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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 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

  2. 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. PMID:27536304

  3. Direct comparison of mice null for liver or intestinal fatty acid-binding proteins reveals highly divergent phenotypic responses to high fat feeding.

    PubMed

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

    2013-10-18

    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

  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. Disease insights through cross-species phenotype comparisons.

    PubMed

    Haendel, Melissa A; Vasilevsky, Nicole; Brush, Matthew; Hochheiser, Harry S; Jacobsen, Julius; Oellrich, Anika; Mungall, Christopher J; Washington, Nicole; Köhler, Sebastian; Lewis, Suzanna E; Robinson, Peter N; Smedley, Damian

    2015-10-01

    New sequencing technologies have ushered in a new era for diagnosis and discovery of new causative mutations for rare diseases. However, the sheer numbers of candidate variants that require interpretation in an exome or genomic analysis are still a challenging prospect. A powerful approach is the comparison of the patient's set of phenotypes (phenotypic profile) to known phenotypic profiles caused by mutations in orthologous genes associated with these variants. The most abundant source of relevant data for this task is available through the efforts of the Mouse Genome Informatics group and the International Mouse Phenotyping Consortium. In this review, we highlight the challenges in comparing human clinical phenotypes with mouse phenotypes and some of the solutions that have been developed by members of the Monarch Initiative. These tools allow the identification of mouse models for known disease-gene associations that may otherwise have been overlooked as well as candidate genes may be prioritized for novel associations. The culmination of these efforts is the Exomiser software package that allows clinical researchers to analyse patient exomes in the context of variant frequency and predicted pathogenicity as well the phenotypic similarity of the patient to any given candidate orthologous gene. PMID:26092691

  7. 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

  8. 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

  9. 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. PMID:27082860

  10. Phenotypic and Evolutionary Consequences of Social Behaviours: Interactions among Individuals Affect Direct Genetic Effects

    PubMed Central

    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. PMID:23226195

  11. Significance of Lewis phenotyping using saliva and gastric tissue: comparison with the Lewis phenotype inferred from Lewis and secretor genotypes.

    PubMed

    Hong, Yun Ji; Hwang, Sang Mee; Kim, Taek Soo; Song, Eun Young; Park, Kyoung Un; Song, Junghan; Han, Kyou-Sup

    2014-01-01

    Lewis phenotypes using various types of specimen were compared with the Lewis phenotype predicted from Lewis and Secretor genotypes. This is the first logical step in explaining the association between the Lewis expression and Helicobacter pylori. We performed a study of the followings on 209 patients who underwent routine gastroscopy: erythrocyte and saliva Lewis phenotyping, gastric Lewis phenotyping by the tissue array, and the Lewis and Secretor genes genotyping. The results of phenotyping were as follows [Le(a-b-), Le(a+b-), Le(a-b+), and Le(a+b+), respectively, in order]: erythrocyte (12.4%, 25.8%, 61.2%, and 0.5%); saliva (2.4%, 27.3%, 70.3%, and 0.0%); gastric mucosa (8.1%, 6.7%, 45.5%, and 39.7%). The frequency of Le, le (59/508) , le (59/1067) , and le (59) alleles was 74.6%, 21.3%, 3.1%, and 1.0%, respectively, among 418 alleles. The saliva Lewis phenotype was completely consistent with the Lewis phenotype inferred from Lewis and Secretor genotypes, but that of gastric mucosa could not be predicted from genotypes. Lewis phenotyping using erythrocytes is only adequate for transfusion needs. Saliva testing for the Lewis phenotype is a more reliable method for determining the peripheral Lewis phenotype of an individual and the gastric Lewis phenotype must be used for the study on the association between Helicobacter pylori and the Lewis phenotype. PMID:24783214

  12. Comparison between multiplex PCR and phenotypic systems for Candida spp. identification.

    PubMed

    Liguori, Giorgio; Gallé, Francesca; Lucariello, Angela; Di Onofrio, Valeria; Albano, Luciana; Mazzarella, Gennaro; D'Amora, Maurizio; Rossano, Fabio

    2010-01-01

    This study evaluated the performances of three phenotypic systems (RapID Yeast panel, Vitek2 YST card, and API 20 C AUX) and multiplex PCR for Candida spp. identification. Four-hundred and fifty clinical strains of Candida spp. were identified with the four systems and results of multiplex PCR were compared with those of phenotypic methods. The best correspondence was obtained between Multiplex PCR and API 20 C AUX (83.7%), but the other comparisons showed similar values (81.7% and 79.3% for Vitek2 and RapID Yeast panel respectively). The correspondence was lower for all the methods in identification of C. krusei; this may be of concern in addition to the azole resistance and the often endogenous origin of this yeast. In the comparison with the three phenotypic methods, multiplex PCR could be reliable and time-saving in the identification of Candida spp. for diagnostics purposes. Nowadays, a large variety of both traditional and molecular methods for Candida spp. identification are commercially available. Multiplex PCR applied in this study may be more rapid and sensitive than phenotypic systems, and less expensive than other molecular methods. PMID:20402415

  13. Tumor morphological evolution: directed migration and gain and loss of the self-metastatic phenotype

    PubMed Central

    2010-01-01

    Background Aside from the stepwise genetic alterations known to underlie cancer cell creation, the microenvironment is known to profoundly influence subsequent tumor development, morphology and metastasis. Invasive cluster formation has been assumed to be dependent on directed migration and a heterogeneous environment - a conclusion derived from complex models of tumor-environment interaction. At the same time, these models have not included the prospect, now supported by a preponderance of evidence, that only a minority of cancer cells may have stem cell capacity. This proves to weigh heavily on the microenvironmental requirements for the display of characteristic tumor growth phenotypes. We show using agent-based modeling that some defining features of tumor growth ascribed to directed migration might also be realized under random migration, and discuss broader implications for cause-and-effect determination in general. Results Considering only the properties of random migration in tumors composed of stem cells and committed cells, we are able to recapitulate a characteristic clustering feature of invasive tumor growth, a property we attribute to "self-metastatic" growth. When the additional influence of directed migrations under chemotactic environments are considered, we find that tumor growth and invasive morphology are supported while the tumor is distant from the source, but are progressively discouraged as the tumor converges about that source. Conclusions We show that invasive clustering can derive from basic kinetic assumptions often neglected in more complex models. While higher-order mechanisms, e.g. directed migration upon chemotactic stimuli, may result in clustering growth morphologies, exclusive attributions of this phenotype to this or other structured microenvironments would be inappropriate, in light of our finding these features are observable in a homogeneous environment. Furthermore, directed migration will result in loss of the invasive

  14. 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

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

    PubMed

    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

  16. 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

  17. Detection of extended-spectrum β-lactamases in Klebsiella pneumoniae: comparison of phenotypic characterization methods

    PubMed Central

    Ejaz, Hasan; ul-Haq, Ikram; Mahmood, Saqib; Zafar, Aizza; Mohsin Javed, Muhammad

    2013-01-01

    Objective: Extended-spectrum β-lactamase producing K. pneumoniae is a serious threat to the patients. This manuscript shows the comparison of phenotypic characterization methods used for ESBL K. pneumoniae and frequency distribution of these isolates in various clinical samples. Methodology: Eleven different types of pathological samples collected on various time intervals were analyzed. K. pneumoniae were identified with API 20E system (bioMerieux) and initial screening of ESBL K. pneumoniae was performed using the ceftazidime antimicrobial disc. Double-disc synergy test (DDST) and CLSI confirmatory test were compared for the phenotypic detection of ESBL K. pneumoniae. Results: A total number of 214 ESBL producing K. pneumoniae were isolated from various clinical samples. Frequency distribution of ESBL producing K. pneumoniae was found to be highest among blood 117 (54.7%) and urine 46 (21.5%) samples. Data regarding the use of various interventions among these patients showed most common presence of intravenous line 209 (97.7%) and urinary catheters 46 (21.5%). Comparison of DDST and CLSI confirmatory test showed that the DDST detected 145 (67.8%) isolates while 213 (99.5%) ESBL K. pneumoniae were characterized by CLSI confirmatory test. Conclusion: The use of CLSI confirmatory test is very efficient in the early detection of ESBL K. pneumoniae especially when the facilities for molecular characterization are not available. PMID:24353625

  18. 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. PMID:24710963

  19. Mathematical learning disabilities in special populations: phenotypic variation and cross-disorder comparisons.

    PubMed

    Dennis, Maureen; Berch, Daniel B; Mazzocco, Michèle M M

    2009-01-01

    What is mathematical learning disability (MLD)? The reviews in this special issue adopt different approaches to defining the construct of MLD. Collectively, they demonstrate the current status of efforts to establish a consensus definition and the challenges faced in this endeavor. In this commentary, we reflect upon the proposed pathways to mathematical learning difficulties and disabilities presented across the reviews. Specifically we consider how each of the reviews contributes to identifying the MLD phenotype by specifying the range of assets and deficits in mathematics, identifying sources of individual variation, and characterizing the natural progression of MLD over the life course. We show how principled comparisons across disorders address issues about the cognitive and behavioral co-morbidities of MLD, and whether commonalities in brain dysmorphology are associated with common mathematics performance profiles. We project the status of MLD research ten years hence with respect to theoretical gains, advances in methodology, and principled intervention studies. PMID:19213019

  20. Effects of a lifestyle modification trial among phenotypically obese metabolically normal and phenotypically obese metabolically abnormal adolescents in comparison with phenotypically normal metabolically obese adolescents.

    PubMed

    Kelishadi, Roya; Hashemipour, Mahin; Sarrafzadegan, Nizal; Mohammadifard, Noushin; Alikhasy, Hasan; Beizaei, Maryam; Sajjadi, Firouzeh; Poursafa, Parinaz; Amin, Zahra; Ghatreh-Samani, Shohreh; Khavarian, Noushin; Siadat, Zahra Dana

    2010-07-01

    This study aimed to assess the effects of a 2-month lifestyle modification trial on cardio-metabolic abnormalities and C-reactive protein (CRP) among obese adolescents with metabolic syndrome [phenotypically obese metabolically abnormal (POMA)] and obese adolescents without a cardio-metabolic disorder [phenotypically obese metabolically normal (POMN)], as well as in normal-weight adolescents with at least one cardio-metabolic disorder [phenotypically normal metabolically obese (PNMO)]. The study comprised 360 adolescents assigned in three groups of equal number of POMN, POMA and PNMO. They were enrolled in a trial consisting of aerobic activity classes, diet and behaviour modification, and were recalled after 6 months. Overall, 94.7% of participants completed the 2-month trial, and 87.3% of them returned after 6 months. The mean CRP was not significantly different between the POMA and PNMO groups, but was higher than in the POMN group. After the trial, body mass index (BMI) and waist circumference (WC) decreased in obese participants, and the mean body fat mass decreased in all groups. At 2 months, the mean total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), triglycerides (TG) and CRP decreased in the POMA and PNMO groups. After 2 and 6 months, the decrease in mean TC, LDL-C, TG, CRP and systolic blood pressure was greater in the POMA than in the POMN group. The magnitude of decrease in CRP correlated with that of BMI, WC, fat mass, TG, TC and LDL-C. Lifestyle modification programmes for primordial/primary prevention of chronic diseases would be beneficial at the population level and should not be limited to obese children. PMID:20929499

  1. 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. Stem Cells 2016;34:832-846. PMID

  2. Metabolic profiling of plant extracts using direct-injection electrospray ionization mass spectrometry allows for high-throughput phenotypic characterization according to genetic and environmental effects.

    PubMed

    García-Flores, Martín; Juárez-Colunga, Sheila; García-Casarrubias, Adrián; Trachsel, Samuel; Winkler, Robert; Tiessen, Axel

    2015-01-28

    In comparison to the exponential increase of genotyping methods, phenotyping strategies are lagging behind in agricultural sciences. Genetic improvement depends upon the abundance of quantitative phenotypic data and the statistical partitioning of variance into environmental, genetic, and random effects. A metabolic phenotyping strategy was adapted to increase sample throughput while saving reagents, reducing cost, and simplifying data analysis. The chemical profiles of stem extracts from maize plants grown under low nitrogen (LN) or control trial (CT) were analyzed using optimized protocols for direct-injection electrospray ionization mass spectrometry (DIESI-MS). Specific ions significantly decreased or increased because of environmental (LN versus CT) or genotypic effects. Biochemical profiling with DIESI-MS had a superior cost-benefit compared to other standard analytical technologies (e.g., ultraviolet, near-infrared reflectance spectroscopy, high-performance liquid chromatography, and gas chromatography with flame ionization detection) routinely used for plant breeding. The method can be successfully applied in maize, strawberry, coffee, and other crop species. PMID:25588121

  3. Comparison Direction and Comparison Dimension among Disabled Individuals: Toward a Refined Conceptualization of Social Comparison under Stress.

    ERIC Educational Resources Information Center

    Buunk, Bram P.

    1995-01-01

    Illuminates the nature and direction of social comparison research using a sample of 168 Dutch individuals. Some of the findings revealed uncertainty and frustration related to a need for social comparison, a desire more for information than affiliation about similar others, and the influence of health problems in evaluating one's situation. (RJM)

  4. Electrical stimulation directs engineered cardiac tissue to an age-matched native phenotype

    PubMed Central

    Lasher, Richard A; Pahnke, Aric Q; Johnson, Jeffrey M; Sachse, Frank B

    2012-01-01

    Quantifying structural features of native myocardium in engineered tissue is essential for creating functional tissue that can serve as a surrogate for in vitro testing or the eventual replacement of diseased or injured myocardium. We applied three-dimensional confocal imaging and image analysis to quantitatively describe the features of native and engineered cardiac tissue. Quantitative analysis methods were developed and applied to test the hypothesis that environmental cues direct engineered tissue toward a phenotype resembling that of age-matched native myocardium. The analytical approach was applied to engineered cardiac tissue with and without the application of electrical stimulation as well as to age-matched and adult native tissue. Individual myocytes were segmented from confocal image stacks and assigned a coordinate system from which measures of cell geometry and connexin-43 spatial distribution were calculated. The data were collected from 9 nonstimulated and 12 electrically stimulated engineered tissue constructs and 5 postnatal day 12 and 7 adult hearts. The myocyte volume fraction was nearly double in stimulated engineered tissue compared to nonstimulated engineered tissue (0.34 ± 0.14 vs 0.18 ± 0.06) but less than half of the native postnatal day 12 (0.90 ± 0.06) and adult (0.91 ± 0.04) myocardium. The myocytes under electrical stimulation were more elongated compared to nonstimulated myocytes and exhibited similar lengths, widths, and heights as in age-matched myocardium. Furthermore, the percentage of connexin-43-positive membrane staining was similar in the electrically stimulated, postnatal day 12, and adult myocytes, whereas it was significantly lower in the nonstimulated myocytes. Connexin-43 was found to be primarily located at cell ends for adult myocytes and irregularly but densely clustered over the membranes of nonstimulated, stimulated, and postnatal day 12 myocytes. These findings support our hypothesis and reveal that the

  5. Comparison of genotypic and virtual phenotypic drug resistance interpretations with laboratory-based phenotypes among CRF01_AE and subtype B HIV-infected individuals.

    PubMed

    Jiamsakul, Awachana; Chaiwarith, Romanee; Durier, Nicolas; Sirivichayakul, Sunee; Kiertiburanakul, Sasisopin; Van Den Eede, Peter; Ditangco, Rossana; Kamarulzaman, Adeeba; Li, Patrick C K; Ratanasuwan, Winai; Sirisanthana, Thira

    2016-02-01

    HIV drug resistance assessments and interpretations can be obtained from genotyping (GT), virtual phenotyping (VP) and laboratory-based phenotyping (PT). We compared resistance calls obtained from GT and VP with those from PT (GT-PT and VP-PT) among CRF01_AE and subtype B HIV-1 infected patients. GT predictions were obtained from the Stanford HIV database. VP and PT were obtained from Janssen Diagnostics BVBA's vircoType(TM) HIV-1 and Antivirogram®, respectively. With PT assumed as the "gold standard," the area under the curve (AUC) and the Bland-Altman plot were used to assess the level of agreement in resistance interpretations. A total of 80 CRF01_AE samples from Asia and 100 subtype B from Janssen Diagnostics BVBA's database were analysed. CRF01_AE showed discordances ranging from 3 to 27 samples for GT-PT and 1 to 20 samples for VP-PT. The GT-PT and VP-PT AUCs were 0.76-0.97 and 0.81-0.99, respectively. Subtype B showed 3-61 discordances for GT-PT and 2-75 discordances for VP-PT. The AUCs ranged from 0.55 to 0.95 for GT-PT and 0.55 to 0.97 for VP-PT. Didanosine had the highest proportion of discordances and/or AUC in all comparisons. The patient with the largest didanosine FC difference in each subtype harboured Q151M mutation. Overall, GT and VP predictions for CRF01_AE performed significantly better than subtype B for three NRTIs. Although discrepancies exist, GT and VP resistance interpretations in HIV-1 CRF01_AE strains were highly robust in comparison with the gold-standard PT. PMID:26147742

  6. Destabilizing Protein Polymorphisms in the Genetic Background Direct Phenotypic Expression of Mutant SOD1 Toxicity

    PubMed Central

    Gidalevitz, Tali; Krupinski, Thomas; Garcia, Susana; Morimoto, Richard I.

    2009-01-01

    Genetic background exerts a strong modulatory effect on the toxicity of aggregation-prone proteins in conformational diseases. In addition to influencing the misfolding and aggregation behavior of the mutant proteins, polymorphisms in putative modifier genes may affect the molecular processes leading to the disease phenotype. Mutations in SOD1 in a subset of familial amyotrophic lateral sclerosis (ALS) cases confer dominant but clinically variable toxicity, thought to be mediated by misfolding and aggregation of mutant SOD1 protein. While the mechanism of toxicity remains unknown, both the nature of the SOD1 mutation and the genetic background in which it is expressed appear important. To address this, we established a Caenorhabditis elegans model to systematically examine the aggregation behavior and genetic interactions of mutant forms of SOD1. Expression of three structurally distinct SOD1 mutants in C. elegans muscle cells resulted in the appearance of heterogeneous populations of aggregates and was associated with only mild cellular dysfunction. However, introduction of destabilizing temperature-sensitive mutations into the genetic background strongly enhanced the toxicity of SOD1 mutants, resulting in exposure of several deleterious phenotypes at permissive conditions in a manner dependent on the specific SOD1 mutation. The nature of the observed phenotype was dependent on the temperature-sensitive mutation present, while its penetrance reflected the specific combination of temperature-sensitive and SOD1 mutations. Thus, the specific toxic phenotypes of conformational disease may not be simply due to misfolding/aggregation toxicity of the causative mutant proteins, but may be defined by their genetic interactions with cellular pathways harboring mildly destabilizing missense alleles. PMID:19266020

  7. Destabilizing protein polymorphisms in the genetic background direct phenotypic expression of mutant SOD1 toxicity.

    PubMed

    Gidalevitz, Tali; Krupinski, Thomas; Garcia, Susana; Morimoto, Richard I

    2009-03-01

    Genetic background exerts a strong modulatory effect on the toxicity of aggregation-prone proteins in conformational diseases. In addition to influencing the misfolding and aggregation behavior of the mutant proteins, polymorphisms in putative modifier genes may affect the molecular processes leading to the disease phenotype. Mutations in SOD1 in a subset of familial amyotrophic lateral sclerosis (ALS) cases confer dominant but clinically variable toxicity, thought to be mediated by misfolding and aggregation of mutant SOD1 protein. While the mechanism of toxicity remains unknown, both the nature of the SOD1 mutation and the genetic background in which it is expressed appear important. To address this, we established a Caenorhabditis elegans model to systematically examine the aggregation behavior and genetic interactions of mutant forms of SOD1. Expression of three structurally distinct SOD1 mutants in C. elegans muscle cells resulted in the appearance of heterogeneous populations of aggregates and was associated with only mild cellular dysfunction. However, introduction of destabilizing temperature-sensitive mutations into the genetic background strongly enhanced the toxicity of SOD1 mutants, resulting in exposure of several deleterious phenotypes at permissive conditions in a manner dependent on the specific SOD1 mutation. The nature of the observed phenotype was dependent on the temperature-sensitive mutation present, while its penetrance reflected the specific combination of temperature-sensitive and SOD1 mutations. Thus, the specific toxic phenotypes of conformational disease may not be simply due to misfolding/aggregation toxicity of the causative mutant proteins, but may be defined by their genetic interactions with cellular pathways harboring mildly destabilizing missense alleles. PMID:19266020

  8. Naked mole-rats: behavioural phenotyping and comparison with C57BL/6 mice.

    PubMed

    Deacon, R M J; Dulu, T D; Patel, N B

    2012-05-16

    Naked mole-rats (NMR) live underground in large eusocial colonies in East Africa. They are extremely long-lived, some individuals having a lifespan of over 30 years. This has attracted research into longevity and possibly neurodegenerative disorders. However, very little is known about their basic behaviour, particularly in tests commonly used to characterise the behaviour of the laboratory rat and mouse, for which there is an enormous database. Recently the authors carried out comprehensive behavioural phenotyping on NMRs, comparing them on most tasks directly with C57BL/6 mice, the strain for which there is the largest behavioural database. The NMR colony had been obtained from the wild originally, but housed in an animal facility for about two years. Large inter-species differences in behaviour were seen between the mice and the NMRs. The latter had generally poor sensorimotor function, including cutaneous sensation, strength and even grasp reflexes. They were often reluctant to enter or head-dip into small holes that mice readily entered. Their vision (generally considered to be very poor) was sufficient to distinguish the two zones of a light-dark box. Although, as expected, the NMRs were capable of burrowing and digging, when individually housed they did not shred cotton material to make nests. Shredding was seen in a colony cage containing a queen, but no nests were made there even when a nesting box was provided. In cognitive testing, although, unlike mice and rats, they did not spontaneously alternate in a T-maze, they learnt rewarded alternation and a cued position task well. This study demonstrates how behaviour uniquely reflects the natural environment in which these unusual animals have evolved and live, and provides baseline data for future work. PMID:22440234

  9. Phenotypic and karyotypic status of Beta vulgaris plants regenerated from direct organogenesis in petiole culture.

    PubMed

    Detrez, C; Sangwan, R S; Sangwan-Norreel, B S

    1989-04-01

    A method for high frequency in vitro regeneration from petiole explants was tested on nine breeding lines of Beta vulgaris L. from the haploid, diploid and tetraploid levels. Regenerants could be obtained without a callus step, from excised petioles derived either from axillary buds sprouted in vitro or from field grown plants, by plating the explants on MS medium supplemented with TIBA (2,3,5-triiodobenzoïc acid) and BAP (6-Benzylaminopurine). The multiple shoots obtained were then rooted in vitro and transferred to soil. In some cases, these adventitious shoots were also used as a petiole explant source for further petiole culture cycles, and the phenotypic characteristics and ploidy status of the regenerants were investigated after one or three petiole culture cycles. Conventional shoot apex culture was used as an in vitro control. Phenotypic variations such as differences in morphology and changes in in vitro growth behaviour, were noticed. Chloroplast and chromosome counts indicated that the alterations in morphogenetic pathway could not be explained by the occurrence of gross cytogenetic abnormalities such as aneuploidy or myxoploidy. Our results suggest that the altered morphology is caused by the presence of the exogenous antiauxin (TIBA) during the in vitro phase. Following transfer to the greenhouse, none of these variations persisted and cytogenetic analyses revealed karyotypic stability in all the plants studied, even after three petiole culture cycles. An assessment of the in vitro petiole culture method as a true-to-type multiplication method for Beta vulgaris is made. PMID:24232710

  10. 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

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

    PubMed

    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

    2016-01-01

    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-chromosomal 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

  12. Breakpoint Mapping and Array CGH in Translocations: Comparison of a Phenotypically Normal and an Abnormal Cohort

    PubMed Central

    Baptista, Julia; Mercer, Catherine; Prigmore, Elena; Gribble, Susan M.; Carter, Nigel P.; Maloney, Viv; Thomas, N. Simon; Jacobs, Patricia A.; Crolla, John A.

    2008-01-01

    We report the analyses of breakpoints in 31 phenotypically normal and 14 abnormal carriers of balanced translocations. Our study assesses the differences between balanced translocations in normal carriers and those in abnormal carriers, focusing on the presence of genomic imbalances at the breakpoints or elsewhere in the genome, presence of cryptic chromosome rearrangements, and gene disruption. Our hypothesis is that all four features will be associated with phenotypic abnormalities and absent or much less frequent in a normal population. In the normal cohort, we identified neither genomic imbalances at the breakpoints or elsewhere in the genome nor cryptic chromosome rearrangements. In contrast, we identified candidate disease-causing imbalances in 4/14 abnormal patients. These were three breakpoint associated deletions and three deletions unrelated to the breakpoints. All six de novo deletions originated on the paternally inherited chromosome. Additional complexity was also present in one of these cases. Gene disruption by the breakpoints was present in 16/31 phenotypically normal individuals and in 5/14 phenotypically abnormal patients. Our results show that translocations in phenotypically abnormal patients are molecularly distinct from those in normal individuals: the former are more likely to be associated with genomic imbalances at the breakpoints or elsewhere and with chromosomal complexity, whereas the frequency of gene disruption is similar in both normal and abnormal translocation carriers. PMID:18371933

  13. Comparison of virulence plasmid (pYV/pCD)-associated phenotypes in Yersinia species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotypic expression of several virulence plasmid (pYV/pCD; 70-kb)-associated genetic determinants were compared among Yesinia species; Yesinia pestis, (an attenuated strain which does not cause plague designated to be used in BSL2 facility), Y. pseudotuberculosis and Y. enterocolitica including lo...

  14. Comparison of CYP1A2 and NAT2 Phenotypes between Black and White Smokers

    PubMed Central

    Muscat, Joshua E.; Pittman, Brian; Kleinman, Wayne; Lazarus, Philip; Stellman, Steven D.; Richie, John P.

