to be healthier than standardised packs for Silk Cut (χ2=158.58, p<0.001), Marlboro (χ2=113.65, p<0.001), and Benson and Hedges (χ2=137.95, p<0.001) brands. Generalized estimating equation binary regressions found that gender was a significant predictor of pack attractiveness for Silk Cut, with females being more likely to find the EU packs attractive (β=−0.45, p=0.007). Gender was a significant predictor for females with regards to the perceived popularity of the Silk Cut brand (β=−0.37, p=0.03). Conclusions The removal of brand identifiers, including colour, font and embossing, reduces the perceived appeal of cigarette packs for young people across all three tested brands. Packs standardised according to Irish legislation are perceived as less attractive, less healthy and smoked by less popular people than packs which conform to the EU TPD 2014 guidelines. PMID:26048206

  5. Impact of experimental design on Drosophila sexual isolation studies: direct effects and comparison to field hybridization data.

    PubMed

    Coyne, Jerry A; Elwyn, Susannah; Rolán-Alvarez, Emilio

    2005-12-01

    Many studies of speciation rely critically on estimates of sexual isolation obtained in the laboratory. Here we examine the sensitivity of sexual isolation to alterations in experimental design and mating environment in two sister species of Drosophila, D. santomea and D. yakuba. We use a newly devised measure of mating frequencies that is able to disentangle sexual isolation from species differences in mating propensity. Variation in fly density, presence or absence of a quasi-natural environment, degree of starvation, and relative frequency of species had little or no effect on sexual isolation, but one factor did have a significant effect: the possibility of choice. Designs that allowed flies to choose between conspecific and heterospecific mates showed significantly more sexual isolation than other designs that did not allow choice. These experiments suggest that sexual isolation between these species (whose ranges overlap on the island of São Tomé) is due largely to discrimination against D. yakuba males by D. santomea females. This suggestion was confirmed by direct observations of mating behavior. Drosophila santomea males also court D. yakuba females less ardently than conspecific females, whereas neither males nor females of D. yakuba show strong mate discrimination. Thus, sexual isolation appears to be a result of evolutionary changes in the derived island endemic D. santomea. Surprisingly, as reported in a companion paper (Llopart et al. 2005), the genotypes of hybrids found in nature do not accord with expectations from these laboratory studies: all F1 hybrids in nature come from matings between D. santomea females and D. yakuba males, matings that occur only rarely in the laboratory.

  6. Direct comparison of the hygroscopic properties of ammonium sulfate and sodium chloride aerosol at relative humidities approaching saturation.

    PubMed

    Walker, Jim S; Wills, Jon B; Reid, Jonathan P; Wang, Liangyu; Topping, David O; Butler, Jason R; Zhang, Yun-Hong

    2010-12-09

    Holographic optical tweezers are used to make comparative measurements of the hygroscopic properties of single component aqueous aerosol containing sodium chloride and ammonium sulfate over a range of relative humidity from 84% to 96%. The change in RH over the course of the experiment is monitored precisely using a sodium chloride probe droplet with accuracy better than ±0.09%. The measurements are used to assess the accuracy of thermodynamic treatments of the relationship between water activity and solute mass fraction with particular attention focused on the dilute solute limit approaching saturation vapor pressure. The consistency of the frequently used Clegg-Brimblecombe-Wexler (CBW) treatment for predicting the hygroscopic properties of sodium chloride and ammonium sulfate aerosol is confirmed. Measurements of the equilibrium size of ammonium sulfate aerosol are found to agree with predictions to within an uncertainty of ±0.2%. Given the accuracy of treating equilibrium composition, the inconsistencies highlighted in recent calibration measurements of critical supersaturations of sodium chloride and ammonium sulfate aerosol cannot be attributed to uncertainties associated with the thermodynamic predictions and must have an alternative origin. It is concluded that the CBW treatment can allow the critical supersaturation to be estimated for sodium chloride and ammonium sulfate aerosol with an accuracy of better than ±0.002% in RH. This corresponds to an uncertainty of ≤1% in the critical supersaturation for typical supersaturations of 0.2% and above. This supports the view that these systems can be used to accurately calibrate instruments that measure cloud condensation nuclei concentrations at selected supersaturations. These measurements represent the first study in which the equilibrium properties of two particles of chemically distinct composition have been compared simultaneously and directly alongside each other in the same environment.

  7. Comparison of advance medical directive inquiry and documentation for hospital inpatients in three medical services: implications for policy changes.

    PubMed

    Anunobi, Echezona; Detweiler, Mark B; Sethi, Roopa; Thomas, Reena; Lutgens, Brian; Detweiler, Jonna G

    2015-01-01

    Following the introduction of the Patient Self-Determination Act of 1990, the Veterans Health Administration developed its own advance medical directive (AMD) policy, which most recently states that documentation is mandatory for all hospital patients in all settings. The object of this study was to assess the effectiveness of AMD documentation at a local Veterans Affairs Medical Center. AMD documentation was compared among three inpatient services: surgery, medicine, and psychiatry. Retrospective in nature, 594 inpatient cases were compared. Results revealed that, overall, the rate of AMD documentation was 37.7%. AMD documentation on surgery was statistically more frequent (45.6%) than for either medicine (33.2%) or psychiatry (34.5%). The difference between the numbers of days to AMD documentation for all three services was not statistically significant. While there was no statistically significant difference across gender, Caucasians had AMDs documented more frequently than African Americans (p < .001). Logistic regression reveals that social worker and physician intervention, not patient-specific variables, are the primary predictors of AMD incidence. Policy makers may need to consider the realities of hospital care, especially in emergency settings, and be more specific in the steps of implementation of the policy in the evenings, weekends, and holidays. True adherence to policy implementation may require hospital administrators to increase staff and educational efforts so that the concept of AMD communication and documentation is completely explained to all staff and patients. Policy should include an electronic record reminder that is renewed every 3 years and provisions for accommodating patients who arrive on weekends and holidays, with special awareness of the particular communication needs of minority groups. The study conclusions are that further inquiry is needed to understand these policy nuances to enable the Veterans Affairs Administration to

  8. Comparisons of purely topological model, betweenness based model and direct current power flow model to analyze power grid vulnerability.

    PubMed

    Ouyang, Min

    2013-06-01

    This paper selects three frequently used power grid models, including a purely topological model (PTM), a betweennness based model (BBM), and a direct current power flow model (DCPFM), to describe three different dynamical processes on a power grid under both single and multiple component failures. Each of the dynamical processes is then characterized by both a topology-based and a flow-based vulnerability metrics to compare the three models with each other from the vulnerability perspective. Taking as an example, the IEEE 300 power grid with line capacity set proportional to a tolerance parameter tp, the results show non-linear phenomenon: under single node failures, there exists a critical value of tp = 1.36, above which the three models all produce identical topology-based vulnerability results and more than 85% nodes have identical flow-based vulnerability from any two models; under multiple node failures that each node fails with an identical failure probability fp, there exists a critical fp = 0.56, above which the three models produce almost identical topology-based vulnerability results at any tp ≥ 1, but producing identical flow-based vulnerability results only occurs at fp = . In addition, the topology-based vulnerability results can provide a good approximation for the flow-based vulnerability under large fp, and the priority of PTM and BBM to better approach the DCPFM for vulnerability analysis mainly depends on the value of fp. Similar results are also found for other failure types, other system operation parameters, and other power grids.

  9. A comparison of different transarterial embolization techniques for direct carotid cavernous fistulas: a single center experience in 32 patients

    PubMed Central

    Lu, Xiaojian; Hussain, Mohammed; Ni, Lanchun; Huang, Qinfeng; Zhou, Fei; Gu, Zhikai; Chen, Jian; Ding, Yuchuan; Xu, Feng

    2014-01-01

    Objective Transarterial treatment of direct carotid cavernous fistulas (DCCF) via embolic materials has been well documented. This study reports, validates, and compares with existing literature our experience treating DCCFs via endovascular approaches by using detachable balloons, coils, and covered stents. Methods Between June 2006 to October 2011, 32 patients (21 male, 11 female) with 32 DCCFs (30 traumatic, 2 spontaneous cavernous ICA aneurysms) were embolized endovascularly. Followup was performed for at least 6 months. Results Among the 32 DCCFs, 21 (65.6%) were embolized using detachable balloons, eight (25.0%) with coils, one (3.1%) with balloons and coils, and two (6.3%) with covered stents. Complete DCCF obliteration was achieved in 31 (96.9%) cases. One fistula failed to respond due to premature balloon detachment. Intracranial bruit in 31 (100%) chemosis and exophthalmos in 28 (100%) cases resolved after embolization. Visual acuity and oculomotor palsy improved in 18 (90%) and 18 (69.2%) cases, respectively. There was no evidence of DCCF recurrence. Thirteen DCCFs were followed up by MRI and five by DSA. In these cases, four (4/13, 30.8%) balloon-embolized DCCFs showed pseudoaneurysms. Three patients were asymptomatic; one had minor left oculomotor palsy. Conclusions Our results correlate and reinforce literature regarding endovascular treatment of DCCFs. Application of Transarterial embolization with detachable balloons, despite extensive use has been decreasing. Coil embolization is an effective and safe alternative for treatment, especially when balloon embolization fails. Covered stent placement may be used as another alternative for selected cases. PMID:25566340

  10. Direct Comparisons of 2D and 3D Dental Microwear Proxies in Extant Herbivorous and Carnivorous Mammals

    PubMed Central

    DeSantis, Larisa R. G.; Scott, Jessica R.; Schubert, Blaine W.; Donohue, Shelly L.; McCray, Brian M.; Van Stolk, Courtney A.; Winburn, Amanda A.; Greshko, Michael A.; O’Hara, Mackie C.