    2008-01-01

    The lower incidence rate of transitional cell carcinoma of the urinary bladder in blacks than in whites may be due to racial differences in the catalytic activity of enzymes that metabolize carcinogenic arylamines in tobacco smoke. To examine this, we compared cytochrome P4501A2 (CYP1A2) and N-acetyltransferase-2 activities (NAT2) in black and white smokers using urinary caffeine metabolites as a probe for enzyme activity in a community-based study of 165 black and 183 white cigarette smokers. The paraxanthine (1,7-dimethylxanthine, 17X)/caffeine (trimethylxanthine, 137X) ratio or [17X + 1,7-dimethyluric acid (17U)]/137X ratio was used as an indicator of CYP1A2 activity. The 5-acetyl-amino-6-formylamino-3-methyluracil (AFMU)/1-methylxanthine (1X) ratio indicated NAT2 activity. The odds ratio for the slow NAT2 phenotype associated with black race was 0.4; 95% confidence intervals 0.2–0.7. The putative combined low risk phenotype (slow CYP1A2/rapid NAT2) was more common in blacks than in whites (25% vs. 15%, P<0.02). There were no significant racial differences in slow and rapid CYP1A2 phenotypes, and in the combined slow NAT2/rapid CYP1A2 phenotype. Age, education, cigarette smoking amount, body mass index, GSTM1 and GSTM3 genotypes were unrelated to CYP1A2 and NAT2 activity. Intake of cruciferous vegetables (primarily broccoli), red meat, carrots, grapefruit and onions predicted CYP1A2 activity either for all subjects or in race-specific analyses. Carrot and grapefruit consumption was related to NAT2 activity. Collectively, these results indicated that phenotypic differences in NAT2 alone or in combination with CYP1A2 might help explain the higher incidence rates of transitional cell bladder cancer in whites. PMID:18703023

  15. Comparison of CYP1A2 and NAT2 phenotypes between black and white smokers.

    PubMed

    Muscat, Joshua E; Pittman, Brian; Kleinman, Wayne; Lazarus, Philip; Stellman, Steven D; Richie, John P

    2008-10-01

    The lower incidence rate of transitional cell carcinoma of the urinary bladder in blacks than in whites may be due to racial differences in the catalytic activity of enzymes that metabolize carcinogenic arylamines in tobacco smoke. To examine this, we compared cytochrome P4501A2 (CYP1A2) and N-acetyltransferase-2 activities (NAT2) in black and white smokers using urinary caffeine metabolites as a probe for enzyme activity in a community-based study of 165 black and 183 white cigarette smokers. The paraxanthine (1,7-dimethylxanthine, 17X)/caffeine (trimethylxanthine, 137X) ratio or [17X+1,7-dimethyluric acid (17U)]/137X ratio was used as an indicator of CYP1A2 activity. The 5-acetyl-amino-6-formylamino-3-methyluracil (AFMU)/1-methylxanthine (1X) ratio indicated NAT2 activity. The odds ratio for the slow NAT2 phenotype associated with black race was 0.4; 95% confidence intervals 0.2-0.7. The putative combined low risk phenotype (slow CYP1A2/rapid NAT2) was more common in blacks than in whites (25% vs. 15%, P<0.02). There were no significant racial differences in slow and rapid CYP1A2 phenotypes, and in the combined slow NAT2/rapid CYP1A2 phenotype. Age, education, cigarette smoking amount, body mass index, GSTM1 and GSTM3 genotypes were unrelated to CYP1A2 and NAT2 activity. Intake of cruciferous vegetables (primarily broccoli), red meat, carrots, grapefruit and onions predicted CYP1A2 activity either for all subjects or in race-specific analyses. Carrot and grapefruit consumption was related to NAT2 activity. Collectively, these results indicated that phenotypic differences in NAT2 alone or in combination with CYP1A2 might help explain the higher incidence rates of transitional cell bladder cancer in whites. PMID:18703023

  16. Surface proteins of Bordetella pertussis: comparison of virulent and avirulent strains and effects of phenotypic modulation.

    PubMed Central

    Armstrong, S K; Parker, C D

    1986-01-01

    The surface proteins of several Bordetella strains and their modulated derivatives were examined by surface radioiodination, cell fractionation, and Western blotting. A surface protein with a high Mr, missing in a mutant lacking the filamentous hemagglutinin, was identified in virulent Bordetella pertussis and Bordetella parapertussis cells and was absent in avirulent B. pertussis strains. The electrophoretic profiles of lipopolysaccharide and the 40,000-Mr anion-selective porin were not determinants which correlated with phase variation or phenotypic modulation. At least three envelope proteins (91,000, 32,000, and 30,000 molecular weight) were found only in virulent B. pertussis strains and were absent or diminished in the avirulent phase and most phenotypically modulated strains. Two transposon-induced mutants unable to produce hemolysin, dermonecrotic toxin, pertussis toxin, and filamentous hemagglutinin also lacked these three envelope proteins, confirming that virulence-associated envelope proteins were genetically regulated with other virulence-associated traits. Images PMID:2876957

  17. Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes.

    PubMed

    Hall, Barry G; Cardenas, Heliodoro; Barlow, Miriam

    2013-01-01

    In clinical settings it is often important to know not just the identity of a microorganism, but also the danger posed by that particular strain. For instance, Escherichia coli can range from being a harmless commensal to being a very dangerous enterohemorrhagic (EHEC) strain. Determining pathogenic phenotypes can be both time consuming and expensive. Here we propose a simple, rapid, and inexpensive method of predicting pathogenic phenotypes on the basis of the presence or absence of short homologous DNA segments in an isolate. Our method compares completely sequenced genomes without the necessity of genome alignments in order to identify the presence or absence of the segments to produce an automatic alignment of the binary string that describes each genome. Analysis of the segment alignment allows identification of those segments whose presence strongly predicts a phenotype. Clinical application of the method requires nothing more that PCR amplification of each of the set of predictive segments. Here we apply the method to identifying EHEC strains of E. coli and to distinguishing E. coli from Shigella. We show in silico that with as few as 8 predictive sequences, if even three of those predictive sequences are amplified the probability of being EHEC or Shigella is >0.99. The method is thus very robust to the occasional amplification failure for spurious reasons. Experimentally, we apply the method to screening a set of 98 isolates to distinguishing E. coli from Shigella, and EHEC from non-EHEC E. coli strains and show that all isolates are correctly identified. PMID:23935901

  18. Estimating the Magnitude and Direction of Altered Arbovirus Transmission Due to Viral Phenotype

    PubMed Central

    Christofferson, Rebecca C.; Mores, Christopher N.

    2011-01-01

    Vectorial capacity is a measure of the transmission potential of a vector borne pathogen within a susceptible population. Vector competence, a component of the vectorial capacity equation, is the ability of an arthropod to transmit an infectious agent following exposure to that agent. Comparisons of arbovirus strain-specific vector competence estimates have been used to support observed or hypothesized differences in transmission capability. Typically, such comparisons are made at a single time point during the extrinsic incubation period, the time in days it takes for the virus to replicate and disseminate to the salivary glands. However, vectorial capacity includes crucial parameters needed to effectively evaluate transmission capability, though often this is based on the discrete vector competence values. Utilization of the rate of change of vector competence over a range of days gives a more accurate measurement of the transmission potential. Accordingly, we investigated the rate of change in vector competence of dengue virus in Aedes aegypti mosquitoes and the resulting vectorial capacity curves. The areas under the curves represent the effective vector competence and the cumulative transmission potentials of arboviruses within a population of mosquitoes. We used the calculated area under the curve for each virus strain and the corresponding variance estimates to test for differences in cumulative transmission potentials between strains of dengue virus based on our dynamic model. To further characterize differences between dengue strains, we devised a displacement index interpreted as the capability of a newly introduced strain to displace the established, dominant circulating strain. The displacement index can be used to better understand the transmission dynamics in systems where multiple strains/serotypes circulate or even multiple arbovirus species. The use of a rate of a rate of change based model of vectorial capacity and the informative calculations of

  19. 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. PMID:15470370

  20. Phenotypic comparison of samdc and spe mutants reveals complex relationships of polyamine metabolism in Ustilago maydis.

    PubMed

    Valdés-Santiago, Laura; Cervantes-Chávez, José Antonio; Winkler, Robert; León-Ramírez, Claudia G; Ruiz-Herrera, José

    2012-03-01

    Synthesis of spermidine involves the action of two enzymes, spermidine synthase (Spe) and S-adenosylmethionine decarboxylase (Samdc). Previously we cloned and disrupted the gene encoding Spe as a first approach to unravel the biological function of spermidine in Ustilago maydis. With this background, the present study was designed to provide a better understanding of the role played by Samdc in the regulation of the synthesis of this polyamine. With this aim we proceeded to isolate and delete the gene encoding Samdc from U. maydis, and made a comparative analysis of the phenotypes of samdc and spe mutants. Both spe and samdc mutants behaved as spermidine auxotrophs, and were more sensitive than the wild-type strain to different stress conditions. However, the two mutants displayed significant differences: in contrast to spe mutants, samdc mutants were more sensitive to LiCl stress, high spermidine concentrations counteracted their dimorphic deficiency, and they were completely avirulent. It is suggested that these differences are possibly related to differences in exogenous spermidine uptake or the differential location of the respective enzymes in the cell. Alternatively, since samdc mutants accumulate higher levels of S-adenosylmethionine (SAM), whereas spe mutants accumulate decarboxylated SAM, the known opposite roles of these metabolites in the processes of methylation and differentiation offer an additional attractive hypothesis to explain the phenotypic differences of the two mutants, and provide insights into the additional roles of polyamine metabolism in the physiology of the cell. PMID:22222500

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

    PubMed Central

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

    2016-01-01

    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 p21WAF1/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. PMID:26918450

  2. 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

    2016-04-01

    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 p21WAF1/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. PMID:26918450

  3. Early Comparison of Inflammatory vs. Fibrostenotic Phenotype in Eosinophilic Esophagitis in a Multicenter Longitudinal Study

    PubMed Central

    Singla, Manish B; Chehade, Mirna; Brizuela, Diana; Maydonovitch, Corinne L; Chen, Yen-Ju; Riffle, Mary Ellen; Achem, Sami R; Moawad, Fouad J

    2015-01-01

    OBJECTIVES: Eosinophilic esophagitis (EoE) is a chronic inflammatory condition that causes esophageal remodeling and stricture formation. We compared the clinical course of symptoms, endoscopic findings, histology, and changes in phenotype over time in EoE patients with inflammatory and fibrostenotic phenotypes. METHODS: Data were obtained from EoE patients from three medical centers and followed prospectively. Endoscopic features and histology from index and follow-up endoscopies were recorded. Behavior was classified as inflammatory if endoscopic findings demonstrated furrows or white plaques and as fibrostenotic if endoscopic findings included fixed rings or strictures. RESULTS: Two hundred and fifty-six EoE patients were included in the analysis. The mean age was 32±18 years, 25% of patients were <18 years, 89% of patients were Caucasians, and 74% of patients were male. The mean duration of symptoms before diagnosis was 6.8±7.2 years with a follow-up of 1.7±1.9 years (maximum follow-up of 12 years). Fifty-four percent of patients presented with fibrostenotic EoE, whereas 46% presented with inflammatory EoE. Patients with inflammatory disease were younger than those with fibrostenotic disease (24±19 vs. 39±15 years, P<0.001). Patients with fibrostenotic disease had a longer duration of symptoms than those with inflammatory disease (8.1±7.7 vs. 5.3±6.3 years, P=0.002). Over the study period, 47 (18%) had remission of inflammatory EoE, 68 (27%) continued to have inflammatory disease, 74 (29%) continued to have fibrostenotic disease, 65 (25%) fibrostenotic patients had regression of fibrosis, and 2 patients (1%) progressed from inflammatory disease to fibrostenotic disease. Patients who had regression from their fibrostenosis were more likely than patients who continued to demonstrate fibrostenosis to have a decrease in proximal (54% vs. 32%, P<0.001) and distal (70% vs. 38%, P<0.001) eosinophilia. CONCLUSIONS: Most EoE patients maintained their phenotype or

  4. Phenotypic and Genotypic Comparison of Epidemic and Non-Epidemic Strains of Pseudomonas aeruginosa from Individuals with Cystic Fibrosis

    PubMed Central

    Duong, Jessica; Booth, Sean C.; McCartney, Nathan K.; Rabin, Harvey R.; Parkins, Michael D.; Storey, Douglas G.

    2015-01-01

    Epidemic strains of Pseudomonas aeruginosa have been found worldwide among the cystic fibrosis (CF) patient population. Using pulse-field gel electrophoresis, the Prairie Epidemic Strain (PES) has recently been found in one-third of patients attending the Calgary Adult CF Clinic in Canada. Using multi-locus sequence typing, PES isolates from unrelated patients were found to consistently have ST192. Though most patients acquired PES prior to enrolling in the clinic, some patients were observed to experience strain replacement upon transitioning to the clinic whereby local non-epidemic P. aeruginosa isolates were displaced by PES. Here we genotypically and phenotypically compared PES to other P. aeruginosa epidemic strains (OES) found around the world as well as local non-epidemic CF P. aeruginosa isolates in order to characterize PES. Since some epidemic strains are associated with worse clinical outcomes, we assessed the pathogenic potential of PES to determine if these isolates are virulent, shared properties with OES, and if its phenotypic properties may offer a competitive advantage in displacing local non-epidemic isolates during strain replacement. As such, we conducted a comparative analysis using fourteen phenotypic traits, including virulence factor production, biofilm formation, planktonic growth, mucoidy, and antibiotic susceptibility to characterize PES, OES, and local non-epidemic isolates. We observed that PES and OES could be differentiated from local non-epidemic isolates based on biofilm growth with PES isolates being more mucoid. Pairwise comparisons indicated that PES produced significantly higher levels of proteases and formed better biofilms than OES but were more susceptible to antibiotic treatment. Amongst five patients experiencing strain replacement, we found that super-infecting PES produced lower levels of proteases and elastases but were more resistant to antibiotics compared to the displaced non-epidemic isolates. This comparative

  5. Comparison of the Phenotype and Approach to Pediatric vs Adult Patients With Nonalcoholic Fatty Liver Disease.

    PubMed

    Nobili, Valerio; Alisi, Anna; Newton, Kimberly P; Schwimmer, Jeffrey B

    2016-06-01

    Nonalcoholic fatty liver disease (NAFLD) is one of the main chronic noncommunicable diseases in Westernized societies; its worldwide prevalence has doubled during the last 20 years. NAFLD has serious health implications not only for adults, but also for children. However, pediatric NAFLD is not only an important global problem in itself, but it is likely to be associated with increases in comorbidities, such as metabolic syndrome and cardiovascular diseases. There are several differences between NAFLD in children and adults, and it is not clear whether the disease observed in children is the initial phase of a process that progresses with age. The increasing prevalence of pediatric NAFLD has serious implications for the future adult population requiring appropriate action. Studies of NAFLD progression, pathogenesis, and management should evaluate disease phenotypes in children and follow these over the patient's lifetime. We review the similarities and differences of NAFLD between children and adults. PMID:27003600

  6. Phenotypic characterization of the archaebacterial genus Sulfolobus: comparison of five wild-type strains.

    PubMed Central

    Grogan, D W

    1989-01-01

    Though amenable to routine manipulation and a popular subject of molecular genetic and biochemical studies on archaebacteria, the genus Sulfolobus has remained poorly described in phenotypic terms. To delineate their physiological capabilities and diversity, five laboratory strains, including type strains of the described species Sulfolobus acidocaldarius and S. solfataricus, were compared with respect to a variety of growth and biochemical parameters, including component profile of the surface-layer cell wall, inhibitors of growth, growth rate as a function of temperature and pH, and compounds used as sole sources of carbon or nitrogen. Motility and photoregulated production of an orange pigment were detected in all five strains tested. The results provide new criteria for distinguishing Sulfolobus strains as well as potential tools for the physiological and genetic manipulation of these extreme thermophiles. Images PMID:2512283

  7. DOORS syndrome: phenotype, genotype and comparison with Coffin-Siris syndrome.

    PubMed

    Campeau, Philippe M; Hennekam, Raoul C

    2014-09-01

    DOORS syndrome (Deafness, Onychodystrophy, Osteodystrophy, mental Retardation, Seizures) is characterized mainly by sensorineural deafness, shortened terminal phalanges with small nails of hands and feet, intellectual deficiency, and seizures. Half of the patients with all clinical features have mutations in TBC1D24. We review here the manifestations of patients clinically diagnosed with DOORS syndrome. In this cohort of 32 families (36 patients) we detected 13 individuals from 10 families with TBC1D24 mutations. Subsequent whole exome sequencing in the cohort showed the same de novoSMARCB1 mutation (c.1130G>A), known to cause Coffin-Siris syndrome, in two patients. Distinguishing features include retinal anomalies, Dandy-Walker malformation, scoliosis, rocker bottom feet, respiratory difficulties and absence of seizures, and 2-oxoglutaric aciduria in the patients with the SMARCB1 mutation. We briefly discuss the heterogeneity of the DOORS syndrome phenotype and the differential diagnosis of this condition. PMID:25169651

  8. 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. PMID:27094849

  9. Comparison of Methods for Identifying Phenotype Subgroups Using Categorical Features Data With Application to Autism Spectrum Disorder

    PubMed Central

    Shotwell, Matthew S; Charles, Jane M; Nicholas, Joyce S

    2011-01-01

    We evaluate the performance of the Dirichlet process mixture (DPM) and the latent class model (LCM) in identifying autism phenotype subgroups based on categorical autism spectrum disorder (ASD) diagnostic features from the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition Text Revision. A simulation study is designed to mimic the diagnostic features in the ASD dataset in order to evaluate the LCM and DPM methods in this context. Likelihood based information criteria and DPM partitioning are used to identify the best fitting models. The Rand statistic is used to compare the performance of the methods in recovering simulated phenotype subgroups. Our results indicate excellent recovery of the simulated subgroup structure for both methods. The LCM performs slightly better than DPM when the correct number of latent subgroups is selected a priori. The DPM method utilizes a maximum a posteriori (MAP) criterion to estimate the number of classes, and yielded results in fair agreement with the LCM method. Comparison of model fit indices in identifying the best fitting LCM showed that adjusted Bayesian information criteria (ABIC) picks the correct number of classes over 90% of the time. Thus, when diagnostic features are categorical and there is some prior information regarding the number of latent classes, LCM in conjunction with ABIC is preferred. PMID:21927523

  10. Waterpipe Tobacco and Cigarette Smoking Direct Comparison of Toxicant Exposure

    PubMed Central

    Eissenberg, Thomas; Shihadeh, Alan

    2009-01-01

    Background Waterpipe (hookah, shisha) tobacco smoking has spread worldwide. Many waterpipe smokers believe that, relative to cigarettes, waterpipes are associated with lower smoke toxicant levels and fewer health risks. For physicians to address these beliefs credibly, waterpipe and cigarette must be compared directly. Purpose The purpose of this study is to provide the first controlled, direct laboratory comparison of the toxicant exposure associated with waterpipe tobacco and cigarette smoking Methods Participants (N=31; mean=21.4 years, SD=2.3) reporting monthly waterpipe use (mean 5.2 uses/month, SD=4.0) and weekly cigarette smoking (mean= 9.9 cigarettes/day, SD=6.4) completed a crossover study in which they each smoked a waterpipe for a maximum of 45 minutes or a single cigarette. Outcomes included expired air carbon monoxide (CO) 5 minutes after session’s end, and blood carboxyhemoglobin (COHb), plasma nicotine, heart rate, and puff topography. Data were collected in 2008–2009 and analyzed in 2009. Results CO increased, on average, by 23.9 ppm for waterpipe (SD=19.8) and 2.7 ppm for cigarette (SD=1.8) while peak waterpipe COHb levels (mean=3.9%, SD=2.5) were three times those observed for the cigarette (mean=1.3%, SD=0.5; Ps<0.001). Peak nicotine levels did not differ (mean ng/ml waterpipe=10.2, SD=7.0; cigarette=10.6, SD=7.7). Significant heart rate increases relative to pre-smoking were observed 5, 10, 15, 20, 25, and 35 minutes during the cigarette session and at every 5-minute interval during the waterpipe session (Ps<0.001). Mean total puff volume was 48.6 liters for waterpipe as compared to 1.0 liters for cigarette (P<0.001). Conclusions Relative to a cigarette, waterpipe use is associated with greater CO, similar nicotine, and dramatically more smoke exposure. Physicians should consider advising their patients that waterpipe tobacco smoking exposes them to some of the same toxicants as cigarette smoking and therefore the two tobacco smoking methods

  11. Effects of vitamin D binding protein phenotypes and vitamin D supplementation on serum total 25(OH)D and directly measured free 25(OH)D

    PubMed Central

    Sollid, Stina T; Hutchinson, Moira Y S; Berg, Vivian; Fuskevåg, Ole M; Figenschau, Yngve; Thorsby, Per M; Jorde, Rolf

    2016-01-01

    Objective To determine the relationship between serum total 25-hydroxyvitamin D (25(OH)D), directly measured free 25(OH)D and calculated free 25(OH)D with regard to vitamin D-binding protein (DBP) phenotypes, sex, BMI, age and season, and their interrelationship to vitamin D supplementation. Design, patients and interventions A randomized controlled trial with 20 000 IU of vitamin D3 per week or placebo for 12 months was designed. A total of 472 subjects, 236 in each of the intervention groups, were included in the analyses. Main outcome measures Baseline serum concentrations and increases in serum total 25(OH)D, directly measured free 25(OH)D, calculated free 25(OH)D and DBP. Results Serum total 25(OH)D and DBP concentrations were significantly lower in subjects with the phenotype Gc2/Gc2 compared to phenotypes with the Gc1S allele, and lower in males compared to females. When using directly measured free 25(OH)D, the differences related to DBP phenotypes and sexes were clearly diminished. All calculated free 25(OH)D concentrations were overestimated compared to the directly measured free 25(OH)D. Serum parathyroid hormone showed an inverse correlation with all vitamin D parameters analyzed. The increases after 12 months of vitamin D supplementation were not significantly different for any of the vitamin D parameters regardless of DBP phenotype, sex or age. Supplementation with vitamin D did not affect serum DBP. Conclusion Direct measurements of free 25(OH)D reduce the differences seen in total 25(OH)D between DBP phenotype groups and sexes, probably caused by differences in DBP concentrations. With conditions affecting serum DBP concentrations, direct measurements of free 25(OH)D should be considered. PMID:26733479

  12. Phenotypic comparison of clinical and plant-beneficial strains of Pantoea agglomerans.

    PubMed

    Bonaterra, Anna; Badosa, Esther; Rezzonico, Fabio; Duffy, Brion; Montesinos, Emilio

    2014-06-01

    Certain strains of Pantoea are used as biocontrol agents for the suppression of plant diseases. However, their commercial registration is hampered in some countries because of biosafety concerns. This study compares clinical and plant-beneficial strains of P. agglomerans and related species using a phenotypic analysis approach in which plant-beneficial effects, adverse effects in nematode models, and toxicity were evaluated. Plant-beneficial effects were determined as the inhibition of apple fruit infection by Penicillium expansum and apple flower infection by Erwinia amylovora. Clinical strains had no general inhibitory activity against infection by the fungal or bacterial plant pathogens, as only one clinical strain inhibited P. expansum and three inhibited E. amylovora. By contrast, all biocontrol strains showed activity against at least one of the phytopathogens, and three strains were active against both. The adverse effects in animals were evaluated in the plant-parasitic nematode Meloidogyne javanica and the bacterial-feeding nematode Caenorhabditis elegans. Both models indicated adverse effects of the two clinical strains but not of any of the plant-beneficial strains. Toxicity was evaluated by means of hemolytic activity in blood, and genotoxicity with the Ames test. None of the strains, whether clinical or plant-beneficial, showed any evidence of toxicity. PMID:26418852

  13. Phenotypic and genotypic comparison of Escherichia coli from pristine tropical waters

    SciTech Connect

    Bermudez, M.; Hazen, T.C.

    1988-04-01

    Nine fecal-coliform-positive strains were isolated from pristine sites in a tropical rain forest. These sites included nonpolluted rivers and water from bromeliads (epiphytes) which were 30 ft (ca. 910 cm) above the ground. Phenotypically, all of these isolates were identified as Escherichia coli. Their DNA was isolated and purified, and the base composition (G+C content) was determined and compared with that of E. coli B (ATCC 11303). The DNA from the environmental isolates was also hybridized to radiolabeled DNA from E. coli B. Eight strains had a DNA base composition similar to that of E. coli B and gave more than 75% homology with E. coli B. One strain had a different DNA base composition and a relatively low percentage of homology with the reference strain. The finding of E. coli in pristine tropical waters suggest that this bacterium could be a natural inhabitant in these environments and is not a reliable indicator or recent human fecal contamination in tropical waters. The indicators that are currently used in the tropics to test the biological quality of water should be reevaluated.

  14. 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…

  15. 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. PMID:26582016

  16. 32 CFR Appendix C to Part 169a - Simplified Cost Comparison and Direct Conversion of CAs

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 1 2013-07-01 2013-07-01 false Simplified Cost Comparison and Direct Conversion of CAs C Appendix C to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF... 169a—Simplified Cost Comparison and Direct Conversion of CAs A. This appendix provides guidance...

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

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 1 2012-07-01 2012-07-01 false Simplified Cost Comparison and Direct Conversion of CAs C Appendix C to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF... 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

    ... 32 National Defense 1 2011-07-01 2011-07-01 false Simplified Cost Comparison and Direct Conversion of CAs C Appendix C to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF... 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, 2010 CFR

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Simplified Cost Comparison and Direct Conversion of CAs C Appendix C to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF... 169a—Simplified Cost Comparison and Direct Conversion of CAs A. This appendix provides guidance...

  20. 32 CFR Appendix C to Part 169a - Simplified Cost Comparison and Direct Conversion of CAs

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 1 2014-07-01 2014-07-01 false Simplified Cost Comparison and Direct Conversion of CAs C Appendix C to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF... 169a—Simplified Cost Comparison and Direct Conversion of CAs A. This appendix provides guidance...

  1. Standard of Calibration for Vacuum Gauges by Direct Comparison with Reference Gauge

    NASA Astrophysics Data System (ADS)

    Akimichi, Hitoshi

    Standards of calibration for vacuum gauges by direct comparison with reference gauge were described. Japanese standard, JIS Z 8750 (Methods of calibration for vacuum gauges), was established in 1962. International standard, ISO/TS 3567 (Vacuum gauges—Calibration by direct comparison with a reference gauge) was established in 2005.

  2. 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…

  3. Performance comparison of phenotypic and molecular methods for detection and differentiation of Candida albicans and Candida dubliniensis

    PubMed Central

    2012-01-01

    Background Candida albicans is the most pathogenic Candida species but shares many phenotypic features with Candida dubliniensis and may, therefore, be misidentified in clinical microbiology laboratories. Candidemia cases due to C. dubliniensis are increasingly being reported in recent years. Accurate identification is warranted since mortality rates are highest for C. albicans infections, however, C. dubliniensis has the propensity to develop resistance against azoles more easily. We developed a duplex PCR assay for rapid detection and differentiation of C. albicans from C. dubliniensis for resource-poor settings equipped with basic PCR technology and compared its performance with three phenotypic methods. Methods Duplex PCR was performed on 122 germ tube positive and 12 germ tube negative isolates of Candida species previously identified by assimilation profiles on Vitek 2 ID-YST system. Typical morphologic characteristics on simplified sunflower seed agar (SSA), and reaction with a commercial (Bichro-Dubli) latex agglutination test were also performed. The assay was further applied on 239 clinical yeast and yeast-like fungi and results were confirmed by DNA sequencing of internal transcribed spacer (ITS) region of rDNA. Results The results of duplex PCR assay for 122 germ tube positive and 12 germ tube negative isolates of Candida species were comparable to their identification by Vitek 2 ID-YST system, colony characteristics on SSA and latex agglutination test. Application of duplex PCR also correctly identified all 148 C. albicans and 50 C. dubliniensis strains among 239 yeast-like fungi. Conclusions The data show that both, duplex PCR and Bichro-Dubli are reliable tests for rapid (within few hours) identification of clinical yeast isolates as C. dubliniensis or C. albicans. However, duplex PCR may be applied directly on clinical yeast isolates for their identification as C. dubliniensis or C. albicans as it does not require prior testing for germ tube

  4. Finding the target after screening the phenotype.

    PubMed

    Hart, Charles P

    2005-04-01

    Although most screening for new drug leads is being directed at known or emerging molecular targets, there has been a renaissance in screening based on changes in cell or organismal phenotypes. Phenotype-based screening is accompanied by the challenge of identifying the molecular target or targets bound by the drug leads and responsible for their pharmacological activity. A variety of technologies and approaches are being explored for target identification after phenotypic screening. Direct approaches employing affinity chromatography, expression cloning and protein microarrays analyze the compound bound to its target. Indirect approaches are based on comparison of the genome-wide activity profile of the compound with databases of the activity profiles of other compounds with known targets or activity profiles following specific genetic changes. This review will use case studies of target identification efforts and highlight the advantages and disadvantages of the various approaches to target identification after phenotypic screening. PMID:15809197

  5. 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 remains rare. Thus, the pertinent question…

  6. 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.

  7. 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.…

  8. Generalized halo independent comparison of direct dark matter detection data

    SciTech Connect

    Nobile, Eugenio Del; Gelmini, Graciela; Huh, Ji-Haeng; Gondolo, Paolo E-mail: gelmini@physics.ucla.edu E-mail: jhhuh@physics.ucla.edu

    2013-10-01

    We extend the halo-independent method to compare direct dark matter detection data, so far used only for spin-independent WIMP-nucleon interactions, to any type of interaction. As an example we apply the method to magnetic moment interactions.

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

    DOE PAGESBeta

    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.

  10. Genotypic and Phenotypic Comparisons of Chromosomal Types within an Indigenous Soil Population of Rhizobium leguminosarum bv. trifolii †

    PubMed Central

    Leung, Kamtin; Strain, Steven R.; de Bruijn, Frans J.; Bottomley, Peter J.

    1994-01-01

    The relative genetic similarities of 200 isolates of Rhizobium leguminosarum bv. trifolii recovered from an Oregon soil were determined at 13 enzyme loci by multilocus enzyme electrophoresis (MLEE). These isolates represented 13 antigenically distinct serotypes recovered from nodules formed on various clover species. The MLEE-derived levels of relatedness among isolates of R. leguminosarum bv. trifolii were found to be in good agreement with the levels of relatedness established by using repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the PCR technique and with levels of relatedness from previously published DNA reassociation studies. BIOLOG substrate utilization patterns showed that isolates within an electrophoretic type (ET) were phenotypically more similar to each other than to isolates of other ETs. The soil isolates were represented by 53 ETs which could be clustered into seven groups (groups B, E, G, H1, H2, I, and J). Evidence for multilocus structure within the population was obtained, and group B was identified as the primary creator of the disequilibrium. Of 75 isolates belonging to the nodule-dominant serotype AS6 complex, 72 were found in group B. Isolates WS2-01 and WS2-02 representing nodule-dominant serotypes recovered from subclover grown at another Oregon site were also found in group B. Isolates representing the most numerous ETs in group B (ETs 2 and 3) were either suboptimally effective or completely ineffective at fixing nitrogen on six different clover species. Another four groups of isolates (groups A, C, D, and F) were identified when 32 strains of diverse origins were analyzed by MLEE and incorporated into the cluster analysis. Group A was most dissimilar in comparisons with other groups and contained strain USDA 2124 (T24), which produces trifolitoxin and has unique symbiotic characteristics. PMID:16349171

  11. 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

  12. Comparison of Techniques for Bonding VCSELs Directly to Ics

    SciTech Connect

    Choquette, K.D.; Geib, K.M.; Hayes, E.M. Wilmsen, C.W.; Hou, H.Q.; Pu, R.

    1999-03-26

    This paper reports the successful bonding of 8 x 8 and 4 x 4 VCSEL arrays to Si CMOS and GaAs MESFET integrated circuits and to GaAs substrates. Three different bonding techniques are demonstrated and their electrical, optical and mechanical characteristics are compared. All three techniques remove the substrate from the VCSEL wafer, leaving individual VCSELs bonded directly to locations within the integrated circuit.

  13. A Comparison of Children's Reading Performance Under Directed and Non-Directed Conditions.

    ERIC Educational Resources Information Center

    Goudey, Charles E.

    Children's reading performances under directed and nondirected conditions were compared in the case of 300 fourth-grade suburban students. Subjects were divided into high, middle, and low achievement groups of 100 each, and each group was subdivided into experimental and control groups. The directed conditions experimental group read the questions…

  14. Partial rescue of a lethal phenotype of fragile bones in transgenic mice with a chimeric antisense gene directed against a mutated collagen gene.

    PubMed Central

    Khillan, J S; Li, S W; Prockop, D J

    1994-01-01

    Previously, transgenic mice were prepared that developed a lethal phenotype of fragile bones because they expressed an internally deleted mini-gene for the pro alpha 1(I) chain of human type I procollagen. The shortened pro alpha 1(I) chains synthesized from the human transgene bound to and produced degradation of normal pro alpha 1(I) chains synthesized from the normal mouse alleles. Here we assembled an antisense gene that was similar to the internally deleted COL1A1 minigene but the 3' half of the gene was inverted so as to code for an antisense RNA. Transgenic mice expressing the antisense gene had a normal phenotype, apparently because the antisense gene contained human sequences instead of mouse sequences. Two lines of mice expressing the antisense gene were bred to two lines of transgenic mice expressing the mini-gene. In mice that inherited both genes, the incidence of the lethal fragile bone phenotype was reduced from 92% to 27%. The effects of the antisense gene were directly demonstrated by an increase in the ratio of normal mouse pro alpha 1(I) chains to human mini-pro alpha 1(I) chains in tissues from mice that inherited both genes and had a normal phenotype. The results raise the possibility that chimeric gene constructs that contain intron sequences and in which only the second half of a gene is inverted may be particularly effective as antisense genes. Images PMID:8022775

  15. Halo independent comparison of direct dark matter detection data

    SciTech Connect

    Gondolo, Paolo; Gelmini, Graciela B. E-mail: gelmini@physics.ucla.edu

    2012-12-01

    We extend the halo-independent method of Fox, Liu, and Weiner to include energy resolution and efficiency with arbitrary energy dependence, making it more suitable for experiments to use in presenting their results. Then we compare measurements and upper limits on the direct detection of low mass ( ∼ 10 GeV) weakly interacting massive particles with spin-independent interactions, including the upper limit on the annual modulation amplitude from the CDMS collaboration. We find that isospin-symmetric couplings are severely constrained both by XENON100 and CDMS bounds, and that isospin-violating couplings are still possible at the lowest energies, while the tension of the higher energy CoGeNT bins with the CDMS modulation constraint remains. We find the CRESST-II signal is not compatible with the modulation signals of DAMA and CoGeNT.

  16. Protein patterning: a comparison of direct spotting versus microcontact printing

    NASA Astrophysics Data System (ADS)

    Clancy, Kathryn F. A.; Nicolau, Dan V.

    2015-03-01

    Protein microarrays are used various research areas including drug discovery, diagnosis, and analysis of protein-ligand interactions. Their efficacy depends on a well-defined pattern of immobilized proteins that also have retained their bioactivity. Protein microarrays are classically fabricated using the robotic spotting drop method ("pin printing"), which can lead to spots with uneven protein concentration within the spotted area, leading to difficult to quantify readings. Among the alternative techniques, microcontact printing (μCP) with a poly(dimethylsiloxane) (PDMS) stamp appears to deliver more defined protein patterns on surfaces, while maintaining bioactivity for a wide range of proteins. Here we have quantitatively compared the distribution of fluorescently labeled proteins deposited using direct pipetting, pin printing and μCP printing with flat stamps onto various functionalized glass surfaces of different contact angles through fluorescent microscopy. The uniformity of the deposited protein spots across deposition techniques was also qualitatively analyzed. It was found that with the use of either the direct pipetting or pin printing techniques that protein concentration on surfaces varied largely across surfaces with different contact angles, whereas adsorption did not vary significantly when using the μCP printing Furthermore, when μCP printing was performed with flat relief structures the spot inhomogeneity was lower than when classical methods were used, and even less so when a pyramid relief structure was used. This suggests that μCP printing with pyramid relief structures could produce protein patterns on various surfaces and with increased spot uniformity to enable more reliable protein microarrays.

  17. Comparison of teacher-directed and student-directed journals on achievement in college chemistry

    NASA Astrophysics Data System (ADS)

    Anderson, Catherine Ann

    The purpose of this research was to use written student journals as a means to improve academic achievement in a one semester introductory college chemistry course designed for nonscience majors. Two kinds of journals were investigated to compare their effectiveness in improving academic achievement and their ability to strengthen conceptual and algorithmic problem solving mastery. Student opinions toward journal writing in college chemistry were also compared. Each journal format was examined for possible differences between the genders. The journal types that were compared were a teacher-directed format and a student-directed format. In the teacher-directed group of 62 students responded to specific topics and readings assigned by the instructor. The 74 students in the student-directed group individually chose the topics that they wrote about. Students wrote two to four entries per week for the duration of the semester (15 weeks). Results showed no significant differences at the alpha=0.05 level between the journal types for improvement of academic achievement as measured by the ACS standardized General-Organic-Biological Chemistry Test. No significant differences in student ability to solve algorithmic and conceptual chemistry problems were detected. Additionally, there were no significant differences between the genders with respect to the journal type analyses. There was a significant difference in the students' opinions toward the journal format that they were assigned to use. The student-directed group gave significantly higher ratings to their format compared to the teacher-directed students. There were no significant differences in the opinion of males and females with regard to journal format. Based on the outcomes of this investigation, for instructors choosing to use written student journals in their college science classes, the use of student-directed journals is recommended. Although there is no benefit in terms of academic achievement or conceptual

  18. Direct comparisons of compressible magnetohydrodynamics and reduced magnetohydrodynamics turbulence

    NASA Astrophysics Data System (ADS)

    Dmitruk, Pablo; Matthaeus, William H.; Oughton, Sean

    2005-11-01

    Direct numerical simulations of low Mach number compressible three-dimensional magnetohydrodynamic (CMHD3D) turbulence in the presence of a strong mean magnetic field are compared with simulations of reduced magnetohydrodynamics (RMHD). Periodic boundary conditions in the three spatial coordinates are considered. Different sets of initial conditions are chosen to explore the applicability of RMHD and to study how close the solution remains to the full compressible MHD solution as both freely evolve in time. In a first set, the initial state is prepared to satisfy the conditions assumed in the derivation of RMHD, namely, a strong mean magnetic field and plane-polarized fluctuations, varying weakly along the mean magnetic field. In those circumstances, simulations show that RMHD and CMHD3D evolve almost indistinguishably from one another. When some of the conditions are relaxed the agreement worsens but RMHD remains fairly close to CMHD3D, especially when the mean magnetic field is large enough. Moreover, the well-known spectral anisotropy effect promotes the dynamical attainment of the conditions for RMHD applicability. Global quantities (mean energies, mean-square current, and vorticity) and energy spectra from the two solutions are compared and point-to-point separation estimations are computed. The specific results shown here give support to the use of RMHD as a valid approximation of compressible MHD with a mean magnetic field under certain but quite practical conditions.

  19. The genetics of maternal care: direct and indirect genetic effects on phenotype in the dung beetle Onthophagus taurus.

    PubMed

    Hunt, John; Simmons, Leigh W

    2002-05-14

    While theoretical models of the evolution of parental care are based on the assumption of underlying genetic variance, surprisingly few quantitative genetic studies of this life-history trait exist. Estimation of the degree of genetic variance in parental care is important because it can be a significant source of maternal effects, which, if genetically based, represent indirect genetic effects. A major prediction of indirect genetic effect theory is that traits without heritable variation can evolve because of the heritable environmental variation that indirect genetic effects provide. In the dung beetle, Onthophagus taurus, females provide care to offspring by provisioning a brood mass. The size of the brood mass has pronounced effects on offspring phenotype. Using a half-sib breeding design we show that the weight of the brood mass females produce exhibits significant levels of additive genetic variance due to sires. However, variance caused by dams is considerably larger, demonstrating that maternal effects are also important. Body size exhibited low additive genetic variance. However, body size exerts a strong maternal influence on the weight of brood masses produced, accounting for 22% of the nongenetic variance in offspring body size. Maternal body size also influenced the number of offspring produced but there was no genetic variance for this trait. Offspring body size and brood mass weight exhibited positive genetic and phenotypic correlations. We conclude that both indirect genetic effects, via maternal care, and nongenetic maternal effects, via female size, play important roles in the evolution of phenotype in this species. PMID:11983863

  20. 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 Ba

    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. PMID:26306646

  1. 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

  2. Direct detection of influenza virus antigen in nasopharyngeal specimens by direct enzyme immunoassay in comparison with quantitating virus shedding.

    PubMed Central

    Döller, G; Schuy, W; Tjhen, K Y; Stekeler, B; Gerth, H J

    1992-01-01

    We developed a direct enzyme immunoassay [EIA; Enzygnost Influenza A(Ag) and Enzygnost Influenza B(Ag)] for the direct detection of influenza A and B virus antigens in nasopharyngeal secretion specimens (NPS). The test is performed without sonification of specimens, and results are obtained within 4 h. A direct comparison between direct EIA and quantitation of virus shedding for influenza A and B virus antigen detection was carried out. A total of 210 NPS and 98 nasopharyngeal wash specimens (NPW) were investigated. We isolated influenza A viruses from 79 (37.6%) of 210 NPS; of these 79 cell-culture-positive NPS, 70 (88.6%) were also positive by direct EIA. Of 29 (13.8%) NPS from which influenza B virus was isolated, 24 (82.8%) NPS were positive by direct EIA. Virus shedding was determined quantitatively in 48 NPS from patients with influenza A and in 24 NPS from patients with influenza B. Only a crude correlation between optical density values and virus concentrations was observed. Detection of influenza virus antigens in NPS by direct EIA showed sensitivities of 89.7% for influenza A virus and 87.9% for influenza B virus and specificities of 99.3% for influenza A virus and 100% for influenza B virus. With direct EIA, all NPW were negative for influenza A virus, although virus was isolated from 21 (21.4%) NPW. Of 15 NPW from which influenza B virus was isolated, 7 showed positive results in direct EIA. In addition, direct EIA is suitable for detecting influenza A and B viruses in cell cultures before the appearance of any cytopathic effects and can be used as a cell culture confirmation test. PMID:1572972

  3. Dynamic stiffening of poly(ethylene glycol)-based hydrogels to direct valvular interstitial cell phenotype in a three-dimensional environment.

    PubMed

    Mabry, Kelly M; Lawrence, Rosa L; Anseth, Kristi S

    2015-05-01

    Valvular interstitial cells (VICs) are active regulators of valve homeostasis and disease, responsible for secreting and remodeling the valve tissue matrix. As a result of VIC activity, the valve modulus can substantially change during development, injury and repair, and disease progression. While two-dimensional biomaterial substrates have been used to study mechanosensing and its influence on VIC phenotype, less is known about how these cells respond to matrix modulus in a three-dimensional environment. Here, we synthesized MMP-degradable poly(ethylene glycol) (PEG) hydrogels with elastic moduli ranging from 0.24 kPa to 12 kPa and observed that cell morphology was constrained in stiffer gels. To vary gel stiffness without substantially changing cell morphology, cell-laden hydrogels were cultured in the 0.24 kPa gels for 3 days to allow VIC spreading, and then stiffened in situ via a second, photoinitiated thiol-ene polymerization such that the gel modulus increased from 0.24 kPa to 1.2 kPa or 13 kPa. VICs encapsulated within soft gels exhibited αSMA stress fibers (∼ 40%), a hallmark of the myofibroblast phenotype. Interestingly, in stiffened gels, VICs became deactivated to a quiescent fibroblast phenotype, suggesting that matrix stiffness directs VIC phenotype independent of morphology, but in a manner that depends on the dimensionality of the culture platform. Collectively, these studies present a versatile method for dynamic stiffening of hydrogels and demonstrate the significant effects of matrix modulus on VIC myofibroblast properties in three-dimensional environments. PMID:25725554

  4. DETECTION OF YERSINIA PESTIS BY COMPARISON OF VIRULENCE PLASMID (PYV/PCD)-ASSOCIATED PHENOTYPES IN YERSINIA SPECIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotypic expression of several virulence plasmid (pYV/pCD; 70-kb)-associated genetic determinants including low calcium response (Lcr; pin point colony, size= 0.36 mm), colony morphology (size= 1.13 mm), crystal violet (CV) binding (dark-violet colony), Congo Red (CR) uptake (red pin point colony;...

  5. 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...

  6. Confirmational identification of Escherichia coli, a comparison of genotypic and phenotypic assays for glutamate decarboxylase and beta-D-glucuronidase.

    PubMed Central

    McDaniels, A E; Rice, E W; Reyes, A L; Johnson, C H; Haugland, R A; Stelma, G N

    1996-01-01

    Genotypic and phenotypic assays for glutamate decarboxylase (GAD) and beta-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 groups of diarrheagenic E. coli, three other non-coli Escherichia species, and various other gram-negative and -positive bacteria found in water. The genotypic assays were performed with hybridization probes generated by PCR amplification of 670- and 623-bp segments of the gadA/B (GAD) and uidA (GUD) genes, respectively. The GAD enzymes catalyze the alpha-decarboxylation of L-glutamic acid to yield gamma-aminobutyric acid and carbon dioxide, which are detected in the phenotypic assay by a pH-sensitive indicator dye. The phenotypic assay for GUD involves the transformation of 4-methylumbelliferyl-beta-D-glucuronide to the fluorogenic compound 4-methylumbelliferone. The GAD phenotypic assay detected the majority of the E. coli strains tested, whereas a number of these strains, including all representatives of the O157:H7 serotype and several nonpathogenic E. coli strains, gave negative results in the GUD assay. Both phenotypic assays detected some but not all strains from each of the four Shigella species. A strain of Citrobacter freundii was also detected by the GUD assay but not by the GAD assay. All E. coli and Shigella strains were detected with both the gadA/B and uidA probes. A few Escherichia fergusonii strains gave weak hybridization signals in response to both probes at 65 degrees C but not at 68 degrees C. None of the other bacterial species tested were detected by either probe. These results were consistent with previous reports which have indicated that the GAD phenotypic assay detects a wider range of E. coli strains than does the GUD assay and is also somewhat more specific for this species. The genotypic assays for the two enzymes were found to be equivalent in both of

  7. 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.

  8. 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

  9. A critical comparison of second order closures with direct numerical simulation of homogeneous turbulence

    NASA Technical Reports Server (NTRS)

    Shih, Tsan-Hsing; Lumley, John L.

    1991-01-01

    Recently, several second order closure models have been proposed for closing the second moment equations, in which the velocity-pressure gradient (and scalar-pressure gradient) tensor and the dissipation rate tensor are two of the most important terms. In the literature, these correlation tensors are usually decomposed into a so called rapid term and a return-to-isotropy term. Models of these terms have been used in global flow calculations together with other modeled terms. However, their individual behavior in different flows have not been fully examined because they are un-measurable in the laboratory. Recently, the development of direct numerical simulation (DNS) of turbulence has given us the opportunity to do this kind of study. With the direct numerical simulation, we may use the solution to exactly calculate the values of these correlation terms and then directly compare them with the values from their modeled formulations (models). Here, we make direct comparisons of five representative rapid models and eight return-to-isotropy models using the DNS data of forty five homogeneous flows which were done by Rogers et al. (1986) and Lee et al. (1985). The purpose of these direct comparisons is to explore the performance of these models in different flows and identify the ones which give the best performance. The modeling procedure, model constraints, and the various evaluated models are described. The detailed results of the direct comparisons are discussed, and a few concluding remarks on turbulence models are given.

  10. A systematic comparison of feature space effects on disease classifier performance for phenotype identification of five diseases.

    PubMed

    Kotfila, Christopher; Uzuner, Özlem

    2015-12-01

    Automated phenotype identification plays a critical role in cohort selection and bioinformatics data mining. Natural Language Processing (NLP)-informed classification techniques can robustly identify phenotypes in unstructured medical notes. In this paper, we systematically assess the effect of naive, lexically normalized, and semantic feature spaces on classifier performance for obesity, atherosclerotic cardiovascular disease (CAD), hyperlipidemia, hypertension, and diabetes. We train support vector machines (SVMs) using individual feature spaces as well as combinations of these feature spaces on two small training corpora (730 and 790 documents) and a combined (1520 documents) training corpus. We assess the importance of feature spaces and training data size on SVM model performance. We show that inclusion of semantically-informed features does not statistically improve performance for these models. The addition of training data has weak effects of mixed statistical significance across disease classes suggesting larger corpora are not necessary to achieve relatively high performance with these models. PMID:26241355

  11. JAK2V617F allele burden and thrombosis: a direct comparison in essential thrombocythemia and polycythemia vera

    PubMed Central

    Carobbio, Alessandra; Finazzi, Guido; Antonioli, Elisabetta; Guglielmelli, Paola; Vannucchi, Alessandro M.; Dellacasa, Chiara M.; Salmoiraghi, Silvia; Delaini, Federica; Rambaldi, Alessandro; Barbui, Tiziano

    2009-01-01

    OBJECTIVE A direct comparison of the incidence and risk factors of major thrombosis in essential thrombocythemia (ET) and polycythemia vera (PV) according to their respective JAK2V617F allele burden is the object of this study. METHODS We compared the rate (%/pts/yr) of major thrombosis in 867 ET patients (57% JAK2V617F) with that of 415 PV patients (all JAK2V617F) and examined risk factors. RESULTS Patients with ET wild type, ET V617F and PV showed a rate of thrombosis of 1.4, 2.1, and 2.7 %/pt/yr respectively. This latter was found to progressively increase according to the time of diagnosis. The actuarial probability of arterial and venous thrombosis in the first 5 years of diagnosis was roughly similar in the three groups. While, in the subsequent periods, the curves of mutated ET patients diverged from wild type and after 10–15 years, ET mutated arm approached PV. CONCLUSION These findings support the concept of a continuum between ET JAK2 mutated and PV not only in reference to the hematological phenotype but also in terms of vascular events PMID:19559071

  12. Antipsychotic-induced metabolic effects in the female rat: Direct comparison between long-acting injections of risperidone and olanzapine.

    PubMed

    Ersland, Kari M; Skrede, Silje; Røst, Therese H; Berge, Rolf K; Steen, Vidar M

    2015-12-01

    Several antipsychotics have well-known adverse metabolic effects. Studies uncovering molecular mechanisms of such drugs in patients are challenging due to high dropout rates, previous use of antipsychotics and restricted availability of biological samples. Rat experiments, where previously unexposed animals are treated with antipsychotics, allow for direct comparison of different drugs, but have been hampered by the short half-life of antipsychotics in rodents. The use of long-acting formulations of antipsychotics could significantly increase the value of rodent models in the molecular characterization of therapeutic and adverse effects of these agents. However, as long-acting formulations have rarely been used in rodents, there is a need to characterize the basic metabolic phenotype of different antipsychotics. Using long-acting olanzapine injections as a positive control, the metabolic effects of intramuscular long-acting risperidone in female rats were investigated for the first time. Like olanzapine, risperidone induced rapid, significant hyperphagia and weight gain, with concomitant increase in several plasma lipid species. Both drugs also induced weight-independent upregulation of several genes encoding enzymes involved in lipogenesis, but this activation was not confirmed at the protein level. Our findings shed light on the role of drug administration, drug dose and nutritional status in the development of rodent models for adverse metabolic effects of antipsychotic agents. PMID:26378122

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

    PubMed

    Jones, C Hal; 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

    2016-01-01

    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

  14. Direct comparisons between absolute and relative geomagnetic paleointensities: Absolute calibration of a relative paleointensity stack

    NASA Astrophysics Data System (ADS)

    Mochizuki, N.; Yamamoto, Y.; Hatakeyama, T.; Shibuya, H.

    2013-12-01

    Absolute geomagnetic paleointensities (APIs) have been estimated from igneous rocks, while relative paleomagnetic intensities (RPIs) have been reported from sediment cores. These two datasets have been treated separately, as correlations between APIs and RPIs are difficult on account of age uncertainties. High-resolution RPI stacks have been constructed from globally distributed sediment cores with high sedimentation rates. Previous studies often assumed that the RPI stacks have a linear relationship with geomagnetic axial dipole moments, and calibrated the RPI values to API values. However, the assumption of a linear relationship between APIs and RPIs has not been evaluated. Also, a quantitative calibration method for the RPI is lacking. We present a procedure for directly comparing API and RPI stacks, thus allowing reliable calibrations of RPIs. Direct comparisons between APIs and RPIs were conducted with virtually no associated age errors using both tephrochronologic correlations and RPI minima. Using the stratigraphic positions of tephra layers in oxygen isotope stratigraphic records, we directly compared the RPIs and APIs reported from welded tuffs contemporaneously extruded with the tephra layers. In addition, RPI minima during geomagnetic reversals and excursions were compared with APIs corresponding to the reversals and excursions. The comparison of APIs and RPIs at these exact points allowed a reliable calibration of the RPI values. We applied this direct comparison procedure to the global RPI stack PISO-1500. For six independent calibration points, virtual axial dipole moments (VADMs) from the corresponding APIs and RPIs of the PISO-1500 stack showed a near-linear relationship. On the basis of the linear relationship, RPIs of the stack were successfully calibrated to the VADMs. The direct comparison procedure provides an absolute calibration method that will contribute to the recovery of temporal variations and distributions of geomagnetic axial dipole

  15. 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.

  16. 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.

  17. 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. PMID:24784665

  18. Dabigatran, a direct thrombin inhibitor, blocks differentiation of normal fibroblasts to a myofibroblast phenotype and demonstrates anti-fibrotic effects on scleroderma lung fibroblasts

    PubMed Central

    Bogatkevich, Galina S.; Ludwicka-Bradley, Anna; Silver, Richard M.

    2010-01-01

    Myofibroblasts are the principal mesenchymal cells responsible for tissue remodeling, collagen deposition, and the restrictive nature of lung parenchyma associated with pulmonary fibrosis. We previously reported that thrombin activates protease-activated receptor (PAR)-1 thereby inducing normal lung fibroblasts to differentiate to a myofibroblast phenotype resembling scleroderma lung myofibroblasts. Here we demonstrate that the thrombin inhibitor dabigatran inhibits in a dose-dependant manner thrombin's induction of myofibroblasts. Dabigatran inhibits thrombin-induced cell proliferation, α-smooth muscle actin (α-SMA) expression and organization, and the production of collagen and connective tissue growth factor (CTGF). Moreover, when treated with dabigatran scleroderma lung myofibroblasts produce less CTGF, α-SMA, and collagen type I. We conclude that dabigatran restrains important profibrotic events in lung fibroblasts and that this oral direct thrombin inhibitor warrants study as a potential anti-fibrotic drug for the treatment of fibrosing lung diseases, e.g. scleroderma lung disease and idiopathic pulmonary fibrosis. PMID:19877031

  19. Comparison of nine phenotypic methods for detection of extended-spectrum beta-lactamase production by Enterobacteriaceae.

    PubMed

    Garrec, Hélène; Drieux-Rouzet, Laurence; Golmard, Jean-Louis; Jarlier, Vincent; Robert, Jérôme

    2011-03-01

    The detection of extended-spectrum β-lactamase-producing (ESBL) bacteria is of importance for infection control and epidemiological surveillance. We aimed to compare phenotypic methods available in the routine laboratory and to evaluate two-step strategies using these methods for the detection of ESBL-positive Enterobacteriaceae. Two methods used for routine susceptibility testing (Vitek2 and disk diffusion methods) and seven methods designed for the detection of ESBL production (ESBL Etests, combination disks, double-disk synergy [DDS] methods on Mueller-Hinton [MH] agar and cloxacillin-containing MH agar, and the Cica-Beta test) were tested against 107 strains of Enterobacteriaceae not susceptible to extended-spectrum cephalosporins. All strains were screened for the presence of acquired ESBL-encoding genes by PCR, and the PCR result was considered the gold standard for evaluation of the other test methods. Among the 107 strains, 52 (49%) were ESBL positive. With Vitek2, sensitivities were the highest when using extended cards (73% to 79%), but 25% to 31% of the strains yielded indeterminate results. For the disk diffusion method, sensitivities were the highest (96%) when testing at least cefotaxime, cefepime, and a third compound (ceftazidime, cefpodoxime, or aztreonam). For the specific methods, specificities ranged from 62% (ceftazidime ESBL Etest) to 100% (DDS using a disk spacing of 20 mm). When a method designed for ESBL detection was used on strains considered ESBL negative or with an indeterminate result by a first routine susceptibility method, sensitivities reached 100% for a majority of combinations. In conclusion, two-step strategies using phenotypic methods available in most clinical laboratories may reach a sensitivity of 100% for ESBL detection among a large panel of species, including AmpC producers, providing a sensible choice of tests. PMID:21248086

  20. 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

  1. 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 Central

    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

  2. The social behavioral phenotype in boys and girls with an extra X chromosome (Klinefelter syndrome and Trisomy X): a comparison with autism spectrum disorder.