    2013-01-01

    The analysis of dental microwear is commonly used by paleontologists and anthropologists to clarify the diets of extinct species, including herbivorous and carnivorous mammals. Currently, there are numerous methods employed to quantify dental microwear, varying in the types of microscopes used, magnifications, and the characterization of wear in both two dimensions and three dimensions. Results from dental microwear studies utilizing different methods are not directly comparable and human quantification of wear features (e.g., pits and scratches) introduces interobserver error, with higher error being produced by less experienced individuals. Dental microwear texture analysis (DMTA), which analyzes microwear features in three dimensions, alleviates some of the problems surrounding two-dimensional microwear methods by reducing observer bias. Here, we assess the accuracy and comparability within and between 2D and 3D dental microwear analyses in herbivorous and carnivorous mammals at the same magnification. Specifically, we compare observer-generated 2D microwear data from photosimulations of the identical scanned areas of DMTA in extant African bovids and carnivorans using a scanning white light confocal microscope at 100x magnification. Using this magnification, dental microwear features quantified in 2D were able to separate grazing and frugivorous bovids using scratch frequency; however, DMTA variables were better able to discriminate between disparate dietary niches in both carnivorous and herbivorous mammals. Further, results demonstrate significant interobserver differences in 2D microwear data, with the microwear index remaining the least variable between experienced observers, consistent with prior research. Overall, our results highlight the importance of reducing observer error and analyzing dental microwear in three dimensions in order to consistently interpret diets accurately. PMID:23936506

  11. Climate Response to Warm Cloud-Aerosol Interactions: Comparisons With Direct Aerosol and Long-Lived Greenhouse Gas Impacts

    NASA Astrophysics Data System (ADS)

    Ramaswamy, V.; Ming, Y.

    2006-12-01

    We employ the NOAA/ GFDL global atmospheric model coupled to a mixed-layer ocean to investigate the mechanisms and quantitative aspects underlying the radiative perturbations and climate response arising due to cloud-aerosol interactions in low-lying clouds. The aerosol species considered include sulfate, sea-salt and carbonaceous species, whose space-time distributions are determined offline by the MOZART 2 chemistry- transport model based on emissions data. The model's prognostic cloud scheme of liquid water and amount is expanded to include cloud droplet concentration in a way that importantly allows them to be computed using the same large-scale and convective updraft velocity field. The equilibrium response of the model's global climate system to the change in aerosols from pre- industrial to present-day is evaluated, in terms of the forcing applied and the role of the large- and cloud-scale feedback mechanisms. The cloud characteristics simulated are compared against observations, while the model's response is compared with that obtained from using a diagnostic aerosol-cloud relationship to highlight the significance of specific cloud microphysical processes. The spatial distributions of the thermal and hydrologic responses are also compared with those resulting from simulations performed for the pre-industrial to present-day direct aerosol effect. The temperature responses in the low and high latitudes, including changes in the large-scale precipitation pattern, are contrasted with those due to the well-mixed greenhouse gases. The forcing-response relationship is examined for the radiative perturbations investigated, with surface radiative forcing included in these considerations. We finally investigate the concept of linear additivity of the responses in various climate variables for the set of radiative perturbations considered above, extending from the global- and zonal-mean to continental scales.

  12. Alternatives for logistic regression in cross-sectional studies: an empirical comparison of models that directly estimate the prevalence ratio

    PubMed Central

    Barros, Aluísio JD; Hirakata, Vânia N

    2003-01-01

    Background Cross-sectional studies with binary outcomes analyzed by logistic regression are frequent in the epidemiological literature. However, the odds ratio can importantly overestimate the prevalence ratio, the measure of choice in these studies. Also, controlling for confounding is not equivalent for the two measures. In this paper we explore alternatives for modeling data of such studies with techniques that directly estimate the prevalence ratio. Methods We compared Cox regression with constant time at risk, Poisson regression and log-binomial regression against the standard Mantel-Haenszel estimators. Models with robust variance estimators in Cox and Poisson regressions and variance corrected by the scale parameter in Poisson regression were also evaluated. Results Three outcomes, from a cross-sectional study carried out in Pelotas, Brazil, with different levels of prevalence were explored: weight-for-age deficit (4%), asthma (31%) and mother in a paid job (52%). Unadjusted Cox/Poisson regression and Poisson regression with scale parameter adjusted by deviance performed worst in terms of interval estimates. Poisson regression with scale parameter adjusted by χ2 showed variable performance depending on the outcome prevalence. Cox/Poisson regression with robust variance, and log-binomial regression performed equally well when the model was correctly specified. Conclusions Cox or Poisson regression with robust variance and log-binomial regression provide correct estimates and are a better alternative for the analysis of cross-sectional studies with binary outcomes than logistic regression, since the prevalence ratio is more interpretable and easier to communicate to non-specialists than the odds ratio. However, precautions are needed to avoid estimation problems in specific situations. PMID:14567763

  13. Phenotypic plasticity in bacterial plasmids.

    PubMed Central

    Turner, Paul E

    2004-01-01

    Plasmid pB15 was previously shown to evolve increased horizontal (infectious) transfer at the expense of reduced vertical (intergenerational) transfer and vice versa, a key trade-off assumed in theories of parasite virulence. Whereas the models predict that susceptible host abundance should determine which mode of transfer is selectively favored, host density failed to mediate the trade-off in pB15. One possibility is that the plasmid's transfer deviates from the assumption that horizontal spread (conjugation) occurs in direct proportion to cell density. I tested this hypothesis using Escherichia coli/pB15 associations in laboratory serial culture. Contrary to most models of plasmid transfer kinetics, my data show that pB15 invades static (nonshaking) bacterial cultures only at intermediate densities. The results can be explained by phenotypic plasticity in traits governing plasmid transfer. As cells become more numerous, the plasmid's conjugative transfer unexpectedly declines, while the trade-off between transmission routes causes vertical transfer to increase. Thus, at intermediate densities the plasmid's horizontal transfer can offset selection against plasmid-bearing cells, but at high densities pB15 conjugates so poorly that it cannot invade. I discuss adaptive vs. nonadaptive causes for the phenotypic plasticity, as well as potential mechanisms that may lead to complex transfer dynamics of plasmids in liquid environments. PMID:15166133

  14. A comparison of FEM-based inversion algorithms, Local frequency estimation and direct inversion approach used in MR elastography.

    PubMed

    Honarvar, Mohammad; Sahebjavaher, Ramin; Rohling, Robert; Salcudean, Septimiu

    2017-03-22

    In quantitative elastography, maps of the mechanical properties of soft tissue, or elastograms, are calculated from the measured displacement data by solving an inverse problem. The model assumptions have a significant effect on elastograms. Motivated by the high sensitivity of imaging results to the model assumptions for in-vivo Magnetic Resonance Elastography (MRE) of the prostate, we compared elastograms obtained with four different methods. Two FEM-based methods developed by our group were compared with two other commonly used methods, Local Frequency Estimator (LFE) and curl-based Direct Inversion (c-DI). All the methods assume a linear isotropic elastic model, but the methods vary in their assumptions, such as local homogeneity or incompressibility, and in the specific approach used. We report results using simulations, phantom, ex-vivo and in-vivo data. The simulation and phantom studies show, for regions with an inclusion, the contrast to noise ratio (CNR) for the FEM methods is about 3-5 times higher than the CNR for the LFE and c-DI and the RMS error is about half. The LFE method produces very smooth results (i.e. low CNR) and is fast. c-DI is faster than the FEM methods but it's only accurate in areas where elasticity variations are small. The artifacts resulting from the homogeneity assumption in c-DI is detrimental in regions with large variations. The ex-vivo and in-vivo results also show similar trends as the simulation and phantom studies. The c-FEM method is more sensitive to noise compared to the mixed-FEM due to higher orders derivatives. This is especially evident at lower frequencies where the wave curvature is smaller and it is more prone to such error, causing a discrepancy in the absolute values between the mixed-FEM and c-FEM in our in-vivo results. In general, the proposed finite element methods use fewer simplifying assumptions and outperform the other methods but they are computationally more expensive.

  15. Airborne measurements of spectral direct aerosol radiative forcing in INTEX/ICARTT (2004) and comparisons to previous campaigns

    NASA Astrophysics Data System (ADS)

    Redemann, J.; Pilewskie, P.; Russell, P.; Livingston, J.; Howard, S.; Schmid, B.; Pommier, J.; Gore, W.; Eilers, J.; Wendisch, M.; Bush, B.; Valero, F.

    2005-12-01

    As part of the INTEX-NA (INtercontinental chemical Transport EXperiment-North America) and ITCT (Intercontinental Transport and Chemical Transformation of anthropogenic pollution) field studies, the NASA Ames 14-channel Airborne Tracking Sunphotometer (AATS-14) and a pair of Solar Spectral Flux Radiometers (SSFR) took measurements from aboard a Jetstream 31 (J31) aircraft during 19 science flights (~ 53 flight hours) over the Gulf of Maine between 12 July and 8 August 2004. AATS-14 measures the direct solar beam transmission at 14 discrete wavelengths (354-2138 nm), yielding aerosol optical depth (AOD) spectra, while the SSFR system yields down- and upwelling solar irradiance at a spectral resolution of ~ 8-12 nm over the wavelength range 300-1700 nm. The combination of simultaneous AATS and SSFR measurements yields plots of net spectral irradiance as a function of aerosol optical depth as measured along horizontal flight legs. From the slope of these plots we determine the instantaneous aerosol-induced change in net radiative flux per change in AOD. By normalization to an aerosol optical depth change of unity we derive the spectral aerosol radiative forcing efficiency [W m-2 nm-1]. Numerical integration of the irradiance measurements over a given spectral range yields the broadband aerosol radiative forcing efficiency [W m-2]. In INTEX/ITCT, we observed a total of 16 horizontal AOD gradients, with 10 gradients well suited for our analysis because of the small changes in solar zenith angle. Within the 10 case studies we found a high variability in the derived instantaneous aerosol forcing efficiencies for the visible wavelength range (350-700 nm), with a mean of -79.6 W m-2 and a standard deviation of 21.8 W m-2 (27%). The mean instantaneous forcing efficiency for the visible plus near-IR wavelength range (350-1670 nm) was derived to be 135.3 W m-2 with a standard deviation of 36.0 W m-2 (27%). An analytical conversion of the instantaneous forcing efficiencies to

  16. Geochemical and Textural Comparison of Modern and Ancient Freshwater Microbial Mud: A Direct Calibration in the Florida Everglades

    NASA Astrophysics Data System (ADS)

    Pederson, C.; Klaus, J.; McNeill, D. F.; Swart, P. K.