    PubMed

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

    2014-02-01

    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 controls, aged 9 to 18 years. We used the Autism Diagnostic Interview, Social Responsiveness Scale, Social Anxiety Scale and Social Skills Rating System. In the extra X group, levels of social dysfunction and autism symptoms were increased, being in between controls and ASD. In contrast to the ASD group, the extra X group showed increased social anxiety. The effects were similar for boys and girls with an extra X chromosome. PMID:23824705

  3. Unique biomaterial compositions direct bone marrow stem cells into specific chondrocytic phenotypes corresponding to the various zones of articular cartilage.

    PubMed

    Nguyen, Lonnissa H; Kudva, Abhijit K; Guckert, Nicole L; Linse, Klaus D; Roy, Krishnendu

    2011-02-01

    Numerous studies have reported generation of cartilage-like tissue from chondrocytes and stem cells, using pellet cultures, bioreactors and various biomaterials, especially hydrogels. However, one of the primary unsolved challenges in the field has been the inability to produce tissue that mimics the highly organized zonal architecture of articular cartilage; specifically its spatially varying mechanical properties and extra-cellular matrix (ECM) composition. Here we show that different combinations of synthetic and natural biopolymers create unique niches that can "direct" a single marrow stem cell (MSC) population to differentiate into the superficial, transitional, or deep zones of articular cartilage. Specifically, incorporating chondroitin sulfate (CS) and matrix metalloproteinase-sensitive peptides (MMP-pep) into PEG hydrogels (PEG:CS:MMP-pep) induced high levels of collagen II and low levels of proteoglycan expression resulting in a low compressive modulus, similar to the superficial zone. PEG:CS hydrogels produced intermediate-levels of both collagen II and proteoglycans, like the transitional zone, while PEG:hyaluronic acid (HA) hydrogels induced high proteoglycan and low collagen II levels leading to high compressive modulus, similar to the deep zone. Additionally, the compressive moduli of these zone-specific matrices following cartilage generation showed similar trend as the corresponding zones of articular cartilage, with PEG:CS:MMP-pep having the lowest compressive modulus, followed by PEG:CS while PEG:HA had the highest modulus. These results underscore the potential for composite scaffold structures incorporating these biomaterial compositions such that a single stem-progenitor cell population can give rise to zonally-organized, functional articular cartilage-like tissue. PMID:21067807

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

    PubMed Central

    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

    2014-01-01

    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. PMID:24682306

  5. Comparison between phenotypic and PCR for detection of OXA-23 type and metallo-beta-lactamases producer Acinetobacter spp.

    PubMed Central

    Azimi, Leila; Lari, Abdolaziz Rastegar; Talebi, Malihe; Namvar, Amirmorteza Ebrahimzadeh; Jabbari, Mosadegh

    2013-01-01

    Background: Resistance to carbapenems is developing around the world and can cause many problems for treatment of patients. Production of metallo-beta-lactamase (MBL) is one of the main mechanism for this type of resistance. So, detection of MBL-producer microorganisms can prevent the spread of this type of resistance. Materials and methods: In this study 94 Acinetobacter spp. were investigated. Resistance to imipenem was conducted after purification and identification. Combination disc (CD) and Double Disc Synergy Test (DDST) were performed for phenotypic detection of MBL and the molecular PCR method was done for vim-1, vim-2, imp-1 and OXA-23 genes. Results: According to TSI, SIM and oxidation-fermentation (OF) test and PCR assay 93 Acinetobacter baumannii and one strain Acinetobacter lwoffii were identified. 85% of them were resistant to imipenem. 34% of them have a positive combination disc test (CD) while Double Disc Synergy Test (DDST) was negative for all of them. The vim-1, vim-2 and imp-1 genes were not detected in PCR molecular method, however in 74% of strains with positive results in combination disc, were positive for the OXA-23 gene after PCR test. This study shows that the blaOXA-23 resistance determinant may become an emerging therapeutic problem. Discussion: According to the results, it seems that combination disc does not have enough specificity for detection of MBL-producer Acinetobacter and using Double Disc Synergy Test (DDST) can be more convenient. PMID:24327942

  6. Comparison of outcomes in mixed phenotype acute leukemia patients treated with chemotherapy and stem cell transplantation versus chemotherapy alone.

    PubMed

    Tian, Hong; Xu, Yang; Liu, Liming; Yan, Lingzhi; Jin, Zhengming; Tang, Xiaowen; Han, Yue; Fu, Zhengzheng; Qiu, Huiying; Sun, Aining; Wu, Depei

    2016-06-01

    The optimal treatment approach for mixed phenotype acute leukemia (MPAL) remains unknown, and prognostic factors for treatment outcomes need to be identified. In this study, 66 patients diagnosed with MPAL according to criteria published by the WHO in 2008 were retrospectively assessed to evaluate the effectiveness of treatment and identify predictive variables. Five patients died of severe infection after the first induction chemotherapy, 29 received alloHSCT after induction (HSCT group), and 32 received only chemotherapy (chemotherapy group). The 3-year OS and DFS estimates for the entire cohort were 45% and 38%, respectively, and the 3-year OS differed significantly between the HSCT and chemotherapy-only groups (77% versus 16%). Using multivariate analyses, we identified disease burden as a prognostic factor for transplantation outcome, with the 3-year OS being 80% among patients who achieved remission and only 45% among patients in cases of nonremission. Our results indicate that alloHSCT after chemotherapy offers a survival advantage compared with chemotherapy only, and patients in remission before transplantation may experience a better outcome. PMID:27088964

  7. Isolation and Molecular Profiling of Primary Mouse Retinal Ganglion Cells: Comparison of Phenotypes from Healthy and Glaucomatous Retinas

    PubMed Central

    Chintalapudi, Sumana R.; Djenderedjian, Levon; Stiemke, Andrew B.; Steinle, Jena J.; Jablonski, Monica M.; Morales-Tirado, Vanessa M.

    2016-01-01

    Loss of functional retinal ganglion cells (RGC) is an element of retinal degeneration that is poorly understood. This is in part due to the lack of a reliable and validated protocol for the isolation of primary RGCs. Here we optimize a feasible, reproducible, standardized flow cytometry-based protocol for the isolation and enrichment of homogeneous RGC with the Thy1.2hiCD48negCD15negCD57neg surface phenotype. A three-step validation process was performed by: (1) genomic profiling of 25-genes associated with retinal cells; (2) intracellular labeling of homogeneous sorted cells for the intracellular RGC-markers SNCG, brain-specific homeobox/POU domain protein 3A (BRN3A), TUJ1, and RNA-binding protein with multiple splicing (RBPMS); and (3) by applying the methodology on RGC from a mouse model with elevated intraocular pressure (IOP) and optic nerve damage. Use of primary RGC cultures will allow for future careful assessment of important cell specific pathways in RGC to provide mechanistic insights into the declining of visual acuity in aged populations and those suffering from retinal neurodegenerative diseases. PMID:27242509

  8. Direct Cell-Cell Contact between Mesenchymal Stem Cells and Endothelial Progenitor Cells Induces a Pericyte-Like Phenotype In Vitro

    PubMed Central

    Richards, R. Geoff; Nerlich, Michael; Alini, Mauro

    2014-01-01

    Tissue engineering techniques for the regeneration of large bone defects require sufficient vascularisation of the applied constructs to ensure a sufficient supply of oxygen and nutrients. In our previous work, prevascularised 3D scaffolds have been successfully established by coculture of bone marrow derived stem cells (MSCs) and endothelial progenitor cells (EPCs). We identified stabilising pericytes (PCs) as part of newly formed capillary-like structures. In the present study, we report preliminary data on the interactions between MSCs and EPCs, leading to the differentiation of pericyte-like cells. MSCs and EPCs were seeded in transwell cultures, direct cocultures, and single cultures. Cells were cultured for 10 days in IMDM 10% FCS or IMDM 5% FCS 5% platelet lysate medium. Gene expression of PC markers, CD146, NG2, αSMA, and PDGFR-β, was analysed using RT-PCR at days 0, 3, 7, and 10. The upregulation of CD146, NG2, and αSMA in MSCs in direct coculture with EPCs advocates the MSCs' differentiation towards a pericyte-like phenotype in vitro. These results suggest that pericyte-like cells derive from MSCs and that cell-cell contact with EPCs is an important factor for this differentiation process. These findings emphasise the concept of coculture strategies to promote angiogenesis for cell-based tissue engineered bone grafts. PMID:24563864

  9. 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.

  10. Direct voxel-based comparisons between grey matter shrinkage and glucose hypometabolism in chronic alcoholism.

    PubMed

    Ritz, Ludivine; Segobin, Shailendra; Lannuzel, Coralie; Boudehent, Céline; Vabret, François; Eustache, Francis; Beaunieux, Hélène; Pitel, Anne L

    2016-09-01

    Alcoholism is associated with widespread brain structural abnormalities affecting mainly the frontocerebellar and the Papez's circuits. Brain glucose metabolism has received limited attention, and few studies used regions of interest approach and showed reduced global brain metabolism predominantly in the frontal and parietal lobes. Even though these studies have examined the relationship between grey matter shrinkage and hypometabolism, none has performed a direct voxel-by-voxel comparison between the degrees of structural and metabolic abnormalities. Seventeen alcoholic patients and 16 control subjects underwent both structural magnetic resonance imaging and (18)F-2-fluoro-deoxy-glucose-positron emission tomography examinations. Structural abnormalities and hypometabolism were examined in alcoholic patients compared with control subjects using two-sample t-tests. Then, these two patterns of brain damage were directly compared with a paired t-test. Compared to controls, alcoholic patients had grey matter shrinkage and hypometabolism in the fronto-cerebellar circuit and several nodes of Papez's circuit. The direct comparison revealed greater shrinkage than hypometabolism in the cerebellum, cingulate cortex, thalamus and hippocampus and parahippocampal gyrus. Conversely, hypometabolism was more severe than shrinkage in the dorsolateral, premotor and parietal cortices. The distinct profiles of abnormalities found within the Papez's circuit, the fronto-cerebellar circuit and the parietal gyrus in chronic alcoholism suggest the involvement of different pathological mechanisms. PMID:26661206

  11. Comparison of Muscle Transcriptome between Pigs with Divergent Meat Quality Phenotypes Identifies Genes Related to Muscle Metabolism and Structure

    PubMed Central

    Damon, Marie; Wyszynska-Koko, Joanna; Vincent, Annie; Hérault, Frédéric; Lebret, Bénédicte

    2012-01-01

    Background Meat quality depends on physiological processes taking place in muscle tissue, which could involve a large pattern of genes associated with both muscle structural and metabolic features. Understanding the biological phenomena underlying muscle phenotype at slaughter is necessary to uncover meat quality development. Therefore, a muscle transcriptome analysis was undertaken to compare gene expression profiles between two highly contrasted pig breeds, Large White (LW) and Basque (B), reared in two different housing systems themselves influencing meat quality. LW is the most predominant breed used in pig industry, which exhibits standard meat quality attributes. B is an indigenous breed with low lean meat and high fat contents, high meat quality characteristics, and is genetically distant from other European pig breeds. Methodology/Principal Findings Transcriptome analysis undertaken using a custom 15 K microarray, highlighted 1233 genes differentially expressed between breeds (multiple-test adjusted P-value<0.05), out of which 635 were highly expressed in the B and 598 highly expressed in the LW pigs. No difference in gene expression was found between housing systems. Besides, expression level of 12 differentially expressed genes quantified by real-time RT-PCR validated microarray data. Functional annotation clustering emphasized four main clusters associated to transcriptome breed differences: metabolic processes, skeletal muscle structure and organization, extracellular matrix, lysosome, and proteolysis, thereby highlighting many genes involved in muscle physiology and meat quality development. Conclusions/Significance Altogether, these results will contribute to a better understanding of muscle physiology and of the biological and molecular processes underlying meat quality. Besides, this study is a first step towards the identification of molecular markers of pork quality and the subsequent development of control tools. PMID:22470472

  12. 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

  13. 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.

  14. Phenotypic and genotypic comparison of ESBL production by Vaginal Escherichia coli isolates from pregnant and non-pregnant women

    PubMed Central

    2013-01-01

    Background Vaginal Escherichia coli is a reservoir along the fecal-vaginal-urinary/neonatal course of transmission in extraintestinal E. coli infections. They also causes genital tract infections especially vaginitis, so that detection of their antibiotic resistance is an important approach to control these infections. One important mechanism of resistance is ESBL production by Enterobacteriaceae especially Klebsiella spp. and Escherichia coli, which is now a worldwide problem that limits therapeutic options. Methods Sixty one vaginal E. coli isolates from pregnant and non-pregnant women, were detected phenotypically and genotypically for ESBL production. Results Most of pregnant and non-pregnant women's isolates, were resistant to cefotaxime (100% vs. 81.5%, respectively) and more than half of them to ceftazidime (56.5% vs. 71.0%, respectively). One hundred percent each, 52.1% vs. 68.4%, and 73.9% vs. 60.5%%, were ESBL producers by screening, confirmatory, and PCR tests, respectively. Pregnant women's isolates had: CTX-M- (69.5%), SHV- and OXA-type (each 4.3%) ESBLs. Only one isolate (4.3%) had two types of ESBLs. All 16 CTX-M-positive (100%) isolates had CTX-M-1. Non-pregnant women's isolates were predominated by SHV and CTX-M -type (44.7% vs. 39.4%, respectively), followed by OXA- (15.7%), and TEM-type (2.6%). Of these isolates, 42.1% had two types of ESBL genes. All 15 CTX-M-positive (100%) isolates had CTX-M-1. Pregnant and non-pregnant women's isolates differed significantly (P≤ 0.05) regarding the expression of SHV- (4.3% vs. 44.7%, respectively) and CTX-M-type (69.5% vs. 39.4%, respectively) ESBLs. In both, CTX-M-1 was the predominant CTX-M group (each 100%). All of the isolates were susceptible to imipenem and meropenem, while the highest rate of resistance was against β-lactams. Multidrug resistance was noted in 56.2% of ESBL-producing isolates. Conclusions Ggenital tracts of pregnant and non-pregnant women represent different environments for

  15. 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.

  16. A direct comparison of CVD-grown and exfoliated MoS2 using optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Plechinger, G.; Mann, J.; Preciado, E.; Barroso, D.; Nguyen, A.; Eroms, J.; Schüller, C.; Bartels, L.; Korn, T.

    2014-06-01

    MoS2 is a highly interesting material, which exhibits a crossover from an indirect band gap in the bulk crystal to a direct gap for single layers. Here, we perform a direct comparison between large-area MoS2 films grown by chemical vapor deposition (CVD) and MoS2 flakes prepared by mechanical exfoliation from mineral bulk crystal. Raman spectroscopy measurements show differences between the in-plane and out-of-plane phonon mode positions in CVD-grown and exfoliated MoS2. Photoluminescence (PL) mapping reveals large regions in the CVD-grown films that emit strong PL at room-temperature, and low-temperature PL scans demonstrate a large spectral shift of the A exciton emission as a function of position. Polarization-resolved PL measurements under near-resonant excitation conditions show a strong circular polarization of the PL, corresponding to a valley polarization.

  17. 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.

  18. Comparison of direct and indirect positron-generation by an ultra-intense femtosecond laser

    SciTech Connect

    Yan, Yonghong; Zhang, Bo; Wu, Yuchi; Dong, Kegong; Gu, Yuqiu; Yao, Zeen

    2013-10-15

    An extensive comparison of the properties of positron beams produced by an ultra-intense femtosecond laser in direct and indirect schemes has been performed with two-dimensional particle-in-cell and Monte Carlo simulations. It is shown that the positron beam generated in the indirect scheme has a higher yield (10{sup 10}), a higher temperature (28.8 MeV), a shorter pulse duration (5 ps), and a smaller divergence (8°) than in the direct case (10{sup 9} yield, 4.4 MeV temperature, 40 ps pulse duration, and 60° divergence). In addition, it was found that the positron/gamma ratio in the indirect scheme is one order of magnitude higher than that in the direct one, which represents a higher signal/noise ratio in positron detection. Nevertheless, the direct generation method still has its own unique advantage, the so-called target normal sheath acceleration, which can result in quasi-monoenergetic positron beams that may serve in some specialized applications.

  19. Comparison of direct and indirect positron-generation by an ultra-intense femtosecond laser

    NASA Astrophysics Data System (ADS)

    Yan, Yonghong; Zhang, Bo; Wu, Yuchi; Dong, Kegong; Yao, Zeen; Gu, Yuqiu

    2013-10-01

    An extensive comparison of the properties of positron beams produced by an ultra-intense femtosecond laser in direct and indirect schemes has been performed with two-dimensional particle-in-cell and Monte Carlo simulations. It is shown that the positron beam generated in the indirect scheme has a higher yield (1010), a higher temperature (28.8 MeV), a shorter pulse duration (5 ps), and a smaller divergence (8°) than in the direct case (109 yield, 4.4 MeV temperature, 40 ps pulse duration, and 60° divergence). In addition, it was found that the positron/gamma ratio in the indirect scheme is one order of magnitude higher than that in the direct one, which represents a higher signal/noise ratio in positron detection. Nevertheless, the direct generation method still has its own unique advantage, the so-called target normal sheath acceleration, which can result in quasi-monoenergetic positron beams that may serve in some specialized applications.

  20. Comparison between Conditional Probability Function and Nonparametric Regression for Fine Particle Source Directions

    NASA Astrophysics Data System (ADS)

    Kim, Eugene; Hopke, Philip K.

    The objective of this study is to examine the use of conditional probability function (CPF) and nonparametric regression (NPR) to identify directions of PM 2.5 (particulate matter ⩽2.5 μm in aerodynamic diameter) sources using data collected from multiple monitoring sites across the US NPR has been used on cyclohexane data from Houston, TX and correctly showed the direction of the source. In recent source apportionment studies using positive matrix factorization (PMF), ambient PM 2.5 compositional data sets from 24-h integrated samples including eight individual carbon fractions collected at four monitoring sites, Atlanta, GA, Washington, DC, Brigantine, NJ, and Seattle, WA, were analyzed identifying 10-11 sources. To analyze local point source impacts from various wind directions, CPF and NPR were calculated using the source contributions estimated from PMF coupled with wind direction measured on site. The comparison between CPF and NPR demonstrated that both methods agreed well with the locations of known local point sources. CPF was simpler and easier to calculate than NPR. In contrast, NPR provided PM 2.5 concentrations and associated uncertainties. This study indicates that both methods can be utilized to enhance source apportionment study of ambient PM 2.5.

  1. Why are estimates of the strength and direction of natural selection from wild populations not congruent with observed rates of phenotypic change?

    PubMed

    Brookfield, John F Y

    2016-09-01

    Observing adaptive evolution is difficult. In the fossil record, phenotypic evolution happens much more slowly than in artificial selection experiments or in experimental evolution. Yet measures of selection on phenotypic traits, with high heritabilities, suggest that phenotypic evolution should also be rapid in the wild, and this discrepancy often remains even after accounting for correlations between different traits (i.e. making predictions using the multivariate version of the breeder's equation). Are fitness correlations with quantitative traits adequate measures of selection in the wild? We should instead view fitnesses as average properties of genotypes, while acknowledging that they can be environment-dependent. Populations will tend to remain at fitness equilibria, once these are attained, and phenotypes will then be stable. Thus, studying the causes of adaptive change at a genotypic rather than phenotypic level may reveal that, typically, it is occurring too slowly to be easily observed. PMID:27401716

  2. 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. PMID:25741361

  3. 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

  4. 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

  5. Simulation of mixture microstructures via particle packing models and their direct comparison with real mixtures

    NASA Astrophysics Data System (ADS)

    Gulliver, Eric A.

    The objective of this thesis to identify and develop techniques providing direct comparison between simulated and real packed particle mixture microstructures containing submicron-sized particles. This entailed devising techniques for simulating powder mixtures, producing real mixtures with known powder characteristics, sectioning real mixtures, interrogating mixture cross-sections, evaluating and quantifying the mixture interrogation process and for comparing interrogation results between mixtures. A drop and roll-type particle-packing model was used to generate simulations of random mixtures. The simulated mixtures were then evaluated to establish that they were not segregated and free from gross defects. A powder processing protocol was established to provide real mixtures for direct comparison and for use in evaluating the simulation. The powder processing protocol was designed to minimize differences between measured particle size distributions and the particle size distributions in the mixture. A sectioning technique was developed that was capable of producing distortion free cross-sections of fine scale particulate mixtures. Tessellation analysis was used to interrogate mixture cross sections and statistical quality control charts were used to evaluate different types of tessellation analysis and to establish the importance of differences between simulated and real mixtures. The particle-packing program generated crescent shaped pores below large particles but realistic looking mixture microstructures otherwise. Focused ion beam milling was the only technique capable of sectioning particle compacts in a manner suitable for stereological analysis. Johnson-Mehl and Voronoi tessellation of the same cross-sections produced tessellation tiles with different the-area populations. Control charts analysis showed Johnson-Mehl tessellation measurements are superior to Voronoi tessellation measurements for detecting variations in mixture microstructure, such as altered

  6. 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

    2016-08-01

    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.

  7. 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…

  8. Direct Comparison of Linear and Macrocyclic Compound Libraries as a Source of Protein Ligands

    PubMed Central

    2015-01-01

    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. PMID:25623285

  9. 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.

  10. Direct Comparison of Electrochemical and Spectrochemical Kinetics for Catalytic Oxygen Reduction

    SciTech Connect

    Wasylenko, Derek J.; Rodriguez, Carlos; Pegis, Michael L.; Mayer, James M.

    2014-09-10

    We describe here a direct comparison of electrochemical and spectrochemical experiments to determine rates and selectivity of oxygen reduction catalyzed by iron 5,10,15,20-meso-tetraphenylporphyrin chloride. Strong agreement was found between the two methods suggesting the same mechanism is occurring under both conditions, with the same overall third order rate constant kcat = (1.1 ± 0.1) × 106 M-2 s-1. This report provides a rare example of characterization of a redox catalytic process by two common but very different methods. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences.

  11. 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.

  12. 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.

  13. Coherent structures in a turbulent mixing layer - A comparison between direct numerical simulations and experiments

    NASA Technical Reports Server (NTRS)

    Metcalfe, R. W.; Menon, S.; Hussain, A. K. M. F.

    1985-01-01

    An eduction scheme has been developed in an attempt to determine the characteristics of large-scale vortical structures in a turbulent mixing layer. This analysis scheme has been applied to a set of experimental data taken in a new, larger mixing layer facility designed to minimize boundary and resonance effects. A similar scheme has been developed to apply to the results of a direct numerical simulation of a temporally growing mixing layer. A comparison of the two approaches shows important similarities in the coherent structures. The numerical simulations indicate that low levels of coherent forcing can dramatically change the evolution of the mixing layer. In the absence of such forcing, the numerical simulations and experiments show a lack of regularity in the transverse position, spacing, amplitude, shape and spanwise coherence of the large-scale vortical structures.

  14. 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

  15. Direct comparison of phosphate uptake by adnate and loosely attached microalgae within an intact biofilm matrix

    SciTech Connect

    Burkholder, J.M.; Wetzel, R.G. ); Klomparens, K.L. )

    1990-09-01

    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 ({sup 33}P)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 ({sup 33}P)phosphate uptake by adnate and loosely attached components of the epiphyte matrix. Loosley 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.

  16. Action-value comparisons in the dorsolateral prefrontal cortex control choice between goal-directed actions

    PubMed Central

    Morris, Richard W.; Dezfouli, Amir; Griffiths, Kristi R.; Balleine, Bernard W.

    2014-01-01

    It is generally assumed that choice between different actions reflects the difference between their action values yet little direct evidence confirming this assumption has been reported. Here we assess whether the brain calculates the absolute difference between action values or their relative advantage, that is, the probability that one action is better than the other alternatives. We use a two-armed bandit task during functional magnetic resonance imaging and modelled responses to determine both the size of the difference between action values (D) and the probability that one action value is better (P). The results show haemodynamic signals corresponding to P in right dorsolateral prefrontal cortex (dlPFC) together with evidence that these signals modulate motor cortex activity in an action-specific manner. We find no significant activity related to D. These findings demonstrate that a distinct neuronal population mediates action-value comparisons, and reveals how these comparisons are implemented to mediate value-based decision-making. PMID:25055179

  17. Direct Comparison of Gyrokinetic Turbulence Simulations with Phase Contrast Imaging Fluctuation Measurements

    NASA Astrophysics Data System (ADS)

    Ernst, Darin; Long, A.; Basse, N.; Lin, L.; Porkolab, M.; Dorland, W.

    2006-04-01

    We have developed a synthetic diagnostic^1 for the GS2 gyrokinetic code for direct comparisons with phase contrast imaging (PCI) measurements of density fluctuations in Alcator C-Mod. The gyrokinetic simulation is carried out in a local, field line following flux-tube, while PCI measures density fluctuations along 32 chords passing vertically through the plasma cross-section.^2 Transforming from Clebsch to cartesian coordinates, and integrating appropriately over portions of the flux tube viewed by the diagnostic, yields a density fluctuation spectrum versus wavenumber kR in the major radius direction. To achieve vertical localization, we examine an ITB case in which the spectrum is dominated by a strong trapped electron mode, localized near the half-radius. The wavelength spectrum from the simulations, using the synthetic diagnostic, closely reproduces the PCI spectrum. Contributions from kψ, where B=∇αx∇ψ, downshift the GS2 kα spectrum to improve upon our previous raw comparison with the PCI kR spectrum.^3 ^1A. Long, D. R. Ernst et al., Bull. Am. Phys. Soc. 50(8) p. 153, GP1.48, also p. 235, LP1.37 http://www.psfc.mit.edu/research/alcator/pubs/APS/APS2005/ernst.pdf. ^2N. P. Basse et al., Phys. Plasmas 12, 052512 (2005). ^3D. R. Ernst et al., 2004 IAEA Fusion Energy Conference, IAEA-CN116/TH/4-1 http://www-naweb.iaea.org/napc/physics/fec/fec2004/datasets/TH4-1.html, see also Phys. Plasmas 11 (2004) 2637.