    2015-12-01

    The goal of this study is to directly calibrate a freshwater microbial carbonate deposit currently forming in the Florida Everglades, to ancient deposits formed during Pleistocene marine transgressions of the South Florida platform. Through textural and geochemical analyses, this project tracks the deposition and early diagenesis of microbial carbonates and their associated organic content as an analogue study applicable to ancient microbialites. In the modern, fine-grained low-Mg calcite crystals are precipitated and buried on a low-lying coastal plain (Paurotis Pond). Geochemical parameters were measured to provide baseline characterization of the deposition and early diagenesis of the freshwater muds. Stable isotopic values of the precipitated muds range from d18O of -1.5 to -2.5‰ and d13C 0.5 to -0.5‰, showing slight increases with depth. This change is likely due to waters from the underlying Pleistocene bedrock, diffusing up and mixing with the surface water. Total organic carbon (TOC) is depleted with depth from 10.4 to 4.2% as a result of the degradation of highly labile organic matter (heavier in d13Corg), leaving the resulting pool of organics increasingly negative (-23‰ to -26‰ in the modern). Pleistocene freshwater limestones were observed in core borings ~20 km north of Paurotis Pond. These units closely resemble the modern muds, and allow us to assess the preservation potential of original microbial, geochemical, and textural signatures. Diagenesis has resulted in lighter d13C values relative to the adjacent altered marine units, as well as their modern equivalent. Organics in the Pleistocene are also characterized by more negative C and O isotopic compositions from interpreted original values, and TOC was reduced to <0.1%. Results suggest that both carbonate and organic fractions are pervasively altered during the burial process, and may not be effective paleoclimate indicators as some research suggests. However, these components may still

  17. Carbon Nanotube Emissions from Arc Discharge Production: Classification of Particle Types with Electron Microscopy and Comparison with Direct Reading Techniques

    PubMed Central

    Ludvigsson, Linus; Isaxon, Christina; Nilsson, Patrik T.; Tinnerberg, Hakan; Messing, Maria E.; Rissler, Jenny; Skaug, Vidar; Gudmundsson, Anders; Bohgard, Mats; Hedmer, Maria; Pagels, Joakim

    2016-01-01

    Introduction: An increased production and use of carbon nanotubes (CNTs) is occurring worldwide. In parallel, a growing concern is emerging on the adverse effects the unintentional inhalation of CNTs can have on humans. There is currently a debate regarding which exposure metrics and measurement strategies are the most relevant to investigate workplace exposures to CNTs. This study investigated workplace CNT emissions using a combination of time-integrated filter sampling for scanning electron microscopy (SEM) and direct reading aerosol instruments (DRIs). Material and Methods: Field measurements were performed during small-scale manufacturing of multiwalled carbon nanotubes using the arc discharge technique. Measurements with highly time- and size-resolved DRI techniques were carried out both in the emission and background (far-field) zones. Novel classifications and counting criteria were set up for the SEM method. Three classes of CNT-containing particles were defined: type 1: particles with aspect ratio length:width >3:1 (fibrous particles); type 2: particles without fibre characteristics but with high CNT content; and type 3: particles with visible embedded CNTs. Results: Offline sampling using SEM showed emissions of CNT-containing particles in 5 out of 11 work tasks. The particles were classified into the three classes, of which type 1, fibrous CNT particles contributed 37%. The concentration of all CNT-containing particles and the occurrence of the particle classes varied strongly between work tasks. Based on the emission measurements, it was assessed that more than 85% of the exposure originated from open handling of CNT powder during the Sieving, mechanical work-up, and packaging work task. The DRI measurements provided complementary information, which combined with SEM provided information on: (i) the background adjusted emission concentration from each work task in different particle size ranges, (ii) identification of the key procedures in each work

  18. Direct comparison of recent cyclone and tsunami deposits from the Tamil Nadu coastline, south-eastern India

    NASA Astrophysics Data System (ADS)

    Gouramanis, C.; Karthikeyan, A.; Seshachalam, S.; Switzer, A.; Pham, D. T.

    2013-12-01

    Storm and tsunami deposits have been identified and described from many siliciclastic coastlines globally. However, as storm and tsunami deposits are both the result of inundation by ocean waves, they can have similar sedimentological and geomorphological signatures. To demarcate storm and tsunami deposits in the geological record, a number of criteria have been proposed to distinguish the two types of deposits. However, these criteria have been assembled from storm and tsunami deposits from coastlines of markedly different onshore and offshore geomorphologies, sedimentary characteristics and sediment sources. Thus, a primary goal for coastal hazard scientists is to define a suite of characteristics that can be used to discern storm from tsunami deposits. This can only be accomplished by identifying recent, known tsunami and storm deposits from the same coastline to directly compare the sedimentary characteristics deposited by these types of events. Here we compare the sedimentology, microfauna and sedimentary structures of two recent events, the 26th December 2004 Indian Ocean Tsunami and the 31st December 2011 Cyclone Thane, from three sites along the Tamil Nadu coastline, south-east India and categorise the similarities and differences between the two deposits. Three sites were investigated, two (SB-1 and SB-2) at Silver Beach, Cuddalore and a third (Pit DPM-3a) at the now blocked Pennai River Mouth north of Cuddalore. At all sites the sedimentary deposits of Cyclone Thane overlie aeolian sands which in turn overly the 2004 Indian Ocean Tsunami deposits. In SB-1 the tsunami deposits have been partially reworked by mangroves that fringed the blocked river. The tsunami deposit found in pit SB-2 overlays a marine intertidal - beach sequence. Pit DPM-3a contains the upper part of the2004 tsunami. In each pit, heavy mineral-rich layers characterise the tsunami and the cyclone deposit, whereas the intervening aeolian sands have only a minor heavy mineral content. Also

  19. A direct comparison of immunological and clinical effects of interleukin 2 with and without interferon-alpha in humans.

    PubMed

    Schiller, J H; Hank, J; Storer, B; Borchert, A A; Moore, K H; Albertini, M; Bechhofer, R; Wesley, O; Brown, R R; Bastin, A M

    1993-03-15

    Interleukin 2 (IL-2) and interferon-alpha (IFN-alpha) are cytokines with synergistic antitumor effects in mouse models. The biological effects of this combination, however, have not been directly compared to each agent alone in humans. We conducted a Phase 1B trial of IL-2 plus or minus IFN-alpha in 38 cancer patients. The objectives of this trial were to determine which doses of IFN-alpha and IL-2 maximally enhanced biological responses, and to determine whether the combined administration of IFN-alpha and IL-2 would result in a potentiation of biological responses over IL-2 alone. Patients received 4 days of IL-2 (1.5 x 10(6) units/m2/day or 3.0 x 10(6) units/m2/day) as a continuous infusion followed by a 3-day rest period, weekly for 3 weeks, with a 3-week rest period between 2 treatment courses. IFN-alpha (0.5 x 10(6) or 5 x 10(6) units/m2/day) was administered s.c. on days 1-4 weekly for 3 weeks with one of the 3-week courses. Patients were randomized to receive either IL-2 alone for course 1, followed by IL-2/IFN-alpha for course 2, or IL-2/IFN-alpha in course 1, followed by IL-2 alone. Immunological parameters were evaluated before treatment, and 24 h after completion of the third week of IL-2. A statistically significant increase in the percentage of circulating natural killer cells (CD56), natural killer cells bearing the Fc receptor (CD16), and activated T cells (CD25) was observed following IL-2 alone, and following IL-2 plus IFN-alpha. Significant increases in lymphocyte-activated killer cell cytotoxicity, antibody cellular cytotoxicity, and serum IL-2 receptor were also observed following both IL-2 and IL-2 plus IFN-alpha. However, no significant differences were observed in the magnitude of the increase in the IL-2-alone group when compared to the IL-2 plus IFN-alpha group. The mean fluorescent intensity of monocytes positive for HLA-DR and Fc receptor expression also increased significantly in both groups, as did serum beta 2-microglobulin expression

  20. Regulatory mechanisms link phenotypic plasticity to evolvability.

    PubMed

    van Gestel, Jordi; Weissing, Franz J

    2016-04-18

    Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticity tend to adopt a phenomenological reaction norm (RN) approach, which neglects the mechanisms underlying plasticity. Focusing on a concrete question - the optimal timing of bacterial sporulation - we here also consider a mechanistic approach, the evolution of a gene regulatory network (GRN) underlying plasticity. Using individual-based simulations, we compare the RN and GRN approach and find a number of striking differences. Most importantly, the GRN model results in a much higher diversity of responsive strategies than the RN model. We show that each of the evolved strategies is pre-adapted to a unique set of unseen environmental conditions. The regulatory mechanisms that control plasticity therefore critically link phenotypic plasticity to the adaptive potential of biological populations.

  1. Single cell dynamic phenotyping

    PubMed Central

    Patsch, Katherin; Chiu, Chi-Li; Engeln, Mark; Agus, David B.; Mallick, Parag; Mumenthaler, Shannon M.; Ruderman, Daniel

    2016-01-01

    Live cell imaging has improved our ability to measure phenotypic heterogeneity. However, bottlenecks in imaging and image processing often make it difficult to differentiate interesting biological behavior from technical artifact. Thus there is a need for new methods that improve data quality without sacrificing throughput. Here we present a 3-step workflow to improve dynamic phenotype measurements of heterogeneous cell populations. We provide guidelines for image acquisition, phenotype tracking, and data filtering to remove erroneous cell tracks using the novel Tracking Aberration Measure (TrAM). Our workflow is broadly applicable across imaging platforms and analysis software. By applying this workflow to cancer cell assays, we reduced aberrant cell track prevalence from 17% to 2%. The cost of this improvement was removing 15% of the well-tracked cells. This enabled detection of significant motility differences between cell lines. Similarly, we avoided detecting a false change in translocation kinetics by eliminating the true cause: varied proportions of unresponsive cells. Finally, by systematically seeking heterogeneous behaviors, we detected subpopulations that otherwise could have been missed, including early apoptotic events and pre-mitotic cells. We provide optimized protocols for specific applications and step-by-step guidelines for adapting them to a variety of biological systems. PMID:27708391

  2. The new mutation theory of phenotypic evolution

    PubMed Central

    Nei, Masatoshi

    2007-01-01

    Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance. PMID:17640887

  3. Comparison of the phenotypes of patients harboring in-frame deletions starting at exon 45 in the Duchenne muscular dystrophy gene indicates potential for the development of exon skipping therapy.

    PubMed

    Nakamura, Akinori; Shiba, Naoko; Miyazaki, Daigo; Nishizawa, Hitomi; Inaba, Yuji; Fueki, Noboru; Maruyama, Rika; Echigoya, Yusuke; Yokota, Toshifumi

    2017-04-01

    Exon skipping therapy has recently received attention for its ability to convert the phenotype of lethal Duchenne muscular dystrophy (DMD) to a more benign form, Becker muscular dystrophy (BMD), by correcting the open reading frame. This therapy has mainly focused on a hot-spot (exons 45-55) mutation in the DMD gene. Exon skipping of an entire stretch of exons 45-55 is an approach applicable to 46.9% of DMD patients. However, the resulting phenotype is not yet fully understood. Here we examined the clinical profiles of 24 patients with BMD resulting from deletions starting at exon 45. The Δ45-55 group ranged in age from 2 to 87 years; no mortality was observed, and one patient was ambulatory at 79 years of age. The age at which patients became wheelchair-bound in the Δ45-48 group (18-88 years old) was approximately 50 years. Cardiomyopathy was well controlled by pharmaceuticals in both deletion groups. In contrast, the Δ45-47 and Δ45-49 groups exhibited more severe phenotypes than those with other mutations: the age at which patients in the Δ45-49 group became wheelchair-bound was around 30-40 years. Our study shows that clinical severity differs between each hot-spot deletion.

  4. [Phenotype specific therapy of COPD].

    PubMed

    Rothe, Thomas

    2014-12-10

    COPD is not a homogenous disease but consists of at least four different phenotypes: Emphysema, COPD with chronic bronchitis, asthma-COPD overlap syndrome (ACOS), and COPD with recurrent exacerbations. With differentiation, treatment can be designed phenotype-specific. Some modern drugs are not indicated in all phenotypes.

  5. Direct comparison of the performance of commonly used e-beam resists during nano-scale plasma etching of Si, SiO2, and Cr

    NASA Astrophysics Data System (ADS)

    Goodyear, Andy; Boettcher, Monika; Stolberg, Ines; Cooke, Mike

    2015-03-01

    Electron beam writing remains one of the reference pattern generation techniques, and plasma etching continues to underpin pattern transfer. We report a systematic study of the plasma etch resistance of several e-beam resists, both negative and positive as well as classical and Chemically Amplified Resists: HSQ[1,2] (Dow Corning), PMMA[3] (Allresist GmbH), AR-P6200 (Allresist GmbH), ZEP520 (Zeon Corporation), CAN028 (TOK), CAP164 (TOK), and an additional pCAR (non-disclosed provider). Their behaviour under plasma exposure to various nano-scale plasma etch chemistries was examined (SF6/C4F8 ICP silicon etch, CHF3/Ar RIE SiO2 etch, Cl2/O2 RIE and ICP chrome etch, and HBr ICP silicon etch). Samples of each resist type were etched simultaneously to provide a direct comparison of their etch resistance. Resist thicknesses (and hence resist erosion rates) were measured by spectroscopic ellipsometer in order to provide the highest accuracy for the resist comparison. Etch selectivities (substrate:mask etch rate ratio) are given, with recommendations for the optimum resist choice for each type of etch chemistry. Silicon etch profiles are also presented, along with the exposure and etch conditions to obtain the most vertical nano-scale pattern transfer. We identify one resist that gave an unusually high selectivity for chlorinated and brominated etches which could enable pattern transfer below 10nm without an additional hard mask. In this case the resist itself acts as a hard mask. We also highlight the differing effects of fluorine and bromine-based Silicon etch chemistries on resist profile evolution and hence etch fidelity.

  6. Virtual environments for the transfer of navigation skills in the blind: a comparison of directed instruction vs. video game based learning approaches.

    PubMed

    Connors, Erin C; Chrastil, Elizabeth R; Sánchez, Jaime; Merabet, Lotfi B

    2014-01-01

    For profoundly blind individuals, navigating in an unfamiliar building can represent a significant challenge. We investigated the use of an audio-based, virtual environment called Audio-based Environment Simulator (AbES) that can be explored for the purposes of learning the layout of an unfamiliar, complex indoor environment. Furthermore, we compared two modes of interaction with AbES. In one group, blind participants implicitly learned the layout of a target environment while playing an exploratory, goal-directed video game. By comparison, a second group was explicitly taught the same layout following a standard route and instructions provided by a sighted facilitator. As a control, a third group interacted with AbES while playing an exploratory, goal-directed video game however, the explored environment did not correspond to the target layout. Following interaction with AbES, a series of route navigation tasks were carried out in the virtual and physical building represented in the training environment to assess the transfer of acquired spatial information. We found that participants from both modes of interaction were able to transfer the spatial knowledge gained as indexed by their successful route navigation performance. This transfer was not apparent in the control participants. Most notably, the game-based learning strategy was also associated with enhanced performance when participants were required to find alternate routes and short cuts within the target building suggesting that a ludic-based training approach may provide for a more flexible mental representation of the environment. Furthermore, outcome comparisons between early and late blind individuals suggested that greater prior visual experience did not have a significant effect on overall navigation performance following training. Finally, performance did not appear to be associated with other factors of interest such as age, gender, and verbal memory recall. We conclude that the highly interactive

  7. From Function to Phenotype: Impaired DNA Binding and Clustering Correlates with Clinical Severity in Males with Missense Mutations in MECP2

    PubMed Central

    Sheikh, Taimoor I.; Ausió, Juan; Faghfoury, Hannah; Silver, Josh; Lane, Jane B.; Eubanks, James H.; MacLeod, Patrick; Percy, Alan K.; Vincent, John B.

    2016-01-01

    Mutations in the MECP2 gene cause Rett syndrome (RTT). MeCP2 binds to chromocentric DNA through its methyl CpG-binding domain (MBD) to regulate gene expression. In heterozygous females the variable phenotypic severity is modulated by non-random X-inactivation, thus making genotype-phenotype comparisons unreliable. However, genotype-phenotype correlations in males with hemizygousMECP2 mutations can provide more accurate insights in to the true biological effect of specific mutations. Here, we compared chromatin organization and binding dynamics for twelve MeCP2 missense mutations (including two novel and the five most common MBD missense RTT mutations) and identifiedacorrelation with phenotype in hemizygous males. We observed impaired interaction of MeCP2-DNA for mutations around the MBD-DNA binding interface, and defective chromatin clustering for distal MBD mutations. Furthermore, binding and mobility dynamics show a gradient of impairment depending on the amino acid properties and tertiary structure within the MBD. Interestingly, a wide range of phenotypic/clinical severity, ranging from neonatal encephalopathy to mild psychiatric abnormalities were observed and all are consistent with our functional/molecular results. Overall, clinical severity showed a direct correlation with the functional impairment of MeCP2. These mechanistic and phenotypic correlations of MeCP2 mutations will enable improved and individualized diagnostics, and may lead to personalized therapeutic interventions. PMID:27929079

  8. `Weak A' phenotypes

    PubMed Central

    Cartron, J. P.; Gerbal, A.; Hughes-Jones, N. C.; Salmon, C.

    1974-01-01

    Thirty-five weak A samples including fourteen A3, eight Ax, seven Aend, three Am and three Ae1 were studied in order to determine their A antigen site density, using an IgG anti-A labelled with 125I. The values obtained ranged between 30,000 A antigen sites for A3 individuals, and 700 sites for the Ae1 red cells. The hierarchy of values observed made it possible to establish a quantitative relationship between the red cell agglutinability of these phenotypes measured under standard conditions, and their antigen site density. PMID:4435836

  9. The differential view of genotype–phenotype relationships

    PubMed Central

    Orgogozo, Virginie; Morizot, Baptiste; Martin, Arnaud

    2015-01-01

    An integrative view of diversity and singularity in the living world requires a better understanding of the intricate link between genotypes and phenotypes. Here we re-emphasize the old standpoint that the genotype–phenotype (GP) relationship is best viewed as a connection between two differences, one at the genetic level and one at the phenotypic level. As of today, predominant thinking in biology research is that multiple genes interact with multiple environmental variables (such as abiotic factors, culture, or symbionts) to produce the phenotype. Often, the problem of linking genotypes and phenotypes is framed in terms of genotype and phenotype maps, and such graphical representations implicitly bring us away from the differential view of GP relationships. Here we show that the differential view of GP relationships is a useful explanatory framework in the context of pervasive pleiotropy, epistasis, and environmental effects. In such cases, it is relevant to view GP relationships as differences embedded into differences. Thinking in terms of differences clarifies the comparison between environmental and genetic effects on phenotypes and helps to further understand the connection between genotypes and phenotypes. PMID:26042146

  10. A Comprehensive Evaluation of Disease Phenotype Networks for Gene Prioritization

    PubMed Central

    Li, Jianhua; Lin, Xiaoyan; Teng, Yueyang; Qi, Shouliang; Xiao, Dayu; Zhang, Jianying; Kang, Yan