  18. Mixed directional false discovery rate control in multiple pairwise comparisons using weighted p-values.

    PubMed

    Zhao, Haibing; Peddada, Shyamal D; Cui, Xinping

    2015-01-01

    In many applications, researchers are interested in making q pairwise comparisons among k test groups on the basis of m outcome variables. Often, m is very large. For example, such situations arise in gene expression microarray studies involving several experimental groups. Researchers are often not only interested in identifying differentially expressed genes between a given pair of experimental groups, but are also interested in making directional inferences such as whether a gene is up- or downregulated in one treatment group relative to another. In such situations, in addition to the usual errors such as false positive (Type I error) and false negative (Type II error), one may commit directional error (Type III error). For example, in a dose response microarray study, a gene may be declared to be upregulated in the high dose group compared to the low dose group when it is not. In this paper, we introduce a mixed directional false discovery rate (mdFDR) controlling procedure using weighted p-values to select positives in different directions. The weights are defined as the inverse of two times the proportion of either positive or negative discoveries. The proposed procedure has been proved mathematically to control the mdFDR at level α and to have a larger power (which is defined as the expected proportion of nontrue null hypotheses) than the GSP10 procedure proposed by Guo et al. (2010). Simulation studies and real data analysis are also conducted to show the outperformance of the proposed procedure than the GSP10 procedure. PMID:25410394

  19. Direct Comparison of the X-Ray Emission and Absorption of Cerium Oxide

    SciTech Connect

    Tobin, J G; Yu, S W; Chung, B W; Waddill, G D; Denlinger, J D

    2010-11-24

    Bremstrahlung Isochromat Spectroscopy (BIS). The XES spectra were collected using a Specs electron gun for the excitation and the XES 350 grating monochromator and channel plate system from Scienta as the photon detection. Spectra were collected in 'normal mode,' where the electron gun kinetic energy (KE) and the energy position of the center of the channel plate were both fixed and the energy distribution in the photon (hv) spectrum was derived from the intensities distributed across the channel plate detector in the energy dispersal direction. The polycrystalline Ce sample was oxidized by exposure to air at ambient pressures. After introduction to the ultra-high vacuum system, the oxidized sample was bombarded with Ar, to clean the topmost surface region and stabilize the surface and near surface regions. Although CeO{sub 2} would be the thermodynamically preferred composition in an oxygen rich environment, the combination of a vacuum environment and ion etching may have driven the near surface region into a Ce{sub 2}O{sub 3} stoichiometry. XES data collection occurred with the sample at or near room temperature. The base pressure of the system was 3 x 10{sup -10} torr, but the pressure changed depending the energy and current of the electron gun. For example, with the XES measurements at KE = 3KeV, the pressure was approximately 8 to 9 x 10{sup -10} torr and the excitation current to the sample was typically 0.01 mA. More detail of the sample preparation and analysis can be found in Reference 1. The XAS experiments were performed at Beamline 8 of the Advance Light Source, as part of a larger collaboration. The ex situ sample used at the ALS was prepared in a fashion similar to that described above. X-ray Emission Spectroscopy (XES) and X-ray Absorption Spectroscopy (XAS), have been used to investigate the photon emission and absorption associated with the Ce3d{sub 5/2} and Ce3d{sub 3/2} core-levels in CeOxide. A comparison of the two processes and their spectra

  20. 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

  1. 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. PMID:25968497

  2. 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. PMID:26876987

  3. 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

  4. Status and solidarity in social comparison: agentic and communal values and vertical and horizontal directions.

    PubMed

    Locke, Kenneth D

    2003-03-01

    Social comparison involves positioning the self relative to others on a vertical or status dimension (ranging from upward to downward comparisons) and a horizontal or solidarity dimension (ranging from contrastive to connective comparisons). Across 3 studies in which 389 undergraduates recorded everyday social comparisons (n = 4,417), downward and connective comparisons were rated as more helpful and mood enhancing than upward and contrastive comparisons. The effects of horizontal comparisons were greater for people for whom solidarity was an important value; however, the effects of vertical comparisons were not greater for people who valued status. The roles of the comparison target, topic, and situation were also explored; for example, noticing undesirable features of the target enhanced status but undermined solidarity. PMID:12635921

  5. 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

  6. Comparison of model estimated and measured direct-normal solar irradiance

    SciTech Connect

    Halthore, R.N.; Schwartz, S.E.; Michalsky, J.J.; Anderson, G.P.; Holben, B.N.; Ten Brink, H.M.

    1997-12-01

    Direct-normal solar irradiance (DNSI), the energy in the solar spectrum incident in unit time at the Earth{close_quote}s surface on a unit area perpendicular to the direction to the Sun, depends only on atmospheric extinction of solar energy without regard to the details of the extinction, whether absorption or scattering. Here we report a set of closure experiments performed in north central Oklahoma in April 1996 under cloud-free conditions, wherein measured atmospheric composition and aerosol optical thickness are input to a radiative transfer model, MODTRAN 3, to estimate DNSI, which is then compared with measured values obtained with normal incidence pyrheliometers and absolute cavity radiometers. Uncertainty in aerosol optical thickness (AOT) dominates the uncertainty in DNSI calculation. AOT measured by an independently calibrated Sun photometer and a rotating shadow-band radiometer agree to within the uncertainties of each measurement. For 36 independent comparisons the agreement between measured and model-estimated values of DNSI falls within the combined uncertainties in the measurement (0.3{endash}0.7{percent}) and model calculation (1.8{percent}), albeit with a slight average model underestimate ({minus}0.18{plus_minus}0.94){percent}; for a DNSI of 839Wm{sup {minus}2} this corresponds to {minus}1.5{plus_minus}7.9Wm{sup {minus}2}. The agreement is nearly independent of air mass and water-vapor path abundance. These results thus establish the accuracy of the current knowledge of the solar spectrum, its integrated power, and the atmospheric extinction as a function of wavelength as represented in MODTRAN 3. An important consequence is that atmospheric absorption of short-wave energy is accurately parametrized in the model to within the above uncertainties. {copyright} 1997 American Geophysical Union

  7. 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.

  8. Comparison of Direct and Array-Derived Strain and Rotation at the Pinon Flat Observatory, California

    NASA Astrophysics Data System (ADS)

    Lin, Chin-Jen; Vernon, Frank; Wassermann, Joachim; Gebauer, André; Schreiber, Ulrich; Carr Agnew, Duncan; Igel, Heiner

    2016-04-01

    To fully understand the wave motion of a deformable body, we need 12 components in total: 3 components of translation, 3 components of rotation, and 6 components of strain. Translation are routinely recorded in the seismology community. Strain measurements are rare and do not routinely enter the inversion procedures for structure and source from seismic observations. Single-component rotational ground motions have been measured just recently. In principle, strains and rotations can be derived from an array of seismic stations, under uniform strain assumption across the array. In a unique instrument setting at the PFO (Pinon Flat Observatory, California), a dense small-aperture seismic array is in the vicinity of a sensor measuring rotations around a vertical axis (ring laser) and three horizontal strain meters. This enables us to compare array derived strain/rotation with observations for 10/12 components of complete ground motion. We show the comparison results between array-derived ground motion and direct observation for tele-seismic events. Several possible errors like tilt couplings, array size, seismometer noise are discussed.

  9. Comparisons of direct extraction methods of microbial DNA from different paddy soils.

    PubMed

    Islam, Md Rashedul; Sultana, Tahera; Melvin Joe, M; Cho, Jang-Cheon; Sa, Tongmin

    2012-07-01

    Molecular analyses for the study of soil microbial communities often depend on the direct extraction of DNA from soils. The present work compares the effectiveness of three different methods of extracting microbial DNA from seven different paddy soils. Comparison among different DNA extraction methods against different paddy soil samples revealed a marked variation in DNA yields from 3.18-20.17 μg DNA/g of dry soil. However, irrespective of the soil samples and extraction methods the DNA fragment size was >10 kb. Among the methods evaluated, method-C (chemical-enzymatic-mechanical) had better cell lysis efficiency and DNA yield. After purification of crude DNA by Purification Kit, A260/A230 and A260/A280 ratios of the DNA obtained by method-C reached up to 2.27 and 1.89, respectively, sustaining the efficacy of this technique in removing humic acid, protein and other contaminants. Results of the comprehensive evaluation of DNA extraction methods suggest that method-C is superior to other two methods (chemical-enzymatic and chemical-mechanical), and was the best choice for extraction of total DNA from soil samples. Since soil type and microbial community characteristics influence DNA recovery, this study provides guidance for choosing appropriate extraction and purification methods according to experimental goals. PMID:23961194

  10. 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. PMID:22712924

  11. 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.

  12. A direct comparison of scan and focal sampling methods for measuring wild chimpanzee feeding behaviour.

    PubMed

    Gilby, Ian C; Pokempner, Amy A; Wrangham, Richard W

    2010-01-01

    Focal sampling is the most accurate method for measuring primate activity budgets but is sometimes impractical. An alternative is scan sampling, in which the behaviour of the group is recorded at regular intervals. The simplest technique is to record whether at least 1 animal is engaged in the behaviour of interest. By direct comparison with focal data collected simultaneously on the same population, we assess the validity of this simple group level sampling method for studying chimpanzee (Pan troglodytes schweinfurthii) feeding behaviour. In a 13-month study at Kanyawara, Kibale National Park, Uganda, group level scan sampling provided statistically similar measures of broad diet composition to those produced by focal data, despite considerable seasonal variation. Monthly means of the percentage of time spent consuming non-fig fruit calculated from group level scan sampling were highly correlated with those from focal sampling. This validates previous methodology used to identify periods of high energy availability. However, group level scans tended to overestimate the percentage of observation time spent feeding, particularly for adult males. We conclude that this method of group level scan sampling provides valuable data for characterizing broad diet choice in chimpanzees and other species, but may be of limited use for estimating individual feeding time. PMID:21196752

  13. Up or down? Reading direction influences vertical counting direction in the horizontal plane – a cross-cultural comparison

    PubMed Central

    Göbel, Silke M.

    2015-01-01

    Most adults and children in cultures where reading text progresses from left to right also count objects from the left to the right side of space. The reverse is found in cultures with a right-to-left reading direction. The current set of experiments investigated whether vertical counting in the horizontal plane is also influenced by reading direction. Participants were either from a left-to-right reading culture (UK) or from a mixed (left-to-right and top-to-bottom) reading culture (Hong Kong). In Experiment 1, native English-speaking children and adults and native Cantonese-speaking children and adults performed three object counting tasks. Objects were presented flat on a table in a horizontal, vertical, and square display. Independent of culture, the horizontal array was mostly counted from left to right. While the majority of English-speaking children counted the vertical display from bottom to top, the majority of the Cantonese-speaking children as well as both Cantonese- and English-speaking adults counted the vertical display from top to bottom. This pattern was replicated in the counting pattern for squares: all groups except the English-speaking children started counting with the top left coin. In Experiment 2, Cantonese-speaking adults counted a square array of objects after they read a text presented to them either in left-to-right or in top-to-bottom reading direction. Most Cantonese-speaking adults started counting the array by moving horizontally from left to right. However, significantly more Cantonese-speaking adults started counting with a top-to-bottom movement after reading the text presented in a top-to-bottom reading direction than in a left-to-right reading direction. Our results show clearly that vertical counting in the horizontal plane is influenced by longstanding as well as more recent experience of reading direction. PMID:25852583

  14. Up or down? Reading direction influences vertical counting direction in the horizontal plane - a cross-cultural comparison.

    PubMed

    Göbel, Silke M

    2015-01-01

    Most adults and children in cultures where reading text progresses from left to right also count objects from the left to the right side of space. The reverse is found in cultures with a right-to-left reading direction. The current set of experiments investigated whether vertical counting in the horizontal plane is also influenced by reading direction. Participants were either from a left-to-right reading culture (UK) or from a mixed (left-to-right and top-to-bottom) reading culture (Hong Kong). In Experiment 1, native English-speaking children and adults and native Cantonese-speaking children and adults performed three object counting tasks. Objects were presented flat on a table in a horizontal, vertical, and square display. Independent of culture, the horizontal array was mostly counted from left to right. While the majority of English-speaking children counted the vertical display from bottom to top, the majority of the Cantonese-speaking children as well as both Cantonese- and English-speaking adults counted the vertical display from top to bottom. This pattern was replicated in the counting pattern for squares: all groups except the English-speaking children started counting with the top left coin. In Experiment 2, Cantonese-speaking adults counted a square array of objects after they read a text presented to them either in left-to-right or in top-to-bottom reading direction. Most Cantonese-speaking adults started counting the array by moving horizontally from left to right. However, significantly more Cantonese-speaking adults started counting with a top-to-bottom movement after reading the text presented in a top-to-bottom reading direction than in a left-to-right reading direction. Our results show clearly that vertical counting in the horizontal plane is influenced by longstanding as well as more recent experience of reading direction. PMID:25852583

  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. 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…

  17. Comparison of Traditional Phenotypic Identification Methods with Partial 5′ 16S rRNA Gene Sequencing for Species-Level Identification of Nonfermenting Gram-Negative Bacilli▿

    PubMed Central

    Cloud, Joann L.; Harmsen, Dag; Iwen, Peter C.; Dunn, James J.; Hall, Gerri; LaSala, Paul Rocco; Hoggan, Karen; Wilson, Deborah; Woods, Gail L.; Mellmann, Alexander

    2010-01-01

    Correct identification of nonfermenting Gram-negative bacilli (NFB) is crucial for patient management. We compared phenotypic identifications of 96 clinical NFB isolates with identifications obtained by 5′ 16S rRNA gene sequencing. Sequencing identified 88 isolates (91.7%) with >99% similarity to a sequence from the assigned species; 61.5% of sequencing results were concordant with phenotypic results, indicating the usability of sequencing to identify NFB. PMID:20164273

  18. Mode-specific tunneling splittings in 9-hydroxyphenalenone: Comparison of two methods for direct tunneling dynamics

    NASA Astrophysics Data System (ADS)

    Fernández-Ramos, Antonio; Smedarchina, Zorka; Zgierski, Marek Z.; Siebrand, Willem

    1998-07-01

    A benchmark comparison is presented of two direct dynamics methods for proton tunneling, namely variational transition-state theory with semiclassical tunneling corrections (VTST/ST) and the instanton method. The molecules chosen for the comparison are 9-hydroxyphenalenone-d0 and -d1, which have 64 vibrational degrees of freedom and show large tunneling splittings for the zero-point level and several vibrationally excited levels of the electronic ground state. Some of the excited-level splittings are larger and some smaller than the zero-level splitting, illustrating the multidimensional nature of the tunneling. Ab initio structure and force field calculations at the Hartree-Fock/6-31G** level are carried out for the two stationary points of the tunneling potential, viz. the equilibrium configuration and the transition state. The VTST/ST calculations are based on both the small- and the large-curvature approximation; the additional quantum-chemical calculations required at intermediate points of the potential are performed at the semiempirical modified neglect of differential overlap (MNDO)/H2 level. The VTST/ST computations use the MORATE 6.5 code developed by Truhlar and co-workers. The instanton dynamics calculations are based on the method we previously developed and applied to tropolone, among others. It uses the transition state rather than the equilibrium configuration as reference structure and approximates the least action analytically. The computations use our "dynamics of instanton tunneling" (DOIT) code. It is found that the large-curvature approximation and the instanton method both reproduce the observed zero-level splitting of the d0 isotopomer if the calculated barrier is reduced by a factor 0.87. With this adjusted barrier, the instanton method also reproduces the zero-level and excited-level splittings of the d1 isotopomer. However, both the small- and the large-curvature approximations severely underestimate all these splittings. These methods

  19. In Nicotiana species, an artificial microRNA corresponding to the virulence modulating region of Potato spindle tuber viroid directs RNA silencing of a soluble inorganic pyrophosphatase gene and the development of abnormal phenotypes.

    PubMed

    Eamens, Andrew L; Smith, Neil A; Dennis, Elizabeth S; Wassenegger, Michael; Wang, Ming-Bo

    2014-02-01

    Potato spindle tuber viroid (PSTVd) is a small non-protein-coding RNA pathogen that can induce disease symptoms in a variety of plant species. How PSTVd induces disease symptoms is a long standing question. It has been suggested that PSTVd-derived small RNAs (sRNAs) could direct RNA silencing of a targeted host gene(s) resulting in symptom development. To test this, we expressed PSTVd sequences as artificial microRNAs (amiRNAs) in Nicotiana tabacum and Nicotiana benthamiana. One amiRNA, amiR46 that corresponds to sequences within the PSTVd virulence modulating region (VMR), induced abnormal phenotypes in both Nicotiana species that closely resemble those displayed by PSTVd infected plants. In N. tabacum amiR46 plants, phenotype severity correlated with amiR46 accumulation and expression down-regulation of the bioinformatically-identified target gene, a Nicotiana soluble inorganic pyrophosphatase (siPPase). Taken together, our phenotypic and molecular analyses suggest that disease symptom development in Nicotiana species following PSTVd infection results from sRNA-directed RNA silencing of the host gene, siPPase. PMID:24503090

  20. 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

  1. Three-Dimensional Stereoscopic Tracking Velocimetry and Experimental/Numerical Comparison of Directional Solidification

    NASA Technical Reports Server (NTRS)

    Lee, David; Ge, Yi; Cha, Soyoung Stephen; Ramachandran, Narayanan; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Measurement of three-dimensional (3-D) three-component velocity fields is of great importance in both ground and space experiments for understanding materials processing and fluid physics. The experiments in these fields most likely inhibit the application of conventional planar probes for observing 3-D phenomena. Here, we present the investigation results of stereoscopic tracking velocimetry (STV) for measuring 3-D velocity fields, which include diagnostic technology development, experimental velocity measurement, and comparison with analytical and numerical computation. STV is advantageous in system simplicity for building compact hardware and in software efficiency for continual near-real-time monitoring. It has great freedom in illuminating and observing volumetric fields from arbitrary directions. STV is based on stereoscopic observation of particles-Seeded in a flow by CCD sensors. In the approach, part of the individual particle images that provide data points is likely to be lost or cause errors when their images overlap and crisscross each other especially under a high particle density. In order to maximize the valid recovery of data points, neural networks are implemented for these two important processes. For the step of particle overlap decomposition, the back propagation neural network is utilized because of its ability in pattern recognition with pertinent particle image feature parameters. For the step of particle tracking, the Hopfield neural network is employed to find appropriate particle tracks based on global optimization. Our investigation indicates that the neural networks are very efficient and useful for stereoscopically tracking particles. As an initial assessment of the diagnostic technology performance, laminar water jets with and without pulsation are measured. The jet tip velocity profiles are in good agreement with analytical predictions. Finally, for testing in material processing applications, a simple directional solidification

  2. Direct comparison of regulators of calcification between bone and vessels in humans.

    PubMed

    Schweighofer, N; Aigelsreiter, A; Trummer, O; Graf-Rechberger, M; Hacker, N; Kniepeiss, D; Wagner, D; Stiegler, P; Trummer, C; Pieber, T; Obermayer-Pietsch, B; Müller, H

    2016-07-01

    Calcification is not only physiologically present in bone but is a main pathophysiological process in vasculature, favouring cardiovascular diseases. Our aim was to investigate changes in the expression of calcification regulators during vascular calcification in bone and vasculature. Levels of gene expression of osteoprotegerin (OPG), receptor activator of NF-κB ligand (RANKL), osteopontin (OPN), matrix gla protein (MGP), bone sialoprotein (BSP), SMAD6, and runt-related transcription factor 2 (RUNX2) were determined in bone, aorta, and external iliac artery tissue samples of transplant donors. Histological stages of atherosclerosis (AS) in vessels are defined as "no changes", "intima thickening", or "intima calcification". Patients' bone samples were subgrouped accordingly. We demonstrate that in vessels BSP and OPN expression significantly increased during intima thickening and decreased during intima calcification, whereas the expression of regulators of calcification did not significantly change in bone during intima thickening and intima calcification. At the stage of intima thickening, MGP, OPG, and SMAD6 expression and at stage of intima calcification only MGP expression was lower in bone than in vessel. The expression of BSP and RANKL was regulated in opposite ways in bone and vessels, whereas the expression of MGP, OC, RUNX2, and OPN was regulated in a tissue-specific manner. Our study is the first direct comparison of gene expression changes during AS progression in bone and vessels. Our results indicate that changes in the expression of regulators of calcification in the vessel wall as well as in bone occur early in the calcification process, even prior to deposition of calcium/phosphate precipitation. PMID:27108945

  3. 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.

  4. Angiotensin II receptor blockade in normotensive subjects: A direct comparison of three AT1 receptor antagonists.

    PubMed

    Mazzolai, L; Maillard, M; Rossat, J; Nussberger, J; Brunner, H R; Burnier, M

    1999-03-01

    Use of angiotensin (Ang) II AT1 receptor antagonists for treatment of hypertension is rapidly increasing, yet direct comparisons of the relative efficacy of antagonists to block the renin-angiotensin system in humans are lacking. In this study, the Ang II receptor blockade induced by the recommended starting dose of 3 antagonists was evaluated in normotensive subjects in a double-blind, placebo-controlled, randomized, 4-way crossover study. At 1-week intervals, 12 subjects received a single dose of losartan (50 mg), valsartan (80 mg), irbesartan (150 mg), or placebo. Blockade of the renin-angiotensin system was assessed before and 4, 24, and 30 hours after drug intake by 3 independent methods: inhibition of the blood pressure response to exogenous Ang II, in vitro Ang II receptor assay, and reactive changes in plasma Ang II levels. At 4 hours, losartan blocked 43% of the Ang II-induced systolic blood pressure increase; valsartan, 51%; and irbesartan, 88% (P<0.01 between drugs). The effect of each drug declined with time. At 24 hours, a residual effect was found with all 3 drugs, but at 30 hours, only irbesartan induced a marked, significant blockade versus placebo. Similar results were obtained when Ang II receptor blockade was assessed with an in vitro receptor assay and by the reactive rise in plasma Ang II levels. This study thus demonstrates that the first administration of the recommended starting dose of irbesartan induces a greater and longer lasting Ang II receptor blockade than that of valsartan and losartan in normotensive subjects. PMID:10082498

  5. Microstructure of ambient and supercritical water. Direct comparison between simulation and neutron scattering experiments

    SciTech Connect

    Chialvo, A.A.; Cummings, P.T. |

    1996-01-25

    Molecular dynamics simulations of SPC, SPC/E, TIP4P, and ST2 water models are performed at ambient and two supercritical conditions make a direct comparison with recent microstructural data obtained by neutron diffraction with isotopic substitution (NDIS) experiments. The models generally fail to accurately predict details of the NDIS results at supercritical conditions, even though they are somewhat successful at ambient conditions. The failure is not as pronounced as that expected by Postorino et al. because of an unusual density dependence in the structure predicted by two of the models. We also evaluate a model for supercritical water denoted SPCG, a modification of the SPC and SPC/E models, in which the dipole moment is reduced to the bare dipole moment of water. For this model, the predicted structure at supercritical conditions is in much better agreement with experiment. A geometric definition of hydrogen bonding is used to gain insight into the angular dependence of the H...O pair distribution function g{sub OH}(r,{omega}). The simulation results for the five models indicate a strong orientational dependence for the g{sub OH}(r,{omega}) along the H-bonding orientations, with an approximately constant relative strength from ambient to supercritical conditions, suggesting that the angle-averaged radial distribution function, g{sub OH}(r), and its volume integral over the first solvation shell, n{sub OH}(r), may not in themselves be good measures of the strength of the H-bonding. 46 refs., 15 figs., 2 tabs.

  6. 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.

  7. 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…

  8. Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.

    PubMed

    Abelin, Jennifer G; Patel, Jinal; Lu, Xiaodong; Feeney, Caitlin M; Fagbami, Lola; Creech, Amanda L; Hu, Roger; Lam, Daniel; Davison, Desiree; Pino, Lindsay; Qiao, Jana W; Kuhn, Eric; Officer, Adam; Li, Jianxue; Abbatiello, Susan; Subramanian, Aravind; Sidman, Richard; Snyder, Evan; Carr, Steven A; Jaffe, Jacob D

    2016-05-01

    Profiling post-translational modifications represents an alternative dimension to gene expression data in characterizing cellular processes. Many cellular responses to drugs are mediated by changes in cellular phosphosignaling. We sought to develop a common platform on which phosphosignaling responses could be profiled across thousands of samples, and created a targeted MS assay that profiles a reduced-representation set of phosphopeptides that we show to be strong indicators of responses to chemical perturbagens.To develop the assay, we investigated the coordinate regulation of phosphosites in samples derived from three cell lines treated with 26 different bioactive small molecules. Phosphopeptide analytes were selected from these discovery studies by clustering and picking 1 to 2 proxy members from each cluster. A quantitative, targeted parallel reaction monitoring assay was developed to directly measure 96 reduced-representation probes. Sample processing for proteolytic digestion, protein quantification, peptide desalting, and phosphopeptide enrichment have been fully automated, making possible the simultaneous processing of 96 samples in only 3 days, with a plate phosphopeptide enrichment variance of 12%. This highly reproducible process allowed ∼95% of the reduced-representation phosphopeptide probes to be detected in ∼200 samples.The performance of the assay was evaluated by measuring the probes in new samples generated under treatment conditions from discovery experiments, recapitulating the observations of deeper experiments using a fraction of the analytical effort. We measured these probes in new experiments varying the treatments, cell types, and timepoints to demonstrate generalizability. We demonstrated that the assay is sensitive to disruptions in common signaling pathways (e.g. MAPK, PI3K/mTOR, and CDK). The high-throughput, reduced-representation phosphoproteomics assay provides a platform for the comparison of perturbations across a range of

  9. Comparison of demographic and direct methods to calculate probabilistic maturation reaction norms for Flemish Cap cod (Gadus morhua)

    PubMed Central

    Pérez-Rodríguez, Alfonso; Morgan, Marie Joanne; Saborido-Rey, Fran

    2009-01-01

    Age and length at maturation have declined in many fish populations and this has been hypothesized to be a genetic change caused by high fishing mortality. Probabilistic Maturation Reaction Norms (PMRNs) have been used as a tool to gain a better understanding of the possible genetic nature of these changes. The demographic and direct methods are two ways to calculate PMRNs. The data requirements are more often met for the demographic method than for the direct method which requires the identification of recruit spawners. However, the demographic method relies on more assumptions than the direct method, typically assuming equality of growth and mortality rates for immature and mature individuals within an age class. This study provides the first direct comparison of demographic and direct methods and shows that both methods produce comparable results. Differences between methods are hypothesized to be owed to possible differences in growth rate between mature and immature individuals in Flemish Cap cod. PMID:25567881

  10. Pheno-Pub: a total support system for the publication of mouse phenotypic data on the web.

    PubMed

    Suzuki, Tomohiro; Furuse, Tamio; Yamada, Ikuko; Motegi, Hiromi; Kozawa, Yasuyo; Masuya, Hiroshi; Wakana, Shigeharu

    2013-12-01

    We have developed an open-source database system named "Pheno-Pub" to support a series of data-handling and publication tasks, including statistical analyses, data review, and web site construction, for mouse phenotyping experiments. This system is composed of three applications. "Mou-Stat" provides semiautomatic statistical analyses for a batch of phenotypic data, including a variety of conditions for group comparisons (e.g., different scales of measurement parameters). "Genotype Viewer" and "Strain Viewer" provide representation of genotype-driven and measurement parameter-driven views of phenotypic data; they highlight significant differences in genotypes and between strains, respectively. Direct links from the Strain Viewer web site to the Genotype Viewer web site provide flexible navigation in the exploration of phenotypic data. With these publication tools, phenotypic data can be made available on the Internet by simple operations. This system is expandable for a wide range of uses in phenotypic comparative analyses, including comparisons among different genotypes and strains and comparisons among groups exposed to different environmental conditions. Finally, Pheno-Pub provides advanced usability for both producers of experimental data and consumers of phenotypic information. Therefore, Pheno-Pub contributes significantly to the publication of data in various fields of phenotyping research and to broad data sharing, thereby promoting the understanding of the functions of the entire mouse genome. PMID:24220852

  11. Direct comparison of different stem cell types and subpopulations reveals superior paracrine potency and myocardial repair efficacy with cardiosphere-derived cells

    PubMed Central

    Li, Tao-Sheng; Cheng, Ke; Malliaras, Konstantinos; Smith, Rachel Ruckdeschel; Zhang, Yiqiang; Sun, Baiming; Matsushita, Noriko; Blusztajn, Agnieszka; Terrovitis, John; Kusuoka, Hideo; Marbán, Linda; Marbán, Eduardo

    2012-01-01

    Objectives To conduct a direct head-to-head comparison of different stem cell types in vitro for various assays of potency, and in vivo for functional myocardial repair in the same mouse model of myocardial infarction. Background Adult stem cells of diverse origins (e.g., bone marrow, fat, heart) and antigenic identity have been studied for repair of the damaged heart, but the relative utility of the various cell types remains unclear. Methods Human cardiosphere-derived stem cells (CDCs), bone marrow-derived mesenchymal stem cells (BM-MSCs), adipose tissue-derived mesenchymal stem cells (AD-MSCs), and bone marrow mononuclear cells (BM-MNCs) were compared. Results CDCs revealed a distinctive phenotype with uniform expression of CD105, partial expression of c-kit and CD90, and negligible expression of hematopoietic markers. In vitro, CDCs showed the greatest myogenic differentiation potency, highest angiogenic potential, and relatively high production of various angiogenic and anti-apoptotic secreted factors. In vivo, injection of CDCs into the infarcted mouse hearts resulted in superior improvement of cardiac function, the highest cell engraftment and myogenic differentiation rates, and the least-abnormal heart morphology 3 weeks after treatment. CDC-treated hearts also exhibited the lowest number of apoptotic cells. The c-kit+ subpopulation purified from CDCs produced lower levels of paracrine factors and inferior functional benefit when compared to unsorted CDCs. To validate the comparison of cells from various human donors, selected results were confirmed in cells of different types derived from individual rats. Conclusions CDCs exhibit a balanced profile of paracrine factor production, and, among various comparator cell types/subpopulations, provide the greatest functional benefit in experimental myocardial infarction. PMID:22381431

  12. 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...