    2016-01-01

    Identification of disease-causing genes is a fundamental challenge for human health studies. The phenotypic similarity among diseases may reflect the interactions at the molecular level, and phenotype comparison can be used to predict disease candidate genes. Online Mendelian Inheritance in Man (OMIM) is a database of human genetic diseases and related genes that has become an authoritative source of disease phenotypes. However, disease phenotypes have been described by free text; thus, standardization of phenotypic descriptions is needed before diseases can be compared. Several disease phenotype networks have been established in OMIM using different standardization methods. Two of these networks are important for phenotypic similarity analysis: the first and most commonly used network (mimMiner) is standardized by medical subject heading, and the other network (resnikHPO) is the first to be standardized by human phenotype ontology. This paper comprehensively evaluates for the first time the accuracy of these two networks in gene prioritization based on protein–protein interactions using large-scale, leave-one-out cross-validation experiments. The results show that both networks can effectively prioritize disease-causing genes, and the approach that relates two diseases using a logistic function improves prioritization performance. Tanimoto, one of four methods for normalizing resnikHPO, generates a symmetric network and it performs similarly to mimMiner. Furthermore, an integration of these two networks outperforms either network alone in gene prioritization, indicating that these two disease networks are complementary. PMID:27415759

  11. Bioimaging for quantitative phenotype analysis.

    PubMed

    Chen, Weiyang; Xia, Xian; Huang, Yi; Chen, Xingwei; Han, Jing-Dong J

    2016-06-01

    With the development of bio-imaging techniques, an increasing number of studies apply these techniques to generate a myriad of image data. Its applications range from quantification of cellular, tissue, organismal and behavioral phenotypes of model organisms, to human facial phenotypes. The bio-imaging approaches to automatically detect, quantify, and profile phenotypic changes related to specific biological questions open new doors to studying phenotype-genotype associations and to precisely evaluating molecular changes associated with quantitative phenotypes. Here, we review major applications of bioimage-based quantitative phenotype analysis. Specifically, we describe the biological questions and experimental needs addressable by these analyses, computational techniques and tools that are available in these contexts, and the new perspectives on phenotype-genotype association uncovered by such analyses.

  12. Phenotypic classification of male pseudohermaphroditism due to steroid 5{alpha}-reductase 2 deficiency

    SciTech Connect

    Sinnecker, G.H.G; Hiort, O.; Kruse, K.; Dibbelt, L.

    1996-05-03

    Conversion of testosterone (T) to dihydrotestosterone (DHT) in genital tissue is catalysed by the enzyme 5{alpha}-reductase 2, which is encoded by the SRD5A2 gene. The potent androgen DHT is required for full masculinization of the external genitalia. Mutations of the SRD5A2 gene inhibit enzyme activity, diminish DHT formation, and hence cause masculinization defects of varying degree. The classical syndrome, formerly described as pseudovaginal perineoscrotal hypospadias, is characterized by a predominantly female phenotype at birth and significant virilization without gynecomastia at puberty. We investigated nine patients with steroid 5{alpha}-reductase 2 deficiency (SRD). T/DHT-ratios were highly increased in the classical syndrome, but variable in the less severe affected patients. Mutations in the SRD5A2 gene had been characterized using PCR-SSCP analysis and direct DNA sequencing. A small deletion was encountered in two patients, while all other patients had single base mutations which result in amino acid substitutions. We conclude that phenotypes may vary widely in patients with SRD5A2 gene mutations spanning the whole range from completely female to normal male without distinctive clinical signs of the disease. Hence, steroid 5{alpha}-reductase deficiency should be considered not only in sex reversed patients with female or ambiguous phenotypes, but also in those with mild symptoms of undermasculinization as encountered in patients with hypospadias and/or micropenis. A classification based on the severity of the masculinization defect may be used for correlation of phenotypes with enzyme activities and genotypes, and for comparisons of phenotypes between different patients as the basis for clinical decisions to be made in patients with pseudohermaphroditism due to steroid 5{alpha}-reductase 2 deficiency. 22 refs., 2 figs., 2 tabs.

  13. The Phenotype of Loneliness

    PubMed Central

    Cacioppo, John T.; Cacioppo, Stephanie

    2012-01-01

    Goossens’ (in press) review nicely maps the progression of scientific research from its early focus on loneliness as a dysphoric state that results from the discrepancy between a person's ideal and actual social relationships to its current emphasis on the centrality of loneliness to our very nature as a social species, and he argues that developmental science throughout Europe has a great deal to contribute to our understanding of this construct. He concludes that psychologists should care about research on loneliness for five reasons: (i) it is a well-defined phenotype, (ii) it shows both high stability and individual differences in rates of change across years, (iii) it has adaptive value and evolutionary significance, (iv) it has a genetic substrate that is moderated by social environments, and (v) it has self-maintaining features that can lead to adverse mental health outcomes. Goossen's (2012) review is rife with information and ideas. We focus here on two additional important reasons and on the phenotype of loneliness. PMID:23024688

  14. From Phenotype to Genotype

    PubMed Central

    2014-01-01

    The progress in phenotype descriptions, measurements, and analyses has been remarkable in the last 50 years. Biomarkers (proteins, carbohydrates, lipids, hormones, various RNAs and cDNAs, microarrays) have been discovered and correlated with diseases and disorders, as well as physiological responses to disease, injury, stress, within blood, urine, and saliva. Three-dimensional digital imaging advanced how we “see” and utilize phenotypes toward diagnosis, treatment, and prognosis. In each example, scientific discovery led to inform clinical health care. In tandem, genetics evolved from Mendelian inheritance (single gene mutations) to include Complex Human Diseases (multiple gene-gene and gene-environment interactions). In addition, epigenetics blossomed with new insights about gene modifiers (e.g., histone and non-histone chromosomal protein methylation, acetylation, sulfation, phosphorylation). We are now at the beginning of a new era using human and microbial whole-genome sequencing to make significant healthcare decisions as to risk, stratification of patients, diagnosis, treatments, and outcomes. Are we as clinicians, scientists, and educators prepared to expand our scope of practice, knowledge base, integration into primary health care (medicine, pharmacy, nursing, and allied health science professions), and clinical approaches to craniofacial-oral-dental health care? The time is now. PMID:24799423

  15. Phenotypic approaches to drought in cassava: review.

    PubMed

    Okogbenin, Emmanuel; Setter, Tim L; Ferguson, Morag; Mutegi, Rose; Ceballos, Hernan; Olasanmi, Bunmi; Fregene, Martin

    2013-01-01

    Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12-18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding.

  16. Phenotypic approaches to drought in cassava: review

    PubMed Central

    Okogbenin, Emmanuel; Setter, Tim L.; Ferguson, Morag; Mutegi, Rose; Ceballos, Hernan; Olasanmi, Bunmi; Fregene, Martin

    2012-01-01

    Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12–18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding. PMID

  17. The social benefits of restoring water quality in the context of the Water Framework Directive: A comparison of willingness to pay and willingness to accept.

    PubMed

    Del Saz-Salazar, Salvador; Hernández-Sancho, Francesc; Sala-Garrido, Ramón

    2009-08-01

    The Water Framework Directive (WFD) is by far the most important piece of water legislation in Europe for the coming decades. Its main aim is to achieve "good ecological status" for all water resources by 2015. The economic valuation of the non-market benefits derived from improving water quality is an important input in assisting the design and implementation of efficient and effective water management policies. In this study, the contingent valuation method has been applied with a double purpose. On the one hand, we have estimated the value of a hypothetical improvement in water quality of a river asking individuals about their willingness to pay, and on the other hand, the issue of exemptions contemplated in the WFD has been addressed surveying people on their willingness to accept compensation if projected improvements were not carried out. Finally, a comparison of costs and benefits in a cost-benefit framework shows that the net present value of the water quality policy is positive both if we consider willingness to pay estimates as willingness to accept estimates, therefore this policy appears desirable from a social perspective.

  18. A Comparison of Staggered-Mesh Lagrange Plus Remap and Cell-Centered Direct Eulerian Godunov Schemes for Rulerian Shock Hydrodynamics

    SciTech Connect

    Pember, R.B.; Anderson, R.W.

    2000-11-22

    We present a comparison of two algorithms for solving the equations of unsteady inviscid compressible flow in a Eulerian frame. The first algorithm is a staggered grid Lagrange plus remap scheme. The Lagrange step in this method is a time-centered version of the scheme due to Tipton, while the remap step employs a variant of the corner transport upwind scheme due to Colella. The second algorithm is a spatially operator-split version of the higher-order Godunov scheme for gas dynamics due to Colella. They use the two methods to compute solutions to a number of one- and two-dimensional problems. The results show the accuracy and performance of the two schemes to be generally equivalent. In a 1984 survey paper by Woodward and Colella, staggered grid, Lagrange plus remap, artificial viscosity schemes did not compare favorably with cell-centered direct Eulerian higher-order Godunov methods. They examine, therefore, how certain features of the staggered grid scheme discussed here contribute to its improved accuracy. They show in particular that the improved accuracy of the present scheme is due in part to the use of a monotonic artificial viscosity in the Lagrange step and the use of an improved upwind method in the remap step.

  19. Assessing the effects of cognitive experiments on the welfare of captive chimpanzees (Pan troglodytes) by direct comparison of activity budget between wild and captive chimpanzees.

    PubMed

    Yamanashi, Yumi; Hayashi, Misato

    2011-12-01

    We investigated the effects of cognitive experiments by direct comparison of activity budgets between wild and captive chimpanzees. One goal of captive management is to ensure that the activity budgets of captive animals are as similar as possible to those of their wild counterparts. However, such similarity has rarely been achieved. We compared the activity budget among three groups of chimpanzees: wild chimpanzees in Bossou (Guinea, n = 10), and captive chimpanzees who participated in cognitive experiments (experimental chimpanzees, n = 6) or did not participate in the experiments (nonexperimental chimpanzees, n = 6) at the Primate Research Institute (Japan). The experimental chimpanzees voluntarily participated in computer-controlled cognitive tasks and small pieces of fruits were provided as rewards. The data from captivity were obtained on the experimental days (weekdays) and nonexperimental days (weekends). In both study sites, we followed each chimpanzee from about 7 a.m. until the time when chimpanzees started to rest in the evening. The behaviors were recorded every 1 min. The results showed that on weekdays, feeding time and resting time of the experimental chimpanzees were almost the same as those of wild chimpanzees. However, for the nonexperimental chimpanzees, feeding time was significantly shorter and resting time was longer than those of the wild chimpanzees. In contrast, no difference was found in feeding time or resting time of the two groups of captive chimpanzees on weekends. The results suggested that the cognitive experiments worked as an efficient method for food-based enrichment.

  20. Comparison of the lattice Boltzmann equation and discrete unified gas-kinetic scheme methods for direct numerical simulation of decaying turbulent flows.

    PubMed

    Wang, Peng; Wang, Lian-Ping; Guo, Zhaoli

    2016-10-01

    The main objective of this work is to perform a detailed comparison of the lattice Boltzmann equation (LBE) and the recently developed discrete unified gas-kinetic scheme (DUGKS) methods for direct numerical simulation (DNS) of the decaying homogeneous isotropic turbulence and the Kida vortex flow in a periodic box. The flow fields and key statistical quantities computed by both methods are compared with those from the pseudospectral method at both low and moderate Reynolds numbers. The results show that the LBE is more accurate and efficient than the DUGKS, but the latter has a superior numerical stability, particularly for high Reynolds number flows. In addition, we conclude that the DUGKS can adequately resolve the flow when the minimum spatial resolution parameter k_{max}η>3, where k_{max} is the maximum resolved wave number and η is the flow Kolmogorov length. This resolution requirement can be contrasted with the requirements of k_{max}η>1 for the pseudospectral method and k_{max}η>2 for the LBE. It should be emphasized that although more validations should be conducted before the DUGKS can be called a viable tool for DNS of turbulent flows, the present work contributes to the overall assessment of the DUGKS, and it provides a basis for further applications of DUGKS in studying the physics of turbulent flows.

  1. Direct Comparisons among Fast Off-Lattice Monte Carlo Simulations, Integral Equation Theories, and Gaussian Fluctuation Theory for Disordered Symmetric Diblock Copolymers

    NASA Astrophysics Data System (ADS)

    Yang, Delian; Zong, Jing; Wang, Qiang

    2012-02-01

    Based on the same model system of symmetric diblock copolymers as discrete Gaussian chains with soft, finite-range repulsions as commonly used in dissipative-particle dynamics simulations, we directly compare, without any parameter-fitting, the thermodynamic and structural properties of the disordered phase obtained from fast off-lattice Monte Carlo (FOMC) simulations^1, reference interaction site model (RISM) and polymer reference interaction site model (PRISM) theories, and Gaussian fluctuation theory. The disordered phase ranges from homopolymer melts (i.e., where the Flory-Huggins parameter χ=0) all the way to the order-disorder transition point determined in FOMC simulations, and the compared quantities include the internal energy, entropy, Helmholtz free energy, excess pressure, constant-volume heat capacity, chain/block dimensions, and various structure factors and correlation functions in the system. Our comparisons unambiguously and quantitatively reveal the consequences of various theoretical approximations and the validity of these theories in describing the fluctuations/correlations in disordered diblock copolymers. [1] Q. Wang and Y. Yin, J. Chem. Phys., 130, 104903 (2009).

  2. A direct comparison of a depth-dependent Radiation stress formulation and a Vortex force formulation within a three-dimensional coastal ocean model

    NASA Astrophysics Data System (ADS)

    Moghimi, Saeed; Klingbeil, Knut; Gräwe, Ulf; Burchard, Hans

    2013-10-01

    In this study a model system consisting of the three-dimensional General Estuarine Transport Model (GETM) and the third generation wind wave model SWAN was developed. Both models were coupled in two-way mode. The effects of waves were included into the ocean model by implementing the depth-dependent Radiation stress formulation (RS) of Mellor (2011a) and the Vortex force formulation (VF) presented by Bennis et al. (2011). Thus, the developed model system offers a direct comparison of these two formulations. The enhancement of the vertical eddy viscosity due to the energy transfer by white capping and breaking waves was taken into account by means of injecting turbulent kinetic energy at the surface. Wave-current interaction inside the bottom boundary layer was considered as well. The implementation of both wave-averaged formulations was validated against three flume experiments. One of these experiments with long period surface waves (swell), had not been evaluated before. The validation showed the capability of the model system to reproduce the three-dimensional interaction of waves and currents. For the flume test cases the wave-induced water level changes (wave set-up and set-down) and the corresponding depth-integrated wave-averaged velocities were similar for RS and VF. Both formulations produced comparable velocity profiles for short period waves. However, for large period waves, VF overestimated the wave set-down near the main breaking points and RS showed artificial offshore-directed transport at the surface where wave shoaling was taking place. Finally the validated model system was applied to a realistic barred beach scenario. For RS and VF the resulting velocity profiles were similar after being significantly improved by a roller evolution method. Both wave-averaged formulations generally provided similar results, but some shortcomings were revealed. Although VF partly showed significant deviations from the measurements, its results were still physically

  3. Electronic transport in a model tetraphenylbenzidine main-chain polymer: Direct comparison of time-of-flight hole drift mobility and electrochemical determinations of hole diffusion

    NASA Astrophysics Data System (ADS)

    Abkowitz, M. A.; Facci, J. S.; Limburg, W. W.; Yanus, J. F.

    1992-09-01

    Electronic transport behavior is analyzed in a model polytetraphenylbenzidine (PTPB) hole transport polymer in which electroactive tetraphenylbenzidine sites are covalently bonded within the polymer main chain. Time-of-flight (TOF) techniques are used to measure the hole drift mobility as a function of electric field and temperature. The TOF data are parametrized using the phenomenological model originally proposed by Gill. For comparative purposes, the disorder model developed by the Marburg group is also used to analyze the data. Transport of holes in PTPB is demonstrated to occur via hopping among the TPB functional units. A pattern of convoluted field and temperature-dependent features, now known to be shared by a broad class of disordered molecular materials, is revealed by the TOF data. Thin solid film electrochemical techniques are applied in parallel with the TOF technique to independently obtain hole diffusion coefficients (Dh) in thin films of PTPB. As a unique consequence of this comparison, it is established that mobilities, computed from solid-state hole diffusion data using the Einstein relation, converge with zero-field extrapolated TOF mobilities over a wide temperature range when the extrapolation is computed from log μ vs E1/2 plots. Therefore, the functional dependence of the logarithm of the drift mobility on the square root of field, a much discussed general feature of electronic transport in disordered molecular materials, is demonstrated to persist through the critical low-field limit. At the same time it is demonstrated that the contribution of thermally driven diffusive broadening, which can now be calculated directly from the independently determined electrochemical hole diffusion coefficients, makes an insignificant contribution to the experimentally observed width of the time-of-flight transit pulse. A comparison of the PTPB data with analogous TOF data on solid solutions of TPD (the functional unit in PTPB) dispersed in polycarbonate

  4. A Direct Comparison of MODIS and COSPEC Sulfur Dioxide Measurements of the May 21, 2003 Eruption Plume of Anatahan Volcano, Mariana Islands

    NASA Astrophysics Data System (ADS)

    Meier, V. L.; Scuderi, L.; Fischer, T.; Hilton, D.

    2007-05-01

    Quantifying the SO2 burden emitted from a volcano is critical to understanding a volcano's current state of activity. Ground-based instruments such as the correlation spectrometer (COSPEC) and the mini-DOAS are most routinely employed to measure volcanic SO2. Both instruments are human operated so they must be deployed on-site to obtain SO2 estimates. This makes it difficult and costly to regularly monitor active volcanoes world- wide. Satellite-based measurements, which can provide SO2 estimates in near real-time, have increasingly been used as a tool for volcanic monitoring. The Moderate Resolution Imaging Spectrometer (MODIS) located on board the Terra and Aqua satellites provides twice daily coverage of the Earth and has the capacity to detect volcanic SO2. The ability of MODIS to accurately detect and quantify SO2 in volcanic plumes using a SO2 retrieval program, MAP_SO2, was compared with COSPEC on the May 21, 2003 plume at Anatahan volcano (16.35oN, 145.67oE). MODIS was able to clearly detect SO2 in the plume and the MAP_SO2 derived SO2 flux was calculated (independently from the COSPEC data) to be more than twice the COSPEC derived flux (10,270 t/d and 3,000 - 4,500 t/d respectively). However, calculating a flux introduces additional errors. Therefore another means of comparing the two methods is utilized: a direct comparison of plume cross-sections from these two different methods. The MODIS image used with the MAP_SO2 program was acquired at 13:25 local time. The COSPEC traverse began at 13:35 local time and ended 14:40 local time. The time of the MODIS image acquisition and the start of the COSPEC traverse occurred within 10 minutes of each other. Although the MODIS image is a snap shot in time and the COSPEC traverse took about an hour to complete, the timing is so close that these two products are ideal for the comparison. The differences in these observations are used to better quantify SO2 emissions, to assess the current mismatch between ground

  5. Phenotype as Agent for Epigenetic Inheritance

    PubMed Central

    Torday, John S.; Miller, William B.