  13. 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...

  14. 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.

  15. Comparison of catalysts for direct transesterification of fatty acids in freeze-dried forage samples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Preparation of fatty acid methyl esters from forages comparing BF3 in CH3OH to HCl in CH3OH as a catalyst in single-step direct transesterification has not been reported. Our objective was to compare 1.09 M methanolic HCl to 7% BF3 in CH3OH as catalysts for direct transesterification of fatty acids ...

  16. 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.

  17. Comparison of deconvolution techniques to measure directional MTF of FDK reconstruction

    NASA Astrophysics Data System (ADS)

    Lee, Changwoo; Park, Junhan; Ko, Youngjun; Baek, Jongduk

    2014-03-01

    To measure a spatial resolution of CT scanner, several methods have been developed using bar pattern, wires and thin plates. While these approaches are effective to measure two dimensional MTF, it is not easy to measure directional MTF using those phantoms. To overcome these limitations, Thornton et al. proposed a method to measure directional MTF using sphere phantoms, which is effective only when the cone angle is small. Recently, Baek et al. developed a method to estimate the directional MTF even with a larger cone angle, but the proposed method was analyzed using a noiseless data set. In this work, we present Wiener and Richardson-Lucy deconvolution techniques to estimate the directional MTF, and compare the estimation performance with that of the previous methods (i.e., Thornton's and Baek's methods). To estimate directional MTF, we reconstructed a sphere object centered at (0.01 cm, 0.01 cm, 10.01 cm) using FDK algorithm, and then calculated plane integrals of the reconstructed sphere object and the ideal sphere object. The plane integrals of sphere objects were used to estimate the directional MTF using Wiener and Richardson-Lucy deconvolution techniques. The estimated directional MTF was compared with the ideal MTF calculated from a point object, and showed an excellent agreement.

  18. Belief propagation in genotype-phenotype networks.

    PubMed

    Moharil, Janhavi; May, Paul; Gaile, Daniel P; Blair, Rachael Hageman

    2016-03-01

    Graphical models have proven to be a valuable tool for connecting genotypes and phenotypes. Structural learning of phenotype-genotype networks has received considerable attention in the post-genome era. In recent years, a dozen different methods have emerged for network inference, which leverage natural variation that arises in certain genetic populations. The structure of the network itself can be used to form hypotheses based on the inferred direct and indirect network relationships, but represents a premature endpoint to the graphical analyses. In this work, we extend this endpoint. We examine the unexplored problem of perturbing a given network structure, and quantifying the system-wide effects on the network in a node-wise manner. The perturbation is achieved through the setting of values of phenotype node(s), which may reflect an inhibition or activation, and propagating this information through the entire network. We leverage belief propagation methods in Conditional Gaussian Bayesian Networks (CG-BNs), in order to absorb and propagate phenotypic evidence through the network. We show that the modeling assumptions adopted for genotype-phenotype networks represent an important sub-class of CG-BNs, which possess properties that ensure exact inference in the propagation scheme. The system-wide effects of the perturbation are quantified in a node-wise manner through the comparison of perturbed and unperturbed marginal distributions using a symmetric Kullback-Leibler divergence. Applications to kidney and skin cancer expression quantitative trait loci (eQTL) data from different mus musculus populations are presented. System-wide effects in the network were predicted and visualized across a spectrum of evidence. Sub-pathways and regions of the network responded in concert, suggesting co-regulation and coordination throughout the network in response to phenotypic changes. We demonstrate how these predicted system-wide effects can be examined in connection with

  19. 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. PMID:22406841

  20. Comparison of indirect and direct blood pressure monitoring in normotensive swine.

    PubMed

    Gladczak, A K; Shires, P K; Stevens, K A; Clymer, J W

    2013-10-01

    The gold standard for blood pressure measurement in pigs is direct monitoring of arterial pressure, but this is an invasive technique adding complexity to surgical procedures. We sought to compare direct measurements obtained via catheterization to more easily-obtained indirect measurements using a sphygmomanometer with an automated cuff. Simultaneous measurements via an arterial pressure transducer and a child-size cuff were performed in pigs undergoing abdominal surgical procedures under normotensive conditions. Correlation between direct and indirect measurements was good (r=0.881). Systolic blood pressures for the cuff were higher than those for arterial measurements, while diastolic pressures were lower for the cuff than arterial. A Bland-Altman analysis confirmed this bias at the extremes of the normotensive range. For highly accurate readings, especially under stressed conditions, direct arterial catheterization remains the preferred method of measuring blood pressure. When monitoring surgical procedures, the more convenient blood pressure cuff can provide reliable measurements. PMID:23790711

  1. Simulation-based comparison of noise effects in wavelength modulation spectroscopy and direct absorption TDLAS

    NASA Astrophysics Data System (ADS)

    Lins, B.; Zinn, P.; Engelbrecht, R.; Schmauss, B.

    2010-08-01

    A simulative investigation of noise effects in wavelength modulation spectroscopy (WMS) and direct absorption diode laser absorption spectroscopy is presented. Special attention is paid to the impact of quantization noise of the analog-to-digital conversion (ADC) of the photodetector signal in the two detection schemes with the goal of estimating the necessary ADC resolution for each technique. With laser relative intensity noise (RIN), photodetector shot noise and thermal amplifier noise included, the strategies used for noise reduction in direct and wavelength modulation spectroscopy are compared by simulating two respective systems. Results show that because of the combined effects of dithering by RIN and signal averaging, the resolutions required for the direct absorption setup are only slightly higher than for the WMS setup. Only for small contributions of RIN an increase in resolution will significantly improve signal quality in the direct scheme.

  2. Comparison of the Spatial Limits on Direction Selectivity in Visual Areas MT and V1

    PubMed Central

    Priebe, Nicholas J.; Lisberger, Stephen G.

    2008-01-01

    We recorded responses to apparent motion from directionally selective neurons in primary visual cortex (V1) of anesthetized monkeys and middle temporal area (MT) of awake monkeys. Apparent motion consisted of multiple stationary stimulus flashes presented in sequence, characterized by their temporal separation (Δt) and spatial separation (Δx). Stimuli were 8° square patterns of 100% correlated random dots that moved at apparent speeds of 16 or 32°/s. For both V1 and MT, the difference between the response to the preferred and null directions declined with increasing flash separation. For each neuron, we estimated the maximum flash separation for which directionally selective responses were observed. For the range of speeds we used, Δx provided a better description of the limitation on directional responses than did Δt. When comparing MT and V1 neurons of similar preferred speed, there was no difference in the maximum Δx between our samples from the two areas. In both V1 and MT, the great majority of neurons had maximal values of Δx in the 0.25-1° range. Mean values were almost identical between the two areas. For most neurons, larger flash separations led to both weaker responses to the preferred direction and increased responses to the opposite direction. The former mechanism was slightly more dominant in MT and the latter slightly more dominant in V1. We conclude that V1 and MT neurons lose direction selectivity for similar values of Δx, supporting the hypothesis that basic direction selectivity in MT is inherited from V1, at least over the range of stimulus speeds represented by both areas. PMID:15483064

  3. 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.

  4. Depth-kymography of vocal fold vibrations: part II. Simulations and direct comparisons with 3D profile measurements

    NASA Astrophysics Data System (ADS)

    de Mul, Frits F. M.; George, Nibu A.; Qiu, Qingjun; Rakhorst, Gerhard; Schutte, Harm K.

    2009-07-01

    We report novel direct quantitative comparisons between 3D profiling measurements and simulations of human vocal fold vibrations. Until now, in human vocal folds research, only imaging in a horizontal plane was possible. However, for the investigation of several diseases, depth information is needed, especially when the two folds act differently, e.g. in the case of tumour growth. Recently, with our novel depth-kymographic laryngoscope, we obtained calibrated data about the horizontal and vertical positions of the visible surface of the vibrating vocal folds. In order to find relations with physical parameters such as elasticity and damping constants, we numerically simulated the horizontal and vertical positions and movements of the human vocal folds while vibrating and investigated the effect of varying several parameters on the characteristics of the phonation: the masses and their dimensions, the respective forces and pressures, and the details of the vocal tract compartments. Direct one-to-one comparison with measured 3D positions presents—for the first time—a direct means of validation of these calculations. This may start a new field in vocal folds research.

  5. Targeting the CD80/CD86 costimulatory pathway with CTLA4-Ig directs microglia toward a repair phenotype and promotes axonal outgrowth.

    PubMed

    Louveau, Antoine; Nerrière-Daguin, Véronique; Vanhove, Bernard; Naveilhan, Philippe; Neunlist, Michel; Nicot, Arnaud; Boudin, Hélène

    2015-12-01

    Among the costimulatory factors widely studied in the immune system is the CD28/cytotoxic T-lymphocyte antigen-4 (CTLA4)-CD80/CD86 pathway, which critically controls the nature and duration of the T-cell response. In the brain, up-regulated expression of CD80/CD86 during inflammation has consistently been reported in microglia. However, the role of CD80/CD86 molecules has mainly been studied in a context of microglia-T cell interactions in pathological conditions, while the function of CD80/CD86 in the regulation of intrinsic brain cells remains largely unknown. In this study, we used a transgenic pig line in which neurons express releasable CTLA4-Ig, a synthetic molecule mimicking CTLA4 and binding to CD80/CD86. The effects of CTLA4-Ig on brain cells were analyzed after intracerebral transplantation of CTLA4-Ig-expressing neurons or wild-type neurons as control. This model provided in vivo evidence that CTLA4-Ig stimulated axonal outgrowth, in correlation with a shift of the nearby microglia from a compact to a ramified morphology. In a culture system, we found that the CTLA4-Ig-induced morphological change of microglia was mediated through CD86, but not CD80. This was accompanied by microglial up-regulated expression of the anti-inflammatory molecule Arginase 1 and the neurotrophic factor BDNF, in an astrocyte-dependent manner through the purinergic P2Y1 receptor pathway. Our study identifies for the first time CD86 as a key player in the modulation of microglia phenotype and suggests that CTLA4-Ig-derived compounds might represent new tools to manipulate CNS microglia. PMID:26212105

  6. Metallothioneins 2 and 3 contribute to the metal-adapted phenotype but are not directly linked to Zn accumulation in the metal hyperaccumulator, Thlaspi caerulescens

    PubMed Central

    Hassinen, V. H.; Tuomainen, M.; Peräniemi, S.; Schat, H.; Kärenlampi, S. O.; Tervahauta, A. I.

    2009-01-01

    To study the role of metallothioneins (MTs) in Zn accumulation, the expression of TcMT2a, TcMT2b, and TcMT3 was analysed in three accessions and 15 F3 families of two inter-accession crosses of the Cd/Zn hyperaccumulator Thlaspi caerulescens, with different degrees of Zn accumulation. The highest expression levels were found in the shoots of a superior metal-accumulating calamine accession from St Laurent le Minier, with >10-fold TcMT3 expression compared with another calamine accession and a non-metallicolous accession. Moreover, F3 sibling lines from the inter-accession crosses that harboured the MT2a or MT3 allele from St Laurent le Minier had higher expression levels. However, there was no co-segregation of TcMT2a or TcMT3 expression and Zn accumulation. To examine the functions of TcMTs in plants, TcMT2a and TcMT3 were ectopically expressed in Arabidopsis. The transformant lines had reduced root length in control medium but not at high metal concentrations, suggesting that the ectopically expressed proteins interfered with the physiological availability of essential metals under limited supply. The Arabidopsis transformant lines did not show increased tolerance to Cd, Cu, or Zn, nor increased Cd or Zn accumulation. Immunohistochemical analysis indicated that in roots, MT2 protein is localized in the epidermis and root hairs of both T. caerulescens and Arabidopsis thaliana. The results suggest that TcMT2a, TcMT2b, and TcMT3 are not primarily involved in Zn accumulation as such. However, the elevated expression levels in the metallicolous accessions suggests that they do contribute to the metal-adapted phenotype, possibly through improving Cu homeostasis at high Zn and Cd body burdens. Alternatively, they might function as hypostatic enhancers of Zn or Cd tolerance. PMID:19033549

  7. 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

  8. An experimental comparison of detector performance for direct and indirect digital radiography systems.

    PubMed

    Samei, Ehsan; Flynn, Michael J

    2003-04-01

    Current flat-panel detectors either directly convert x-ray energy to electronic charge or use indirect conversion with an intermediate optical process. The purpose of this work was to compare direct and indirect detectors in terms of their modulation transfer function (MTF), noise power spectrum (NPS), and detective quantum efficiency (DQE). Measurements were made on three flat-panel detectors, Hologic Direct-Ray DR-1000 (DRC), GE Revolution XQ/i (XQ/i), and Philips Digital Diagnost (DiDi) using the IEC-defined RQA5 (approximately 74 kVp, 21 mm Al) and RQA9 (approximately 120 kVp, 40 mm Al) radiographic techniques. The presampled MTFs of the systems were measured using an edge method [Samei et al., Med. Phys. 25, 102 (1998)]. The NPS of the systems were determined for a range of exposure levels by two-dimensional (2D) Fourier analysis of uniformly exposed radiographs [Flynn and Samei, Med. Phys. 26, 1612 (1999)]. The DQEs were assessed from the measured MTF, NPS, exposure, and estimated ideal signal-to-noise ratios. For the direct system, the MTF was found to be significantly higher than that for the indirect systems and very close to an ideal function associated with the detector pixel size. The NPS for the direct system was found to be constant in relation to frequency. For the XQ/i and DRC systems, the DQE results reflected expected differences based on the absorption efficiency of the different detector materials. Using RQA5, the measured DQE values in the diagonal (and axial) direction(s) at spatial frequencies of 0.15 mm(-1) and 2.5 mm(-1) were 64% (64%) and 20% (15%) for the XQ/i system, and 38% (38%) and 20% (20%) for the DRC, respectively. The DQE results of the DiDi system were difficult to interpret due to additional preprocessing steps in that system. PMID:12722813

  9. 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.

  10. Field Comparison of Direct-Push Approaches for Determination of K-Profiles

    NASA Astrophysics Data System (ADS)

    Dietrich, P.; Butler, J. J.; Yaramanci, U.; Wittig, V.; Tiggelmann, L.; Schoofs, S.

    2003-12-01

    A large body of theoretical and experimental research has shown that spatial variations in hydraulic conductivity (K) are a significant factor in determining how groundwater and accompanying contaminants move in the subsurface. Therefore, a wide variety of direct and indirect techniques have been developed for the characterization of K variations at a site. Methods based on direct-push technology have much potential for use in shallow unconsolidated settings. However, the various direct-push methods differ in their expense, in terms of time, money, and effort, and the nature (qualitative vs. quantitative) of the information that they can provide. A field study was carried out at a test site near Nauen, Germany to evaluate and compare several direct-push methods for determination of spatial variations in K. The test site was established by the Department of Applied Geophysics of the Technical University of Berlin in collaboration with the German Federal Institute for Geosciences and Natural Resources. Extensive geophysical surface measurements (surface nuclear magnetic resonance, georadar, refraction seismic, and 2D dc geoelectrics), as well as data from a continuously cored borehole, are available. These data provide a controlled framework for the evaluation of different direct-push methods for the characterization of spatial variations in hydraulic conductivity. The following direct-push methods were investigated in this study: electrical conductivity (EC) and cone penetrometer (CPT) logging, slug tests, injection logging, and the direct-push permeameter (DPP). In addition, natural gamma (NG) logging was performed in pipe installed with direct-push technology. EC, CPT, and NG logging are very fast, but do not provide direct estimates of K. Their successful use for site characterization depends on the appropriateness of the applied empirical relationships. As shown by the results from Nauen, EC, CPT, and NG logging are often limited to the delineation of major

  11. 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

  12. COMPARISONS OF THE INTERSTELLAR MAGNETIC FIELD DIRECTIONS OBTAINED FROM THE IBEX RIBBON AND INTERSTELLAR POLARIZATIONS

    SciTech Connect

    Frisch, Priscilla C.; Andersson, B-G; Berdyugin, Andrei; Piirola, Vilppu; Funsten, Herbert O.; Magalhaes, Antonio M.; McComas, David J.; Schwadron, Nathan A.; Slavin, Jonathan D.; Wiktorowicz, Sloane J. E-mail: bgandersson@sofia.usra.ed E-mail: piirola@utu.f E-mail: mario@astro.iag.usp.b E-mail: nschwadron@guero.sr.unh.ed E-mail: sloane@berkeley.ed

    2010-12-01

    Variations in the spatial configuration of the interstellar magnetic field (ISMF) near the Sun can be constrained by comparing the ISMF direction at the heliosphere found from the Interstellar Boundary Explorer (IBEX) spacecraft observations of a 'Ribbon' of energetic neutral atoms (ENAs), with the ISMF direction derived from optical polarization data for stars within {approx}40 pc. Using interstellar polarization observations toward {approx}30 nearby stars within {approx}90{sup 0} of the heliosphere nose, we find that the best fits to the polarization position angles are obtained for a magnetic pole directed toward ecliptic coordinates of {lambda}, {beta} {approx} 263{sup 0}, 37{sup 0} (or galactic coordinates of l, b {approx} 38{sup 0}, 23{sup 0}), with uncertainties of {+-}35{sup 0} based on the broad minimum of the best fits and the range of data quality. This magnetic pole is 33{sup 0} from the magnetic pole that is defined by the center of the arc of the ENA Ribbon. The IBEX ENA ribbon is seen in sight lines that are perpendicular to the ISMF as it drapes over the heliosphere. The similarity of the polarization and Ribbon directions for the local ISMF suggests that the local field is coherent over scale sizes of tens of parsecs. The ISMF vector direction is nearly perpendicular to the flow of local interstellar material (ISM) through the local standard of rest, supporting a possible local ISM origin related to an evolved expanding magnetized shell. The local ISMF direction is found to have a curious geometry with respect to the cosmic microwave background dipole moment.

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

    PubMed

    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

  14. 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

  15. Teratogenic effects of triphenyltin on embryos of amphibian (Xenopus tropicalis): a phenotypic comparison with the retinoid X and retinoic acid receptor ligands.

    PubMed

    Yu, Lin; Zhang, Xiaoli; Yuan, Jing; Cao, Qinzhen; Liu, Junqi; Zhu, Pan; Shi, Huahong

    2011-09-15

    Triphenyltin (TPT) has high binding affinity with the retinoid X receptor (RXR) in animals. The natural ligand of RXR, 9-cis-retinoic acid (RA), is known to induce featured malformations in vertebrate embryos by disrupting RA signal. Limited information is available on the TPT effects on amphibians. We exposed embryos of amphibian (Xenopus tropicalis) to TPT, 9-cis-RA, all-trans-RA (ligand of retinoic acid receptor, RAR), and LGD1069 (a selective ligand of RXR). The 72h LC50 of TPT was 5.25 μg Sn/L, and 72h EC50 was 0.96 μg Sn/L. TPT induced multiple malformations including enlarged proctodaeum and narrow fins. TPT at 5 μg Sn/L inhibited the differentiation of skins and muscles. The reduced brain, loss of external eyes and bent axis were observed in RXR and RAR ligands treatments. TPT and tributyltin (TBT) inhibited the mRNA expression of RXRα and increased that of TRβ. The phenotypes of malformations induced by TPT were similar to those by TBT and were much different from those by the RXR and RAR ligands. These results indicated that TPT was acute toxic and had high teratogenicity to amphibian embryos, and that TPT induced phenotypes of malformations. TPT and TBT might have a similar teratogenic mechanism, which seems not to be mainly mediated through RA signal. PMID:21820800

  16. Comparison of the Bruker MALDI-TOF Mass Spectrometry System and Conventional Phenotypic Methods for Identification of Gram-Positive Rods

    PubMed Central

    Barberis, Claudia; Almuzara, Marisa; Join-Lambert, Olivier; Ramírez, María Soledad; Famiglietti, Angela; Vay, Carlos

    2014-01-01

    In recent years, MALDI-TOF Mass Spectrometry (MS) method has emerged as a promising and a reliable tool for bacteria identification. In this study we compared Bruker MALDI-TOF MS and conventional phenotypic methods to identify a collection of 333 Gram-positive clinical isolates comprising 22 genera and 60 species. 16S rRNA sequencing was the reference molecular technique, and rpoB gene sequecing was used as a secondary gene target when 16Sr RNA did not allow species identification of Corynebacterium spp. We also investigate if score cut-offs values of ≥1,5 and ≥1,7 were accurate for genus and species-level identification using the Bruker system. Identification at species level was obtained for 92,49% of Gram-positive rods by MALDI-TOF MS compared to 85,89% by phenotypic method. Our data validates the score ≥1,5 for genus level and ≥1,7 for species-level identification in a large and diverse collection of Gram-positive rods. The present study has proved the accuracy of MALDI-TOF MS as an identification method in Gram-positive rods compared to currently used methods in routine laboratories. PMID:25184254

  17. 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.

  18. A direct comparison of unconscious face processing under masking and interocular suppression.

    PubMed

    Izatt, Gregory; Dubois, Julien; Faivre, Nathan; Koch, Christof

    2014-01-01

    Different combinations of forward and backward masking as well as interocular suppression have been used extensively to render stimuli invisible and to study those aspects of visual stimuli that are processed in the absence of conscious experience. Although the two techniques-masking vs. interocular suppression-obviously differ both in their applications and mechanisms, only little effort has been made to compare them systematically. Yet, such a comparison is crucial: existing discrepancies in the extent of unconscious processing inferred from these two techniques must be reconciled, as our understanding of unconscious vision should be independent of the technique used to prevent visibility. Here, we studied similarities and differences between faces rendered invisible by masking vs. interocular suppression using a priming paradigm. By carefully equating stimulus strength across the two techniques, we analyzed the effects of face primes with the same viewpoint (repetition priming, Experiment 1) and of face primes with a different viewpoint (identity priming, Experiment 2) on the reaction times for a fame categorization task. Overall, we found that the magnitude of both repetition and identity priming largely depended on stimulus visibility. Moreover, when the primes were subjectively invisible, both repetition and identity priming were found to be qualitatively stronger under masking than under interocular suppression. Taken together, these results help refine our understanding of which level of visual processing each technique disrupts, and illustrate the importance of systematic methodological comparisons in the field of unconscious vision. PMID:25071634

  19. ATTITUDE AND ACHIEVEMENT COMPARISONS FOR DIRECT AND TELEVISION CLASSES IN BIOLOGICAL SCIENCE - REPORT 3.

    ERIC Educational Resources Information Center

    WOODWARD, JOHN C.

    TO DETERMINE WHICH TEACHING METHOD WAS MORE EFFECTIVE, STUDENT ATTITUDE AND STUDENT ACHIEVEMENT WERE COMPARED BETWEEN TELEVISION (TV) LECTURES AND DIRECT CLASS LECTURES GIVEN BY THE SAME INSTRUCTOR AND COVERING THE SAME MATERIAL. THE LECTURE GROUP (126 STUDENTS) HAD SIGNIFICANTLY GREATER NUMBERS OF UPPERCLASSMEN, AND MORE OF THE STUDENTS PLANNED…

  20. Comparison of Direct Instruction and Simultaneous Prompting Procedure on Teaching Concepts to Individuals with Intellectual Disability

    ERIC Educational Resources Information Center

    Celik, Semiha; Vuran, Sezgin

    2014-01-01

    The purpose of this study was to compare the efficiency, effectiveness, maintenance effects and social validity of two instructional methods, Direct Instruction and Simultaneous Prompting Procedure, on teaching concepts (long, old, few and thick) using a parallel treatments design. All sessions were conducted at a private special education center…

  1. 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…

  2. Comparison between direct and reverse electroporation of cells in situ: a simulation study.

    PubMed

    Towhidi, Leila; Khodadadi, Delaram; Maimari, Nataly; Pedrigi, Ryan M; Ip, Henry; Kis, Zoltan; Kwak, Brenda R; Petrova, Tatiana W; Delorenzi, Mauro; Krams, Rob

    2016-03-01

    The discovery of the human genome has unveiled new fields of genomics, transcriptomics, and proteomics, which has produced paradigm shifts on how to study disease mechanisms, wherein a current central focus is the understanding of how gene signatures and gene networks interact within cells. These gene function studies require manipulating genes either through activation or inhibition, which can be achieved by temporarily permeabilizing the cell membrane through transfection to delivercDNAorRNAi. An efficient transfection technique is electroporation, which applies an optimized electric pulse to permeabilize the cells of interest. When the molecules are applied on top of seeded cells, it is called "direct" transfection and when the nucleic acids are printed on the substrate and the cells are seeded on top of them, it is termed "reverse" transfection. Direct transfection has been successfully applied in previous studies, whereas reverse transfection has recently gained more attention in the context of high-throughput experiments. Despite the emerging importance, studies comparing the efficiency of the two methods are lacking. In this study, a model for electroporation of cells in situ is developed to address this deficiency. The results indicate that reverse transfection is less efficient than direct transfection. However, the model also predicts that by increasing the concentration of deliverable molecules by a factor of 2 or increasing the applied voltage by 20%, reverse transfection can be approximately as efficient as direct transfection. PMID:27009275

  3. Comparison of CaOH with MTA for direct pulp capping: a PBRN randomized clinical trial.

    PubMed

    Hilton, T J; Ferracane, J L; Mancl, L

    2013-07-01

    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. PMID:23690353

  4. COMPARISON BETWEEN CONDITIONAL PROBABILITY FUNCTION AND NONPARAMETRIC REGRESSION FOR FINE PARTICLE SOURCE DIRECTIONS. (R831078)

    EPA Science Inventory

    The objective of this study is to examine the use of conditional probability function (CPF) and nonparametric regression (NPR) to identify directions of PM2.5 (particulate matter 2.5 m in aerodynamic diameter) sources using data collected from multiple monitoring sites across ...

  5. 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…

  6. 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…

  7. 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…

  8. Comparison of Direct Inoculation and Copan Transport Systems for Isolation of Neisseria gonorrhoeae from Endocervical Specimens

    PubMed Central

    Olsen, C. C.; Schwebke, J. R.; Benjamin, W. H.; Beverly, A.; Waites, K. B.