    2016-01-01

    The conventional understanding of phenotype is as a derivative of descent with modification through Darwinian random mutation and natural selection. Recent research has revealed Lamarckian inheritance as a major transgenerational mechanism for environmental action on genomes whose extent is determined, in significant part, by germ line cells during meiosis and subsequent stages of embryological development. In consequence, the role of phenotype can productively be reconsidered. The possibility that phenotype is directed towards the effective acquisition of epigenetic marks in consistent reciprocation with the environment during the life cycle of an organism is explored. It is proposed that phenotype is an active agent in niche construction for the active acquisition of epigenetic marks as a dominant evolutionary mechanism rather than a consequence of Darwinian selection towards reproductive success. The reproductive phase of the life cycle can then be appraised as a robust framework in which epigenetic inheritance is entrained to affect growth and development in continued reciprocal responsiveness to environmental stresses. Furthermore, as first principles of physiology determine the limits of epigenetic inheritance, a coherent justification can thereby be provided for the obligate return of all multicellular eukaryotes to the unicellular state. PMID:27399791

  6. Parasitism and phenotypic change in colonial hosts.

    PubMed

    Hartikainen, Hanna; Fontes, Inês; Okamura, Beth

    2013-09-01

    Changes in host phenotype are often attributed to manipulation that enables parasites to complete trophic transmission cycles. We characterized changes in host phenotype in a colonial host–endoparasite system that lacks trophic transmission (the freshwater bryozoan Fredericella sultana and myxozoan parasite Tetracapsuloides bryosalmonae). We show that parasitism exerts opposing phenotypic effects at the colony and module levels. Thus, overt infection (the development of infectious spores in the host body cavity) was linked to a reduction in colony size and growth rate, while colony modules exhibited a form of gigantism. Larger modules may support larger parasite sacs and increase metabolite availability to the parasite. Host metabolic rates were lower in overtly infected relative to uninfected hosts that were not investing in propagule production. This suggests a role for direct resource competition and active parasite manipulation (castration) in driving the expression of the infected phenotype. The malformed offspring (statoblasts) of infected colonies had greatly reduced hatching success. Coupled with the severe reduction in statoblast production this suggests that vertical transmission is rare in overtly infected modules. We show that although the parasite can occasionally infect statoblasts during overt infections, no infections were detected in the surviving mature offspring, suggesting that during overt infections, horizontal transmission incurs a trade-off with vertical transmission.

  7. Engineering complex phenotypes in industrial strains.

    PubMed

    Patnaik, Ranjan

    2008-01-01

    The global demand is rising for greener manufacturing processes that are cost-competitive and available in a timely manner. This has led to the development of a series of new tools and integrative platforms enabling rapid engineering of complex phenotypes in industrial microbes. By blending "old classical methods" of strain isolation with "newer approaches" of cell engineering, researchers are demonstrating the ability to stack multiple complex phenotypes in industrial hosts with some level of certainty. Newer tools for dissecting the genotype-phenotype correlation include association analysis (Precision Engineering), multiSCale Analysis of Library Enrichment (SCALE) in competition experiments, whole-genome transcriptional analysis, and proteomics and metabolomics technology. These newer and older tools of metabolic engineering and synthetic biology when combined with recent whole cell engineering approaches like whole genome shuffling, global transciptome machinery engineering, and directed evolutionary engineering, provide a powerful platform for engineering complex phenotypes in industrial strains. This review attempts to highlight and compare these newer tools and approaches with traditional strain isolation procedures as it applies to genome engineering with examples taken from literature.

  8. Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes

    PubMed Central

    Arbogast, Thomas; Ouagazzal, Abdel-Mouttalib; Chevalier, Claire; Kopanitsa, Maksym; Afinowi, Nurudeen; Migliavacca, Eugenia; Cowling, Belinda S.; Birling, Marie-Christine; Champy, Marie-France; Reymond, Alexandre; Herault, Yann

    2016-01-01

    The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+) or a duplication (Dup/+) of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice. PMID:26872257

  9. Phenotype and Function of CD209+ Bovine Blood Dendritic Cells, Monocyte-Derived-Dendritic Cells and Monocyte-Derived Macrophages

    PubMed Central

    Bannantine, John P.; Mack, Victoria; Fry, Lindsay M.; Davis, William C.

    2016-01-01

    Phylogenic comparisons of the mononuclear phagocyte system (MPS) of humans and mice demonstrate phenotypic divergence of dendritic cell (DC) subsets that play similar roles in innate and adaptive immunity. Although differing in phenotype, DC can be classified into four groups according to ontogeny and function: conventional DC (cDC1 and cDC2), plasmacytoid DC (pDC), and monocyte derived DC (MoDC). DC of Artiodactyla (pigs and ruminants) can also be sub-classified using this system, allowing direct functional and phenotypic comparison of MoDC and other DC subsets trafficking in blood (bDC). Because of the high volume of blood collections required to study DC, cattle offer the best opportunity to further our understanding of bDC and MoDC function in an outbred large animal species. As reported here, phenotyping DC using a monoclonal antibody (mAb) to CD209 revealed CD209 is expressed on the major myeloid population of DC present in blood and MoDC, providing a phenotypic link between these two subsets. Additionally, the present study demonstrates that CD209 is also expressed on monocyte derived macrophages (MoΦ). Functional analysis revealed each of these populations can take up and process antigens (Ags), present them to CD4 and CD8 T cells, and elicit a T-cell recall response. Thus, bDC, MoDC, and MoΦ pulsed with pathogens or candidate vaccine antigens can be used to study factors that modulate DC-driven T-cell priming and differentiation ex vivo. PMID:27764236

  10. Comparison of phenotypes produced in response to transient expression of genes encoded by four distinct begomoviruses in Nicotiana benthamiana and their correlation with the levels of developmental miRNAs

    PubMed Central

    2011-01-01

    Background Whitefly-transmitted geminiviruses (begomoviruses) are a major limiting factor for the production of numerous dicotyledonous crops throughout the world. Begomoviruses differ in the number of components that make up their genomes and association with satellites, and yet they cause strikingly similar phenotypes, such as leaf curling, chlorosis and stunted plant growth. MicroRNAs (miRNAs) are small endogenous RNAs that regulate plant growth and development. The study described here was aimed at investigating the effects of each virus encoded gene on the levels of developmental miRNAs to identify common trends between distinct begomoviruses. Results All genes encoded by four distinct begomoviruses (African cassava mosaic virus [ACMV], Cabbage leaf curl virus [CbLCuV], Tomato yellow leaf curl virus [TYLCV] and Cotton leaf curl virus/Cotton leaf curl betasatellite [CLCuV/CLCuMB]) were expressed from a Potato virus X (PVX) vector in Nicotiana benthamiana. Changes in the levels of ten miRNAs in response to the virus genes were determined by northern blotting using specific miRNA probes. For the monopartite begomoviruses (TYLCV and CLCuMV) the V2 gene product was identified as the major symptom determinant while for bipartite begomoviruses (ACMV and CbLCuV) more than one gene appears to contribute to symptoms and this is reflected in changes in miRNA levels. The phenotype induced by expression of the βC1 gene of the betasatellite CLCuMB was the most distinct and consisted of leaf curling, vein swelling, thick green veins and enations and the pattern of changes in miRNA levels was the most distinct. Conclusions Our results have identified symptom determinants encoded by begomoviruses and show that developmental abnormalities caused by transient expression of begomovirus genes correlates with altered levels of developmental miRNAs. Additionally, all begomovirus genes were shown to modulate miRNA levels, the first time this has been shown to be the case. PMID

  11. High-throughput mouse phenotyping.

    PubMed

    Gates, Hilary; Mallon, Ann-Marie; Brown, Steve D M

    2011-04-01

    Comprehensive phenotyping will be required to reveal the pleiotropic functions of a gene and to uncover the wider role of genetic loci within diverse biological systems. The challenge will be to devise phenotyping approaches to characterise the thousands of mutants that are being generated as part of international efforts to acquire a mutant for every gene in the mouse genome. In order to acquire robust datasets of broad based phenotypes from mouse mutants it is necessary to design and implement pipelines that incorporate standardised phenotyping platforms that are validated across diverse mouse genetics centres or mouse clinics. We describe here the rationale and methodology behind one phenotyping pipeline, EMPReSSslim, that was designed as part of the work of the EUMORPHIA and EUMODIC consortia, and which exemplifies some of the challenges facing large-scale phenotyping. EMPReSSslim captures a broad range of data on diverse biological systems, from biochemical to physiological amongst others. Data capture and dissemination is pivotal to the operation of large-scale phenotyping pipelines, including the definition of parameters integral to each phenotyping test and the associated ontological descriptions. EMPReSSslim data is displayed within the EuroPhenome database, where a variety of tools are available to allow the user to search for interesting biological or clinical phenotypes.

  12. EHR Big Data Deep Phenotyping

    PubMed Central

    Lenert, L.; Lopez-Campos, G.

    2014-01-01

    Summary Objectives Given the quickening speed of discovery of variant disease drivers from combined patient genotype and phenotype data, the objective is to provide methodology using big data technology to support the definition of deep phenotypes in medical records. Methods As the vast stores of genomic information increase with next generation sequencing, the importance of deep phenotyping increases. The growth of genomic data and adoption of Electronic Health Records (EHR) in medicine provides a unique opportunity to integrate phenotype and genotype data into medical records. The method by which collections of clinical findings and other health related data are leveraged to form meaningful phenotypes is an active area of research. Longitudinal data stored in EHRs provide a wealth of information that can be used to construct phenotypes of patients. We focus on a practical problem around data integration for deep phenotype identification within EHR data. The use of big data approaches are described that enable scalable markup of EHR events that can be used for semantic and temporal similarity analysis to support the identification of phenotype and genotype relationships. Conclusions Stead and colleagues’ 2005 concept of using light standards to increase the productivity of software systems by riding on the wave of hardware/processing power is described as a harbinger for designing future healthcare systems. The big data solution, using flexible markup, provides a route to improved utilization of processing power for organizing patient records in genotype and phenotype research. PMID:25123744

  13. Hierarchical compression of Caenorhabditis elegans locomotion reveals phenotypic differences in the organization of behaviour

    PubMed Central

    2016-01-01

    Regularities in animal behaviour offer insights into the underlying organizational and functional principles of nervous systems and automated tracking provides the opportunity to extract features of behaviour directly from large-scale video data. Yet how to effectively analyse such behavioural data remains an open question. Here, we explore whether a minimum description length principle can be exploited to identify meaningful behaviours and phenotypes. We apply a dictionary compression algorithm to behavioural sequences from the nematode worm Caenorhabditis elegans freely crawling on an agar plate both with and without food and during chemotaxis. We find that the motifs identified by the compression algorithm are rare but relevant for comparisons between worms in different environments, suggesting that hierarchical compression can be a useful step in behaviour analysis. We also use compressibility as a new quantitative phenotype and find that the behaviour of wild-isolated strains of C. elegans is more compressible than that of the laboratory strain N2 as well as the majority of mutant strains examined. Importantly, in distinction to more conventional phenotypes such as overall motor activity or aggregation behaviour, the increased compressibility of wild isolates is not explained by the loss of function of the gene npr-1, which suggests that erratic locomotion is a laboratory-derived trait with a novel genetic basis. Because hierarchical compression can be applied to any sequence, we anticipate that compressibility can offer insights into the organization of behaviour in other animals including humans. PMID:27581484

  14. Hierarchical compression of Caenorhabditis elegans locomotion reveals phenotypic differences in the organization of behaviour.

    PubMed

    Gomez-Marin, Alex; Stephens, Greg J; Brown, André E X

    2016-08-01

    Regularities in animal behaviour offer insights into the underlying organizational and functional principles of nervous systems and automated tracking provides the opportunity to extract features of behaviour directly from large-scale video data. Yet how to effectively analyse such behavioural data remains an open question. Here, we explore whether a minimum description length principle can be exploited to identify meaningful behaviours and phenotypes. We apply a dictionary compression algorithm to behavioural sequences from the nematode worm Caenorhabditis elegans freely crawling on an agar plate both with and without food and during chemotaxis. We find that the motifs identified by the compression algorithm are rare but relevant for comparisons between worms in different environments, suggesting that hierarchical compression can be a useful step in behaviour analysis. We also use compressibility as a new quantitative phenotype and find that the behaviour of wild-isolated strains of C. elegans is more compressible than that of the laboratory strain N2 as well as the majority of mutant strains examined. Importantly, in distinction to more conventional phenotypes such as overall motor activity or aggregation behaviour, the increased compressibility of wild isolates is not explained by the loss of function of the gene npr-1, which suggests that erratic locomotion is a laboratory-derived trait with a novel genetic basis. Because hierarchical compression can be applied to any sequence, we anticipate that compressibility can offer insights into the organization of behaviour in other animals including humans.

  15. Characterizing the in vitro biofilm phenotype of Staphylococcus epidermidis isolates from central venous catheters.

    PubMed

    Van Kerckhoven, Marian; Hotterbeekx, An; Lanckacker, Ellen; Moons, Pieter; Lammens, Christine; Kerstens, Monique; Ieven, Margareta; Delputte, Peter; Jorens, Philippe G; Malhotra-Kumar, Surbhi; Goossens, Herman; Maes, Louis; Cos, Paul

    2016-08-01

    Central venous catheter (CVC)-related infections are commonly caused by Staphylococcus epidermidis that is able to form a biofilm on the catheter surface. Many studies involving biofilm formation by Staphylococcus have been published each adopting an own in vitro model. Since the capacity to form a biofilm depends on multiple environmental factors, direct comparison of results obtained in different studies remains challenging. This study characterized the phenotype (strong versus weak biofilm-producers) of S. epidermidis from CVCs in four different in vitro biofilm models, covering differences in material type (glass versus polymer) and nutrient presentation (static versus continuous flow). A good correlation in phenotype was obtained between glass and polymeric surfaces independent of nutrient flow, with 85% correspondence under static growth conditions and 80% under dynamic conditions. A 80% correspondence between static and dynamic conditions on polymeric surfaces could be demonstrated as well. Incubation time had a significant influence on the biofilm phenotype with only 55% correspondence between the dynamic models at different incubation times (48h versus 17h). Screening for the presence of biofilm-related genes only revealed that ica A was correlated with biofilm formation under static but not under dynamic conditions. In conclusion, this study highlights that a high level of standardization is necessary to interpret and compare results of different in vitro biofilm models.

  16. Do convergent developmental mechanisms underlie convergent phenotypes?

    NASA Technical Reports Server (NTRS)

    Wray, Gregory A.

    2002-01-01

    Convergence is a pervasive evolutionary process, affecting many aspects of phenotype and even genotype. Relatively little is known about convergence in developmental processes, however, nor about the degree to which convergence in development underlies convergence in anatomy. A switch in the ecology of sea urchins from feeding to nonfeeding larvae illustrates how convergence in development can be associated with convergence in anatomy. Comparisons to more distantly related taxa, however, suggest that this association may be limited to relatively close phylogenetic comparisons. Similarities in gene expression during development provide another window into the association between convergence in developmental processes and convergence in anatomy. Several well-studied transcription factors exhibit likely cases of convergent gene expression in distantly related animal phyla. Convergence in regulatory gene expression domains is probably more common than generally acknowledged, and can arise for several different reasons. Copyright 2002 S. Karger AG, Basel.

  17. Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

    PubMed Central

    2014-01-01

    Our enhanced iRRL approach greatly facilitates genotyping-by-sequencing and thus direct estimates of allele frequencies. Our direct comparison of three commonly used SNP callers emphasizes the need to question the accuracy of SNP and genotype calling, as we obtained considerably different SNP datasets depending on caller algorithms, sequencing depths and filtering criteria. These differences affected scans for signatures of natural selection, but will also exert undue influences on demographic inferences. This study presents the first effort to generate a population genomic dataset for wild-born orangutans with known population provenance. PMID:24405840

  18. A direct morphometric comparison of five labeling protocols for multi-atlas driven automatic segmentation of the hippocampus in Alzheimer's disease.

    PubMed

    Nestor, Sean M; Gibson, Erin; Gao, Fu-Qiang; Kiss, Alex; Black, Sandra E

    2013-02-01

    Hippocampal volumetry derived from structural MRI is increasingly used to delineate regions of interest for functional measurements, assess efficacy in therapeutic trials of Alzheimer's disease (AD) and has been endorsed by the new AD diagnostic guidelines as a radiological marker of disease progression. Unfortunately, morphological heterogeneity in AD can prevent accurate demarcation of the hippocampus. Recent developments in automated volumetry commonly use multi-template fusion driven by expert manual labels, enabling highly accurate and reproducible segmentation in disease and healthy subjects. However, there are several protocols to define the hippocampus anatomically in vivo, and the method used to generate atlases may impact automatic accuracy and sensitivity - particularly in pathologically heterogeneous samples. Here we report a fully automated segmentation technique that provides a robust platform to directly evaluate both technical and biomarker performance in AD among anatomically unique labeling protocols. For the first time we test head-to-head the performance of five common hippocampal labeling protocols for multi-atlas based segmentation, using both the Sunnybrook Longitudinal Dementia Study and the entire Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) baseline and 24-month dataset. We based these atlas libraries on the protocols of (Haller et al., 1997; Killiany et al., 1993; Malykhin et al., 2007; Pantel et al., 2000; Pruessner et al., 2000), and a single operator performed all manual tracings to generate de facto "ground truth" labels. All methods distinguished between normal elders, mild cognitive impairment (MCI), and AD in the expected directions, and showed comparable correlations with measures of episodic memory performance. Only more inclusive protocols distinguished between stable MCI and MCI-to-AD converters, and had slightly better associations with episodic memory. Moreover, we demonstrate that protocols including more posterior

  19. Quantification of the Relative Biological Effectiveness for Ion Beam Radiotherapy: Direct Experimental Comparison of Proton and Carbon Ion Beams and a Novel Approach for Treatment Planning

    SciTech Connect

    Elsaesser, Thilo; Weyrather, Wilma K.; Friedrich, Thomas; Durante, Marco; Iancu, Gheorghe; Kraemer, Michael; Kragl, Gabriele; Brons, Stephan; Winter, Marcus; Weber, Klaus-Josef; Scholz, Michael

    2010-11-15

    Purpose: To present the first direct experimental in vitro comparison of the biological effectiveness of range-equivalent protons and carbon ion beams for Chinese hamster ovary cells exposed in a three-dimensional phantom using a pencil beam scanning technique and to compare the experimental data with a novel biophysical model. Methods and Materials: Cell survival was measured in the phantom after irradiation with two opposing fields, thus mimicking the typical patient treatment scenario. The novel biophysical model represents a substantial extension of the local effect model, previously used for treatment planning in carbon ion therapy for more than 400 patients, and potentially can be used to predict effectiveness of all ion species relevant for radiotherapy. A key feature of the new approach is the more sophisticated consideration of spatially correlated damage induced by ion irradiation. Results: The experimental data obtained for Chinese hamster ovary cells clearly demonstrate that higher cell killing is achieved in the target region with carbon ions as compared with protons when the effects in the entrance channel are comparable. The model predictions demonstrate agreement with these experimental data and with data obtained with helium ions under similar conditions. Good agreement is also achieved with relative biological effectiveness values reported in the literature for other cell lines for monoenergetic proton, helium, and carbon ions. Conclusion: Both the experimental data and the new modeling approach are supportive of the advantages of carbon ions as compared with protons for treatment-like field configurations. Because the model predicts the effectiveness for several ion species with similar accuracy, it represents a powerful tool for further optimization and utilization of the potential of ion beams in tumor therapy.

  20. Molecular Anchors for Self-Assembled Monolayers on ZnO: A Direct Comparison of the Thiol and Phosphic Acid Moieties

    SciTech Connect

    Perkins, C. L.

    2009-01-01

    Two of the most promising schemes for attaching organic molecules to metal oxides are based on the chemistry of the thiol and phosphonic acid moieties. We have made a direct comparison of the efficacy of these two molecular anchors on zinc oxide by comparing the chemical and physical properties of n-hexane derivatives of both. The surface properties of polycrystalline ZnO thin films and ZnO(000)-O crystals modified with 1-hexanethiol and 1-hexanephosphonic acid were examined with a novel quartz crystal microbalance (QCM)-based flow cell reactor, angle-resolved and temperature-dependent photoelectron spectroscopy, and contact angle measurements. A means of using ammonium chloride as a probe of molecule-ZnO interactions is introduced and used to ascertain the relative quality of self-assembled monolayers (SAMs) based on thiols and phosphonic acids. QCM data shows that a phosphonic acid-anchored alkyl chain only six carbons long can provide significant corrosion protection for ZnO against Bron