    1999-01-01

    Two commercial swab transport systems, Copan Amies gel agar with and without charcoal (Copan Diagnostics, Corona, Calif.), were compared to direct inoculation onto modified Thayer-Martin medium for detection of Neisseria gonorrhoeae in 1,490 endocervical specimens obtained from women attending a sexually transmitted disease clinic. Copan swabs were held in the transport system for 24 h at room temperature prior to inoculation onto modified Thayer-Martin medium. All cultures were incubated at 35°C in 5% CO2, and bacteria were identified on the basis of Gram stain, oxidase, and biochemical reactions. Copan Amies gel agar transport system without charcoal detected 77 of 81 (95%) direct inoculation culture-positive specimens, and Copan Amies gel agar transport system with charcoal detected 53 of 56 (95%) directly inoculated culture-positive specimens. Copan Amies gel agar without charcoal inoculated after 6 h supported growth of 56 (98%) positive cultures out of only 55 directly inoculated culture-positive specimens. This study demonstrates that Copan swabs represent a reasonable alternative, providing convenience, low cost, and ease of use while still maintaining a satisfactory recovery rate of N. gonorrhoeae from clinical specimens, if specimens can be inoculated onto selective media within a relatively short time period not involving overnight shipment. PMID:10523556

  9. Ethical aspects of directly observed treatment for tuberculosis: a cross-cultural comparison

    PubMed Central

    2013-01-01

    Background Tuberculosis is a major global public health challenge, and a majority of countries have adopted a version of the global strategy to fight Tuberculosis, Directly Observed Treatment, Short Course (DOTS). Drawing on results from research in Ethiopia and Norway, the aim of this paper is to highlight and discuss ethical aspects of the practice of Directly Observed Treatment (DOT) in a cross-cultural perspective. Discussion Research from Ethiopia and Norway demonstrates that the rigid enforcement of directly observed treatment conflicts with patient autonomy, dignity and integrity. The treatment practices, especially when imposed in its strictest forms, expose those who have Tuberculosis to extra burdens and costs. Socially disadvantaged groups, such as the homeless, those employed as day labourers and those lacking rights as employees, face the highest burdens. Summary From an ethical standpoint, we argue that a rigid practice of directly observed treatment is difficult to justify, and that responsiveness to social determinants of Tuberculosis should become an integral part of the management of Tuberculosis. PMID:23819555

  10. 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...

  11. Optimization and Comparison of Direct and Indirect Supercritical Carbon Dioxide Power Plant Cycles for Nuclear Applications

    SciTech Connect

    Edwin A. Harvego; Michael G. McKellar

    2011-11-01

    There have been a number of studies involving the use of gases operating in the supercritical mode for power production and process heat applications. Supercritical carbon dioxide (CO2) is particularly attractive because it is capable of achieving relatively high power conversion cycle efficiencies in the temperature range between 550 C and 750 C. Therefore, it has the potential for use with any type of high-temperature nuclear reactor concept, assuming reactor core outlet temperatures of at least 550 C. The particular power cycle investigated in this paper is a supercritical CO2 Recompression Brayton Cycle. The CO2 Recompression Brayton Cycle can be used as either a direct or indirect power conversion cycle, depending on the reactor type and reactor outlet temperature. The advantage of this cycle when compared to the helium Brayton cycle is the lower required operating temperature; 550 C versus 850 C. However, the supercritical CO2 Recompression Brayton Cycle requires an operating pressure in the range of 20 MPa, which is considerably higher than the required helium Brayton cycle operating pressure of 8 MPa. This paper presents results of analyses performed using the UniSim process analyses software to evaluate the performance of both a direct and indirect supercritical CO2 Brayton Recompression cycle for different reactor outlet temperatures. The direct supercritical CO2 cycle transferred heat directly from a 600 MWt reactor to the supercritical CO2 working fluid supplied to the turbine generator at approximately 20 MPa. The indirect supercritical CO2 cycle assumed a helium-cooled Very High Temperature Reactor (VHTR), operating at a primary system pressure of approximately 7.0 MPa, delivered heat through an intermediate heat exchanger to the secondary indirect supercritical CO2 Brayton Recompression cycle, again operating at a pressure of about 20 MPa. For both the direct and indirect cycles, sensitivity calculations were performed for reactor outlet temperature

  12. 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. PMID:15364649

  13. GaAs quantum structures: Comparison between direct pseudopotential and single-band truncated-crystal calculations

    NASA Astrophysics Data System (ADS)

    Franceschetti, Alberto; Zunger, Alex

    1996-04-01

    A single-band approach for semiconductor clusters which accounts for the nonparabolicity of the energy bands was recently used by Rama Krishna and Friesner [M.V. Rama Krishna and R.A. Friesner, Phys. Rev. Lett. 67, 629 (1991)]. We compare the results of this method (denoted here as single-band truncated-crystal, or SBTC, approximation) with a direct pseudopotential band-structure calculation for free-standing hydrogen-passivated GaAs quantum films, wires, and dots. The direct pseudopotential calculation, which includes coupling between all bands, shows that isolated GaAs quantum films, wires, and dots have an indirect band gap for thicknesses below 16, 28, and at least 30 Å (8, 14, and at least 15 ML), respectively; beyond these critical dimensions the transition becomes direct. A comparison of the SBTC approximation with the direct pseudopotential calculation shows that (i) the confinement energy of the valence-band maximum is overestimated by the SBTC method, because the zero-confinement character of this state is neglected; (ii) the confinement energy of the Γ-derived conduction state (direct band gap) is slightly overestimated by the SBTC approximation, mainly because of the assumption of infinite potential barriers at the boundaries; (iii) the confinement energy of the X-derived conduction state (indirect band gap) is severely underestimated by the SBTC method; (iv) while the SBTC approximation predicts ``quantum deconfinement'' (i.e., reduction of gap as size is reduced) for the direct gap of thin GaAs quantum wires, such effect is not present in the direct pseudopotential calculation.

  14. GaAs quantum structures: Comparison between direct pseudopotential and single-band truncated-crystal calculations

    SciTech Connect

    Franceschetti, A.; Zunger, A.

    1996-04-01

    A single-band approach for semiconductor clusters which accounts for the nonparabolicity of the energy bands was recently used by Rama Krishna and Friesner [M.V. Rama Krishna and R.A. Friesner, Phys. Rev. Lett. {bold 67}, 629 (1991)]. We compare the results of this method (denoted here as single-band truncated-crystal, or SBTC, approximation) with a direct pseudopotential band-structure calculation for free-standing hydrogen-passivated GaAs quantum films, wires, and dots. The direct pseudopotential calculation, which includes coupling between all bands, shows that isolated GaAs quantum films, wires, and dots have an indirect band gap for thicknesses below 16, 28, and at least 30 A (8, 14, and at least 15 ML), respectively; beyond these critical dimensions the transition becomes direct. A comparison of the SBTC approximation with the direct pseudopotential calculation shows that (i) the confinement energy of the valence-band maximum is overestimated by the SBTC method, because the zero-confinement character of this state is neglected; (ii) the confinement energy of the {Gamma}-derived conduction state (direct band gap) is slightly overestimated by the SBTC approximation, mainly because of the assumption of infinite potential barriers at the boundaries; (iii) the confinement energy of the {ital X}-derived conduction state (indirect band gap) is severely underestimated by the SBTC method; (iv) while the SBTC approximation predicts {open_quote}{open_quote}quantum deconfinement{close_quote}{close_quote} (i.e., {ital reduction} of gap as size is reduced) for the direct gap of thin GaAs quantum wires, such effect is not present in the direct pseudopotential calculation. {copyright} {ital 1996 American Institute of Physics.}

  15. Aerosol microphysical retrievals from precision filter radiometer direct solar radiation measurements and comparison with AERONET

    NASA Astrophysics Data System (ADS)

    Kazadzis, S.; Veselovskii, I.; Amiridis, V.; Gröbner, J.; Suvorina, A.; Nyeki, S.; Gerasopoulos, E.; Kouremeti, N.; Taylor, M.; Tsekeri, A.; Wehrli, C.

    2014-07-01

    Synchronized sun-photometric measurements from the AERONET-CIMEL (AErosol RObotic NETwork) and GAW-PFR (Global Atmospheric Watch-Precision Filter Radiometer) aerosol networks are used to compare retrievals of the aerosol optical depth (AOD), effective radius, and volume concentration during a high-temporal-resolution measurement campaign at the Athens site in the Mediterranean Basin from 14 to 22 July 2009. During this period, direct-sun AOD retrievals from both instruments exhibited small differences in the range 0.01-0.02. The AODs measured with CIMEL and PFR instruments were inverted to retrieve particle microphysical properties using the linear estimation (LE) technique. For low aerosol loads (AOD < 0.2), measurements of the effective radius by the PFR were found to be -20% to +30% different from CIMEL values for both direct-sun data and inversion data. At higher loads (AOD > 0.4), measurements of the effective radius by the PFR are consistently 20 % lower than CIMEL for both direct-sun and inversion data. Volume concentrations at low aerosol loads from the PFR are up to 80% higher than the CIMEL for direct-sun data but are up to 20% lower when derived from inversion data under these same conditions. At higher loads, the percentage difference in volume concentrations from the PFR and CIMEL is systematically negative, with inversion data predicting differences 30% lower than those obtained from direct-sun data. An assessment of the effect of errors in the AOD retrieval on the estimation of PFR bulk parameters was performed and demonstrates that it is possible to estimate the particle volume concentration and effective radius with an uncertainty < 65% when AOD < 0.2 and when input errors are as high as 10%.

  16. 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. PMID:20039757

  17. Direct comparison between two γ-alumina structural models by DFT calculations

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

    We selected two important γ-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.

  18. 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.

  19. Scattering directionality parameters of fractal black carbon aerosols and comparison with the Henyey-Greenstein approximation.

    PubMed

    Pandey, Apoorva; Chakrabarty, Rajan K

    2016-07-15

    Current radiation transfer schemes employ the Henyey-Greenstein (HG) phase function to connect three single parameter representations of aerosol scattering directionality-the hemispherical upscatter fraction (β), the backscatter fraction (b), and the asymmetry parameter (g). The HG phase function does not account for particle morphology, which could lead to significant errors. In this Letter, we compute these single parameters for fractal black carbon (BC) aerosols using the numerically exact superposition T-matrix method. The variations in β, g, and b as a function of aerosol morphology are examined. Corrected empirical relationships connecting these parameters are proposed. We find that the HG phase function could introduce up to a 35% error in β and g estimates. Interestingly, these errors are suppressed by the large mass absorption cross-sections of BC aerosols in radiative transfer calculations and contribute to ≤8% error in direct forcing efficiencies. PMID:27420533

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

    PubMed

    Chestnut, Eleanor K; Markman, Ellen M

    2016-03-01

    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 (i.e., reference points) to be placed in the complement position. Three experiments with children ages 4-8 (N = 181) explored whether children share this sensitivity to directional syntax. Children of this age showed an incipient preference for framing reference points as complements. Stating, "Girls do math as well as boys," which frames boys as the reference point for girls, may therefore actually teach children that boys set the standard. PMID:26727987

  1. 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

  2. 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

  3. Comparison between iterative wavefront control algorithm and direct gradient wavefront control algorithm for adaptive optics system

    NASA Astrophysics Data System (ADS)

    Cheng, Sheng-Yi; Liu, Wen-Jin; Chen, Shan-Qiu; Dong, Li-Zhi; Yang, Ping; Xu, Bing

    2015-08-01

    Among all kinds of wavefront control algorithms in adaptive optics systems, the direct gradient wavefront control algorithm is the most widespread and common method. This control algorithm obtains the actuator voltages directly from wavefront slopes through pre-measuring the relational matrix between deformable mirror actuators and Hartmann wavefront sensor with perfect real-time characteristic and stability. However, with increasing the number of sub-apertures in wavefront sensor and deformable mirror actuators of adaptive optics systems, the matrix operation in direct gradient algorithm takes too much time, which becomes a major factor influencing control effect of adaptive optics systems. In this paper we apply an iterative wavefront control algorithm to high-resolution adaptive optics systems, in which the voltages of each actuator are obtained through iteration arithmetic, which gains great advantage in calculation and storage. For AO system with thousands of actuators, the computational complexity estimate is about O(n2) ˜ O(n3) in direct gradient wavefront control algorithm, while the computational complexity estimate in iterative wavefront control algorithm is about O(n) ˜ (O(n)3/2), in which n is the number of actuators of AO system. And the more the numbers of sub-apertures and deformable mirror actuators, the more significant advantage the iterative wavefront control algorithm exhibits. Project supported by the National Key Scientific and Research Equipment Development Project of China (Grant No. ZDYZ2013-2), the National Natural Science Foundation of China (Grant No. 11173008), and the Sichuan Provincial Outstanding Youth Academic Technology Leaders Program, China (Grant No. 2012JQ0012).

  4. Comparison of direct mercury analyzer and FIA-CV-AAS in determination of methylmercury in fish

    NASA Astrophysics Data System (ADS)

    Ulrich, J. C.; Hortellani, M. A.; Sarkis, J. E. S.; Nakatsubo, M. A.

    2016-07-01

    Methylmercury (MeHg) has been determined in fish reference materials by direct mercury analyzer (DMA 80) and FIA-CV-AAS. In order to evaluate accuracy, certified reference materials (Fish protein, NRCC - Dorm 4 and fish material, Ipen - Dourada 1) were analyzed after extraction and separation of mercury species. Good agreement of the results have been obtained (relative error of the determination between the methods varied from 1.5% to 39%). The repeatability of the results varied from 4% to 26%.

  5. 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.

  6. Toward isometric force capabilities evaluation by using a musculoskeletal model: Comparison with direct force measurement.

    PubMed

    Hernandez, Vincent; Rezzoug, Nasser; Gorce, Philippe

    2015-09-18

    Developing formalisms to determine force capabilities of human limbs by using musculoskeletal models could be useful for biomechanical and ergonomic applications. In this framework, the purpose of this study was to compare measured maximal isometric force capabilities at the hand in a set of Cartesian directions with forces computed from a musculoskeletal model of the upper-limb. The results were represented under the form of a measured force polytope (MFP) and a musculoskeletal force polytope (MSFP). Both of them were obtained from the convex hull of measured and simulated force vectors endpoints. Nine subjects participated to the experiment. For one posture recorded with an optoelectronic system, maximum isometric forces exerted at the hand were recorded in twenty six directions of the Cartesian space with a triaxial force sensor. Results showed significant differences between the polytopes global shapes. The MSFP was more elongated than the MFP. Concerning the polytopes volumes, no significant difference was found. Mean maximal isometric forces provided by MFP and MSFP were 509.6 (118.4)N and 627.9 (73.3)N respectively. Moreover, the angle between the main axes of the two polytopes was 5.5 (2.3)° on average. Finally, RMS error values between MFP and MSFP were lower than 100N in 88% of the considered directions. The proposed MSFP based on a musculoskeletal model gave interesting information on optimal force orientation parameters. The possible applications in the frame of ergonomics, rehabilitation and biomechanics are proposed and discussed. PMID:26206551

  7. Comparison of aortic annulus size by transesophageal echocardiography and computed tomography angiography with direct surgical measurement.

    PubMed

    Wang, Hanghang; Hanna, Jennifer M; Ganapathi, Asvin; Keenan, Jeffrey E; Hurwitz, Lynne M; Vavalle, John P; Kiefer, Todd L; Wang, Andrew; Harrison, J Kevin; Hughes, G Chad

    2015-06-01

    This study sought to compare the accuracy of 2-dimensional transesophageal echocardiography (TEE) and computed tomography angiography (CTA) for noninvasive aortic annular sizing as required for transcatheter aortic valve implantation (TAVI). Direct intraoperative (OR) sizing is the gold standard for aortic annular measurement in surgical aortic valve replacement. Unlike surgical aortic valve replacement, TAVI requires noninvasive assessment of aortic annular dimensions for determining the size of prosthesis to be implanted and controversy exists regarding the best imaging technique for TAVI sizing. Preoperative CTA and OR TEE images of the aortic annulus in 227 patients who underwent proximal aortic surgery with OR annular sizing at the Duke University Medical Center were reviewed. Both imaging techniques were compared with direct OR measurements of aortic annulus diameter using metric sizers as the gold standard. CTA overestimated aortic annulus diameter in 72.2% of cases, with 46.3% >1 TAVI valve-size (>3 mm) overestimations, whereas TEE underestimated aortic annulus diameter in 51.1% of cases, with 16.7% >1 valve-size underestimations. Combining both techniques improved the estimation of aortic annular size. In conclusion, there are limitations to current imaging techniques for noninvasive determination of aortic annular dimensions compared with direct OR sizing. Undersizing by TEE and oversizing by CTA are common and may be related to differences in methods for sizing an elliptical structure. Combining measurements from both techniques would decrease the false exclusion rate for TAVI eligibility because of size mismatch. PMID:25846765

  8. 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.

  9. 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.

  10. Phenotypic and Genotypic Comparisons of Human T-Cell Leukemia Virus Type 1 Reverse Transcriptases from Infected T-Cell Lines and Patient Samples▿

    PubMed Central

    Mitchell, Michael S.; Bodine, Ellen T.; Hill, Shawn; Princler, Gerald; Lloyd, Patricia; Mitsuya, Hiroaki; Matsuoka, Masao; Derse, David

    2007-01-01

    It is well established that cell-free infection with human T-cell leukemia virus type 1 (HTLV-1) is less efficient than that with other retroviruses, though the specific infectivities of only a limited number of HTLV-1 isolates have been quantified. Earlier work indicated that a postentry step in the infectious cycle accounted for the poor cell-free infectivity of HTLV-1. To determine whether variations in the pol gene sequence correlated with virus infectivity, we sequenced and phenotypically tested pol genes from a variety of HTLV-1 isolates derived from primary sources, transformed cell lines, and molecular clones. The pol genes and deduced amino acid sequences from 23 proviruses were sequenced and compared with 14 previously published sequences, revealing a limited number of amino acid variations among isolates. The variations appeared to be randomly dispersed among primary isolates and proviruses from cell lines and molecular clones. In addition, there was no correlation between reverse transcriptase sequence and the disease phenotype of the original source of the virus isolate. HTLV-1 pol gene fragments encoding reverse transcriptase were amplified from a variety of isolates and were subcloned into HTLV-1 vectors for both single-cycle infection and spreading-infection assays. Vectors carrying pol genes that matched the consensus sequence had the highest titers, and those with the largest number of variations from the consensus had the lowest titers. The molecular clone from CS-1 cells had four amino acid differences from the consensus sequence and yielded infectious titers that were approximately eight times lower than those of vectors encoding a consensus reverse transcriptase. PMID:17287279

  11. Comparison of the phenotype of NK1R-/- mice with pharmacological blockade of the substance P (NK1 ) receptor in assays for antidepressant and anxiolytic drugs.

    PubMed

    Rupniak, N M; Carlson, E J; Webb, J K; Harrison, T; Porsolt, R D; Roux, S; de Felipe, C; Hunt, S P; Oates, B; Wheeldon, A

    2001-11-01

    The phenotype of NK1R-/- mice was compared with that of acute pharmacological blockade of the tachykinin NK1 receptor on sensorimotor function and in assays relevant to depressive illness and anxiety. The dose range for L-760735 and GR205171 that was associated with functional blockade of central NK1 receptors in the target species was established by antagonism of the behavioural effects of intracerebroventricular NK1 agonist challenge in gerbils, mice and rats. The caudal grooming and scratching response to GR73632 was absent in NK1R-/- mice, confirming that the receptor had been genetically ablated. There was no evidence of sedation or motor impairment in NK1R-/- mice or following administration of L-760735 to gerbils, even at doses in excess of those required for central NK1 receptor occupancy. In the resident-intruder and forced swim test, the behaviour of NK1R-/- mice, or animals treated acutely with L-760735 or GR205171, resembled that seen with the clinically used antidepressant drug fluoxetine. However, the effects of GR205171 were not clearly enantioselective in mice. In contrast, although NK1R-/- mice also exhibited an increase in the duration of struggle behaviour in the tail suspension test, this was not observed following pharmacological blockade with L-760735 in gerbils or GR205171 in mice, suggesting that this may reflect a developmental alteration in the knockout mouse. There was no effect of NK1 receptor blockade with L-760735 in guinea-pigs or GR205171 in rats, or deletion of the NK1 receptor in mice, on behaviour in the elevated plus-maze test for anxiolytic activity. These findings extend previous observations on the phenotype of the NK1R-/- mouse and establish a broadly similar profile following acute pharmacological blockade of the receptor. These studies also serve to underscore the limitations of currently available antagonists that are suitable for use in rat and mouse behavioural assays. PMID:11742144

  12. A direct comparison of next generation sequencing enrichment methods using an aortopathy gene panel- clinical diagnostics perspective

    PubMed Central

    2012-01-01

    Background Aortopathies are a group of disorders characterized by aneurysms, dilation, and tortuosity of the aorta. Because of the phenotypic overlap and genetic heterogeneity of diseases featuring aortopathy, molecular testing is often required for timely and correct diagnosis of affected individuals. In this setting next generation sequencing (NGS) offers several advantages over traditional molecular techniques. Methods The purpose of our study was to compare NGS enrichment methods for a clinical assay targeting the nine genes known to be associated with aortopathy. RainDance emulsion PCR and SureSelect RNA-bait hybridization capture enrichment methods were directly compared by enriching DNA from eight samples. Enriched samples were barcoded, pooled, and sequenced on the Illumina HiSeq2000 platform. Depth of coverage, consistency of coverage across samples, and the overlap of variants identified were assessed. This data was also compared to whole-exome sequencing data from ten individuals. Results Read depth was greater and less variable among samples that had been enriched using the RNA-bait hybridization capture enrichment method. In addition, samples enriched by hybridization capture had fewer exons with mean coverage less than 10, reducing the need for followup Sanger sequencing. Variants sets produced were 77% concordant, with both techniques yielding similar numbers of discordant variants. Conclusions When comparing the design flexibility, performance, and cost of the targeted enrichment methods to whole-exome sequencing, the RNA-bait hybridization capture enrichment gene panel offers the better solution for interrogating the aortopathy genes in a clinical laboratory setting. PMID:23148498

  13. 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.

  14. Comparison of performance capabilities of spread spectrum coherent and direct detection CO2 DIAL systems

    NASA Astrophysics Data System (ADS)

    Hasson, Victor H.; Kovacs, Mark A.

    2002-02-01

    This paper compares the performance of a conventional direct detection CO2 Differential Absorption Lidar (DIAL) system with the coherent spread spectrum approach developed and patented by Textron. The analysis shows that the coherent approach is far superior in terms of maximum attainable standoff range at a specified transmitter average power and substantially reduced system power and associated size and weight at a predetermined range. The requirements on local oscillator stability are fairly relaxed and the spread spectrum/coherent DIAL concept is fairly easy to implement. Some comparative validation data are provided.

  15. 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.

  16. 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.

  17. Comparison between Agrobacterium-mediated and direct gene transfer using the gene gun.

    PubMed

    Gao, Caixia; Nielsen, Klaus K

    2013-01-01

    Agrobacterium-mediated transformation and direct gene transfer using the gene gun (microparticle -bombardment) are the two most widely used methods for plant genetic modification. The Agrobacterium method has been successfully practiced in dicots for many years, but only recently have efficient protocols been developed for grasses. Microparticle bombardment has evolved as a method delivering exogenous nucleic acids into plant genome and is a commonly employed technique in plant science. Here these two systems are compared for transformation efficiency, transgene integration, and transgene expression when used to transform tall fescue (Festuca arundinacea Schreb.). The tall fescue transformation protocols lead to the production of large numbers of fertile, independent transgenic lines. PMID:23104329

  18. Social responsiveness and competence in Prader-Willi syndrome: direct comparison to autism spectrum disorder.

    PubMed

    Dimitropoulos, Anastasia; Ho, Alan; Feldman, Benjamin

    2013-01-01

    Prader-Willi syndrome (PWS), a neurodevelopmental disorder primarily characterized by hyperphagia and food preoccupations, is caused by the absence of expression of the paternally active genes in the proximal arm of chromosome 15. Although maladaptive behavior and the cognitive profile in PWS have been well characterized, social functioning has only more recently been systematically examined. Findings to date indicate the social impairment exhibited may reflect specific difficulty interpreting and using social information effectively. In addition, evidence suggests that there is an increased risk of social deficits in people with the maternally-derived uniparental disomy (mUPD) subtype of PWS in comparison to those with 15q11-13 paternal deletion (DEL). Using the Social Responsiveness Scale (SRS) and the Social Competence Inventory, our goal was to compare social functioning in PWS to individuals with autism spectrum disorder (ASD). Participants with mUPD scored similarly to the ASD group across most SRS domains. All groups had difficulty with social competence, although the DEL group scored highest on prosocial behavior. Findings suggest further characterization of social behavior in PWS is necessary to aid in advancing the understanding of the contributions of genes in the 15q11-13 critical region to ASD susceptibility, particularly with respect to the overexpression of maternally expressed genes in this region, as well as aiding in awareness and development/implementation of interventions. PMID:22576167

  19. 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.

  20. 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.

  1. 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.

  2. Comparison of six commercially-available DNA polymerases for direct PCR.

    PubMed

    Miura, Masashi; Tanigawa, Chihiro; Fujii, Yoshito; Kaneko, Satoshi

    2013-01-01

    The use of a "direct PCR" DNA polymerase enables PCR amplification without any prior DNA purification from blood samples due to the enzyme's resistance to inhibitors present in blood components. Such DNA polymerases are now commercially available. We compared the PCR performance of six direct PCR-type DNA polymerases (KOD FX, Mighty Amp, Hemo KlenTaq, Phusion Blood II, KAPA Blood, and BIOTAQ) in dried blood eluted from a filter paper with TE buffer. GoTaq Flexi was used as a standard DNA polymerase. PCR performance was evaluated by a nested PCR technique for detecting Plasmodium falciparum genomic DNA in the presence of the blood components. Although all six DNA polymerases showed resistance to blood components compared to the standard Taq polymerase, the KOD FX and BIOTAQ DNA polymerases were resistant to inhibitory blood components at concentrations of 40%, and their PCR performance was superior to that of other DNA polymerases. When the reaction mixture contained a mild detergent, only KOD FX DNA polymerase retained the original amount of amplified product. These results indicate that KOD FX DNA polymerase is the most resistant to inhibitory blood components and/or detergents. Thus, KOD FX DNA polymerase could be useful in serological studies to simultaneously detect antibodies and DNA in eluents for antibodies. KOD FX DNA polymerase is thus not limited to use in detecting malaria parasites, but could also be employed to detect other blood-borne pathogens. PMID:24213192

  3. Physico-chemical comparison of famotidine tablets prepared via dry granulation and direct compression techniques.

    PubMed

    Baseer, Abdul; Hassan, Fouzia; Hassan, Sm Fareed; Jabeen, Sabahat; Israr, Fozia; Murtaza, Ghulam; Haque, Naheed

    2013-05-01

    Famotidine is generally employed for the treatment of gastric ulcer. The present study was conducted to fabricate famotidine tablets using various diluents. The binder was incorporated to the formulations in different proportions. Both the dry granulation and direct compression techniques were employed to develop the tablets. Physical evaluation of tablets i.e. tablets hardness, friability, weight variation, thickness and diameter was determined. In vitro dissolution studies of the prepared tablets were carried out for 60 min using the USP apparatus II and 900 ml 0.1 M HCl stirred at 37 ± 0.5°C with a speed of 50 rpm. Physical analysis of tablets prepared via direct compression showed satisfactory results regarding the weight variation, hardness and friability, since their respective values were within the BP limits. All the prepared famotidine tablets exhibited diffusion based mode of drug release. 100% release of drug occurred in less than 60 min. The drug release from all the formulated tablets has elaborated the involvement of diffusion (Higuchian drug release). This comparative study exhibited that physical parameters of tablets are affected by the technique of tabletting. PMID:23625414

  4. A comparison of directed evolution approaches using the beta-glucuronidase model system.

    PubMed

    Rowe, Lori A; Geddie, Melissa L; Alexander, Omar B; Matsumura, Ichiro

    2003-09-26

    Protein engineers can alter the properties of enzymes by directing their evolution in vitro. Many methods to generate molecular diversity and to identify improved clones have been developed, but experimental evolution remains as much an art as a science. We previously used DNA shuffling (sexual recombination) and a histochemical screen to direct the evolution of Escherichia coli beta-glucuronidase (GUS) variants with improved beta-galactosidase (BGAL) activity. Here, we employ the same model evolutionary system to test the efficiencies of several other techniques: recursive random mutagenesis (asexual), combinatorial cassette mutagenesis (high-frequency recombination) and a versatile high-throughput microplate screen. GUS variants with altered specificity evolved in each trial, but different combinations of mutagenesis and screening techniques effected the fixation of different beneficial mutations. The new microplate screen identified a broader set of mutations than the previously employed X-gal colony screen. Recursive random mutagenesis produced essentially asexual populations, within which beneficial mutations drove each other into extinction (clonal interference); DNA shuffling and combinatorial cassette mutagenesis led instead to the accumulation of beneficial mutations within a single allele. These results explain why recombinational approaches generally increase the efficiency of laboratory evolution. PMID:12972256

  5. Estimating Am-241 activity in the body: comparison of direct measurements and radiochemical analyses

    SciTech Connect

    Lynch, Timothy P.; Tolmachev, Sergei Y.; James, Anthony C.

    2009-06-01

    The assessment of dose and ultimately the health risk from intakes of radioactive materials begins with estimating the amount actually taken into the body. An accurate estimate provides the basis to best assess the distribution in the body, the resulting dose, and ultimately the health risk. This study continues the time-honored practice of evaluating the accuracy of results obtained using in vivo measurement methods and techniques. Results from the radiochemical analyses of the 241Am activity content of tissues and organs from four donors to the United States Transuranium and Uranium Registries were compared to the results from direct measurements of radioactive material in the body performed in vivo and post mortem. Two were whole body donations and two were partial body donations The skeleton was the organ with the highest deposition of 241Am activity in all four cases. The activities ranged from 30 Bq to 300 Bq. The skeletal estimates obtained from measurements over the forehead were within 20% of the radiochemistry results in three cases and differed by 78% in one case. The 241Am lung activity estimates ranged from 1 Bq to 30 Bq in the four cases. The results from the direct measurements were within 40% of the radiochemistry results in 3 cases and within a factor of 3 for the other case. The direct measurement estimates of liver activity ranged from 2 Bq to 60 Bq and were generally lower than the radiochemistry results. The results from this study suggest that the measurement methods and calibration techniques used at the In Vivo Radiobioassay and Research Facility to quantify the activity in the lungs, skeleton and liver are reasonable under the most challenging conditions where there is 241Am activity in multiple organs. These methods and techniques are comparable to those used at other Department of Energy sites. This suggests that the current in vivo methods and calibration techniques provide reasonable estimates of radioactive material in the body. Not

  6. Quantitative comparison of direct phase retrieval algorithms in in-line phase tomography

    SciTech Connect

    Langer, Max; Cloetens, Peter; Guigay, Jean-Pierre; Peyrin, Francoise

    2008-10-15

    A well-known problem in x-ray microcomputed tomography is low sensitivity. Phase contrast imaging offers an increase of sensitivity of up to a factor of 10{sup 3} in the hard x-ray region, which makes it possible to image soft tissue and small density variations. If a sufficiently coherent x-ray beam, such as that obtained from a third generation synchrotron, is used, phase contrast can be obtained by simply moving the detector downstream of the imaged object. This setup is known as in-line or propagation based phase contrast imaging. A quantitative relationship exists between the phase shift induced by the object and the recorded intensity and inversion of this relationship is called phase retrieval. Since the phase shift is proportional to projections through the three-dimensional refractive index distribution in the object, once the phase is retrieved, the refractive index can be reconstructed by using the phase as input to a tomographic reconstruction algorithm. A comparison between four phase retrieval algorithms is presented. The algorithms are based on the transport of intensity equation (TIE), transport of intensity equation for weak absorption, the contrast transfer function (CTF), and a mixed approach between the CTF and TIE, respectively. The compared methods all rely on linearization of the relationship between phase shift and recorded intensity to yield fast phase retrieval algorithms. The phase retrieval algorithms are compared using both simulated and experimental data, acquired at the European Synchrotron Radiation Facility third generation synchrotron light source. The algorithms are evaluated in terms of two different reconstruction error metrics. While being slightly less computationally effective, the mixed approach shows the best performance in terms of the chosen criteria.

  7. 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

  8. Complementation of sugary-1 phenotype in rice endosperm with the wheat isoamylase1 gene supports a direct role for isoamylase1 in amylopectin biosynthesis.

    PubMed

    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

  9. 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.

  10. COMPARISON OF THE COMPLETE FOURIER DIRECT MRI WITH EXISTING DIFFUSION WEIGHTED MRI METHODS

    PubMed Central

    Özcan, Alpay

    2011-01-01

    The Complete Fourier Direct (CFD) MRI method introduced in earlier work for modeling the diffusion weighted MRI signal is compared with the existing methods. The preservation of Hermitian symmetry in the diffusion weighted MRI signal without affecting its energy is the key point that differentiates CFD–MRI from the existing methods. By keeping the correct Fourier relationship intact, the joint distribution function is represented ‘as it is’, without any constraints, e.g. being symmetric. The necessity to model or assume models for spin motion and try to fit the model to the samples of the Fourier transform as in case of model matching methods is not required because the Discrete Fourier Transform applied to correctly processed signal in CFD–MRI gives more accurate results. PMID:21918715

  11. 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.

  12. Comparison of direct and indirect blood pressure measurements in anesthetized dogs.

    PubMed Central

    Gains, M J; Grodecki, K M; Jacobs, R M; Dyson, D; Foster, R A

    1995-01-01

    The precision and accuracy of an indirect oscillometric blood pressure measurement technique (Dinamap 8100) was assessed in 11 anesthetized Beagle dogs weighing 8 to 11.5 kg. Direct blood pressure measurements were made by catheterization of the lingual artery, and simultaneous indirect measurements were determined by placing a cuff over the median artery (midradial area). Blood pressure measurements at 2 different planes of anesthesia (light and deep) were recorded in triplicate. At a light plane of anesthesia, the Dinamap 8100 underestimated diastolic and mean arterial pressure, and at a deep anesthetic plane overestimated systolic pressure. The indirect technique had good repeatability of systolic pressures. Regression analysis for the 2 techniques showed excellent correlation (r = 0.93). The results indicate that the indirect oscillometric blood pressure measurement technique provides a good estimate of systolic, diastolic, and mean arterial pressure in dogs weighing 8-11.5 kg. PMID:8521360

  13. 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.

  14. The anharmonic oscillator driven by Gaussian noise. Comparison between direct perturbation and Markov approximation methods

    NASA Astrophysics Data System (ADS)

    Pesquera, L.; Blanco, R.

    1987-04-01

    The anharmonic oscillator driven by Gaussian noise is studied in the limit of weak damping using the direct perturbation (DPM) and Markov approximation (MAM) methods. Mean values are obtained to first order in the anharmonic coupling constant g. From a careful treatment of the high-frequency behavior it is concluded that to first order in g the DPM takes high-frequency contributions into account whereas the MAM does not, while both agree if high-frequency contributions are not important. It is also shown that both methods give the same results to second order in g for the quartic anharmonic oscillator. The spectral density of the noise used in stochastic electrodynamics is considered as a particular example.

  15. Acceleration of heavy and light particles in turbulence: Comparison between experiments and direct numerical simulations

    NASA Astrophysics Data System (ADS)

    Volk, R.; Calzavarini, E.; Verhille, G.; Lohse, D.; Mordant, N.; Pinton, J.-F.; Toschi, F.

    2008-08-01

    We compare experimental data and numerical simulations for the dynamics of inertial particles with finite density in turbulence. In the experiment, bubbles and solid particles are optically tracked in a turbulent flow of water using an Extended Laser Doppler Velocimetry technique. The probability density functions (PDF) of particle accelerations and their auto-correlation in time are computed. Numerical results are obtained from a direct numerical simulation in which a suspension of passive pointwise particles is tracked, with the same finite density and the same response time as in the experiment. We observe a good agreement for both the variance of acceleration and the autocorrelation time scale of the dynamics; small discrepancies on the shape of the acceleration PDF are observed. We discuss the effects induced by the finite size of the particles, not taken into account in the present numerical simulations.

  16. Matching is not Naming: A direct comparison of lexical manipulations in explicit and implicit reading tasks

    PubMed Central

    Vogel, Alecia C.; Petersen, Steven E.; Schlaggar, Bradley L.

    2014-01-01

    The neurobiological basis of reading is of considerable interest, yet analyzing data from subjects reading words aloud during functional MRI data collection can be difficult. Therefore, many investigators use surrogate tasks such as visual matching or rhyme matching to eliminate the need for spoken output. Use of these tasks has been justified by the presumption of “automatic activation” of reading-related neural processing when a word is viewed. We have tested the efficacy of using a non-reading task for studying “reading effects” by directly comparing BOLD activity in subjects performing a visual matching task and an item naming task on words, pseudowords (meaningless but legal letter combinations), and nonwords (meaningless and illegal letter combinations). When compared directly, there is significantly more activity during the naming task in “reading-related” regions such as the inferior frontal gyrus (IFG) and supramarginal gyrus. More importantly, there are differing effects of lexicality in the tasks. A whole-brain task (matching vs naming) by string type (word vs pseudoword vs nonword) by BOLD timecourse analysis identifies regions showing this three-way interaction, including the left IFG and left angular gyrus (AG). In the majority of the identified regions (including the left IFG and left AG), there is a string type by timecourse interaction in the naming but not the matching task. These results argue that the processing performed in specific regions is contingent on task, even in reading-related regions, and is thus non-automatic. Such differences should be taken into consideration when designing studies intended to investigate reading. PMID:22711620

  17. 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

    2012-05-01

    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. PMID:22444428

  18. 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.

  19. Comparisons of the F and HN gene sequences of different strains of bovine parainfluenza virus type 3: relationship to phenotype and pathogenicity.

    PubMed Central

    Breker-Klassen, M M; Yoo, D; Babiuk, L A

    1996-01-01

    The genes for the F and HN glycoprotein of a pathogenic field isolate of bovine parainfluenza virus type 3 (BPIV3) were isolated, converted to cDNA, and sequenced using dideoxynucleotides. The resulting nucleotide sequences were converted to protein sequence and were compared to previously sequenced glycoprotein genes with amino acid differences in the glycoproteins of isolates expressing different phenotypes. The HN glycoprotein, involved in the attachment and release of the virus, and the F glycoprotein, involved in penetration and spread of the virus, have been shown to affect pathogenicity of the virus and are the immunodominant proteins of the virus. Both the F and HN proteins have been shown to be required for syncytium formation. Our results suggest that BPIV3 viruses that exhibit greater syncytium-inducing activity in vitro have greater pathogenicity in vivo. By determining which epitopes are involved in syncytium formation and comparing the sequences and enzymatic activities of different strains of virus, it may be possible to design subunit vaccines that protect against disease. Images Figure 1. PMID:8809388

  20. Phenotypic plasticity in life-history traits of Daphnia galeata in response to temperature - a comparison across clonal lineages separated in time.

    PubMed

    Henning-Lucass, Nicole; Cordellier, Mathilde; Streit, Bruno; Schwenk, Klaus

    2016-02-01

    Climatic changes are projected to result in rapid adaptive events with considerable phenotypic shifts. In order to reconstruct the impact of increased mean water temperatures during past decades and to reveal possible thermal micro-evolution, we applied a resurrection ecology approach using dormant eggs of the freshwater keystone species Daphnia galeata. To this end, we compared the adaptive response of D. galeata clones from Lake Constance of two different time periods, 1965-1974 ("historical") versus 2000-2009 ("recent"), to experimentally increased temperature regimes. In order to distinguish between genetic versus environmentally induced effects, we performed a common garden experiment in a flow-through system and measured variation in life-history traits. Experimental thermal regimes were chosen according to natural temperature conditions during the reproductive period of D. galeata in Central European lakes, with one additional temperature regime exceeding the currently observable maximum (+2°C). Increased water temperatures were shown to significantly affect measured life-history traits, and significant "temperature × clonal age" interactions were revealed. Compared to historical clones, recent clonal lineages exhibited a shorter time to first reproduction and a higher survival rate, which may suggest temperature-driven micro-evolution over time but does not allow an explicit conclusion on the adaptive nature of such responses. PMID:26941934

  1. 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

  2. Power matters in closing the phenotyping gap

    NASA Astrophysics Data System (ADS)

    Meyer, Carola W.; Elvert, Ralf; Scherag, André; Ehrhardt, Nicole; Gailus-Durner, Valerie; Fuchs, Helmut; Schäfer, Helmut; Hrabé de Angelis, Martin; Heldmaier, Gerhard; Klingenspor, Martin

    2007-05-01

    Much of our understanding of physiology and metabolism is derived from investigating mouse mutants and transgenic mice, and open-access platforms for standardized mouse phenotyping such as the German Mouse Clinic (GMC) are currently viewed as one powerful tool for identifying novel gene-function relationships. Phenotyping or phenotypic screening involves the comparison of wild-type control mice with their mutant or transgenic littermates. In our study, we explored the extent to which standardized phenotyping will succeed in detecting biologically relevant phenotypic differences in mice generated and provided by different collaborators. We analyzed quantitative metabolic data (body mass, energy intake, and energy metabolized) collected at the GMC under the current workflow, and used them for statistical power considerations. Our results demonstrate that there is substantial variability in these parameters among lines of wild-type C57BL/6 (B6) mice from different sources. Given this variable background noise in mice that serve as controls, subtle phenotypes in mutant or transgenic littermates may be overlooked. Furthermore, a phenotype observed in one cohort of a mutant line may not be reproducible (to the same extent) in mice coming from a different environment or supplier. In the light of these constraints, we encourage researchers to incorporate information on intrastrain variability into future study planning, or to perform advanced hierarchical analyses. Both will ultimately improve the detectability of novel phenotypes by phenotypic screening.

  3. 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

  4. A comparison of alternating current and direct current electrospray ionization for mass spectrometry.

    PubMed

    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. PMID:24464359

  5. Comparison of the diagnostic accuracy of direct digital radiography system, filtered images, and subtraction radiography

    PubMed Central

    Takeshita, Wilton Mitsunari; Vessoni Iwaki, Lilian Cristina; Da Silva, Mariliani Chicarelli; Filho, Liogi Iwaki; Queiroz, Alfredo De Franco; Geron, Lucas Bachegas Gomes

    2013-01-01

    Background: To compare the diagnostic accuracy of three different imaging systems: Direct digital radiography system (DDR-CMOS), four types of filtered images, and a priori and a posteriori registration of digital subtraction radiography (DSR) in the diagnosis of proximal defects. Materials and Methods: The teeth were arranged in pairs in 10 blocks of vinyl polysiloxane, and proximal defects were performed with drills of 0.25, 0.5, and 1 mm diameter. Kodak RVG 6100 sensor was used to capture the images. A posteriori DSR registrations were done with Regeemy 0.2.43 and subtraction with Image Tool 3.0. Filtered images were obtained with Kodak Dental Imaging 6.1 software. Images (n = 360) were evaluated by three raters, all experts in dental radiology. Results: Sensitivity and specificity of the area under the receiver operator characteristic (ROC) curve (Az) were higher for DSR images with all three drills (Az = 0.896, 0.979, and 1.000 for drills 0.25, 0.5, and 1 mm, respectively). The highest values were found for 1-mm drills and the lowest for 0.25-mm drills, with negative filter having the lowest values of all (Az = 0.631). Conclusion: The best method of diagnosis was by using a DSR. The negative filter obtained the worst results. Larger drills showed the highest sensitivity and specificity values of the area under the ROC curve. PMID:24124300

  6. 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

  7. 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.

  8. 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. PMID:26960783

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

    PubMed Central

    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. PMID:24910629

  10. Comparison of advection and steam fogs: From direct observation over the sea

    NASA Astrophysics Data System (ADS)

    Heo, Ki-Young; Ha, Kyung-Ja; Mahrt, Larry; Shim, Jae-Seol

    2010-11-01

    Sea fog occurs frequently over the Yellow Sea in spring and summer, which causes costly or even catastrophic events including property damage, marine accidents, public health and financial losses. Case studies of advection and steam fogs using direct observation over the sea are constructed to better understand their formation, evolution and dissipation. A southerly wind supplies moisture to initiate advection fog events (AFs). Approximately -100 to -200 W m-2 of latent heat flux and -70 W m-2 of sensible heat flux during mature AFs are characterized with stable stratification which maintains dense fog by limiting downward mixing of dryer air. Steam fogs (SFs) develop from flow of cold air over warmer water, but are normally of limited persistence. During the SFs, a northerly wind decreases the air temperature below the sea surface temperature, which increases the relative humidity through evaporation from the warmer ocean. During mature SF, 360 W m-2 of latent heat flux and 150 W m-2 of sensible heat flux are characterized with neutral and unstable atmospheric conditions. The increase in wind speed and wind shear mixes dry air downward to the surface and limits the duration of the SF.

  11. A Comparison of Direct and Two-Stage Transportation of Patients to Hospital in Poland

    PubMed Central

    Rosiek, Anna; Rosiek-Kryszewska, Aleksandra; Leksowski, Łukasz; Leksowski, Krzysztof

    2015-01-01

    Background: The rapid international expansion of telemedicine reflects the growth of technological innovations. This technological advancement is transforming the way in which patients can receive health care. Materials and Methods: The study was conducted in Poland, at the Department of Cardiology of the Regional Hospital of Louis Rydygier in Torun. The researchers analyzed the delay in the treatment of patients with acute coronary syndrome. The study was conducted as a survey and examined 67 consecutively admitted patients treated invasively in a two-stage transport system. Data were analyzed statistically. Results: Two-stage transportation does not meet the timeframe guidelines for the treatment of patients with acute myocardial infarction. Intervals for the analyzed group of patients were statistically significant (p < 0.0001). Conclusions: Direct transportation of the patient to a reference center with interventional cardiology laboratory has a significant impact on reducing in-hospital delay in case of patients with acute coronary syndrome. Perspectives: This article presents the results of two-stage transportation of the patient with acute coronary syndrome. This measure could help clinicians who seek to assess time needed for intervention. It also shows how time from the beginning of pain in chest is important and may contribute to patient disability, death or well-being. PMID:25918911

  12. 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

  13. 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.

  14. 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.

  15. Template-directed molecular assembly on silicon carbide nanomesh: comparison between CuPc and pentacene.

    PubMed

    Shi, Chen; Wei, Chen; Han, Huang; Xingyu, Gao; Dongchen, Qi; Yuzhan, Wang; Wee, Andrew T S

    2010-02-23

    The template-directed assembly of two planar molecules (copper phthalocyanine (CuPc) and pentacene) on SiC nanomesh has been studied by scanning tunneling microscopy and photoelectron spectroscopy, respectively. Both molecules are trapped as single molecules in the cells of SiC nanomesh at low coverage. At high coverage, CuPc forms a highly ordered single-molecular array with identical symmetry and periodicity as the substrate, whereas pentacene forms a quasi-amorphous layer due to the random mixture of three different adsorption configurations. This difference in adsorption behavior is attributed to differences in molecular geometries. The measured changes of work functions reveal weak charge transfer between the molecules and substrate. Both molecules are preferentially adsorbed on the SiC nanomesh rather than on graphene. The CuPc single-molecular array possesses good long-range order, large area coverage, and a molecular density of over 3.0 x 10(13) molecules/cm(2). PMID:20050639

  16. 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.

  17. Fixation of acetabular fractures via the ilioinguinal versus pararectus approach: a direct comparison.

    PubMed

    Märdian, S; Schaser, K D; Hinz, P; Wittenberg, S; Haas, N P; Schwabe, P

    2015-09-01

    This study compared the quality of reduction and complication rate when using a standard ilioinguinal approach and the new pararectus approach when treating acetabular fractures surgically. All acetabular fractures that underwent fixation using either approach between February 2005 and September 2014 were retrospectively reviewed and the demographics of the patients, the surgical details and complications were recorded. A total of 100 patients (69 men, 31 women; mean age 57 years, 18 to 93) who were consecutively treated were included for analysis. The quality of reduction was assessed using standardised measurement of the gaps and steps in the articular surface on pre- and post-operative CT-scans. There were no significant differences in the demographics of the patients, the surgical details or the complications between the two approaches. A significantly better reduction of the gap, however, was achieved with the pararectus approach (axial: p = 0.025, coronal: p = 0.013, sagittal: p = 0.001). These data suggest that the pararectus approach is at least equal to, or in the case of reduction of the articular gap, superior to the ilioinguinal approach. This approach allows direct buttressing of the dome of the acetabulum and the quadrilateral plate, which is particularly favourable in geriatric fracture patterns. PMID:26330596

  18. Comparison: Direct thrust nuclear engine, nuclear electric engine, and a chemical engine for future space missions

    SciTech Connect

    Ramsthaler, J.H.; Sulmeisters, T.K.

    1988-01-01

    The need for an advanced direct thrust nuclear rocket propulsion engine has been identified in Project Forecast 2, Air Force Systems Command report which looks into future Air Force needs. The Air Force Astronautical Laboratory (AFAL) has been assigned responsibility for developing the nuclear engine, and they in turn have requested support from teams of contractors who have the full capability to assist in the development of the nuclear engine. The Idaho National Engineering Laboratory (INEL) has formed a team of experts with Martin Marietta for mission analysis. Science Applications International (SAIC) for flight safety analysis, Westinghouse for the nuclear subsystem, and Rocketdyne for the engine system. INEL is the overall program manager and manager for test facility design, construction and operation. The INEL team has produced plans for both the engine system and the ground test facility. AFAL has funded the INEL team to perform mission analyses to evaluate the cost, performance and operational advantages for a nuclear rocket engine in performing Air Force Space Missions. For those studies, the Advanced Nuclear Rocket Engine (ANRE), a scaled down NERVA derivative, was used as the baseline nuclear engine to compare against chemical engines and nuclear electric engines for performance of orbital transfer and maneuvering missions. 3 tabs.

  19. 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.

  20. 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.

  1. Direct numerical simulation of pore-scale flow in a bead pack: Comparison with magnetic resonance imaging observations

    NASA Astrophysics Data System (ADS)

    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 uncertainty 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. 2012 Elsevier Science.

  2. 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.

  3. 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. PMID:23454220

  4. Direct Stimulatory Effects of Oxytocin in Female Rat Gonadotrophs and Somatotrophs In Vitro: Comparison With Lactotrophs

    PubMed Central

    Fletcher, Patrick A.; Arias-Cristancho, José A.; Cristancho-Gordo, Ruth; Helena, Cleyde V.; Bertram, Richard; Tabak, Joël

    2015-01-01

    The peptide oxytocin (OT) is secreted by hypothalamic neurons and exerts numerous actions related to reproduction. OT stimulation of prolactin secretion in female rats is important during the estrous cycle, pregnancy, and lactation. Here we report that OT also stimulates transients of intracellular Ca2+ concentration in somatotrophs and gonadotrophs as well as the release of GH and LH in a dose-dependent manner with EC50 values that closely correspond to the ligand affinity of the OT receptor (OTR). Remarkably, the hormone-releasing effect of OT in these two cell types is 2 orders of magnitude more sensitive than that in lactotrophs. The specific OTR agonist [Thr4,Gly7]-oxytocin acutely stimulated the release of LH, GH, and prolactin from female rat pituitary cells in primary culture and increased intracellular Ca2+ concentration in gonadotrophs, somatotrophs, and lactotrophs. In these three cell types, the effects on hormone release and intracellular Ca2+ of both OT and [Thr4,Gly7]oxytocin were abolished by the specific OT receptor antagonist desGly-NH2-d(CH2)5[D-Tyr2,Thr4]OVT but not by the highly selective vasopressin V1a receptor antagonist, d(CH2)5[Tyr(Me)2,Dab5]AVP. Furthermore, 10 nM arginine vasopressin stimulated LH and GH release comparably with a dose of OT that was at least 10 times lower. Finally, the presence of the OTR-like immunoreactivity could be observed in all three cell types. Taken together, these results show that OT directly stimulates gonadotrophs, somatotrophs, and lactotrophs through OT receptors and suggest that OT signaling may serve to coordinate the release of different pituitary hormones during specific physiological conditions. PMID:25406939

  5. Direct Comparison of Rat- and Human-Derived Ganglionic Eminence Tissue Grafts on Motor Function.

    PubMed

    Lelos, Mariah J; Roberton, Victoria H; Vinh, Ngoc-Nga; Harrison, Carl; Eriksen, Peter; Torres, Eduardo M; Clinch, Susanne P; Rosser, Anne E; Dunnett, Stephen B

    2016-01-01

    Huntington's disease (HD) is a debilitating, genetically inherited neurodegenerative disorder that results in early loss of medium spiny neurons from the striatum and subsequent degeneration of cortical and other subcortical brain regions. Behavioral changes manifest as a range of motor, cognitive, and neuropsychiatric impairments. It has been established that replacement of the degenerated medium spiny neurons with rat-derived fetal whole ganglionic eminence (rWGE) tissue can alleviate motor and cognitive deficits in preclinical rodent models of HD. However, clinical application of this cell replacement therapy requires the use of human-derived (hWGE), not rWGE, tissue. Despite this, little is currently known about the functional efficacy of hWGE. The aim of this study was to directly compare the ability of the gold standard rWGE grafts, against the clinically relevant hWGE grafts, on a range of behavioral tests of motor function. Lister hooded rats either remained as unoperated controls or received unilateral excitotoxic lesions of the lateral neostriatum. Subsets of lesioned rats then received transplants of either rWGE or hWGE primary fetal tissue into the lateral striatum. All rats were tested postlesion and postgraft on the following tests of motor function: staircase test, apomorphine-induced rotation, cylinder test, adjusting steps test, and vibrissae-evoked touch test. At 21 weeks postgraft, brain tissue was taken for histological analysis. The results revealed comparable improvements in apomorphine-induced rotational bias and the vibrissae test, despite larger graft volumes in the hWGE cohort. hWGE grafts, but not rWGE grafts, stabilized behavioral performance on the adjusting steps test. These results have implications for clinical application of cell replacement therapies, as well as providing a foundation for the development of stem cell-derived cell therapy products. PMID:26727032

  6. Direct comparison of NPPB and DPC as probes of CFTR expressed in Xenopus oocytes.

    PubMed

    Zhang, Z R; Zeltwanger, S; McCarty, N A

    2000-05-01

    Blockers of CFTR with well-characterized kinetics and mechanism of action will be useful as probes of pore structure. We have studied the mechanism of block of CFTR by the arylaminobenzoates NPPB and DPC. Block of macroscopic currents by NPPB and DPC exhibited similar voltage-dependence, suggestive of an overlapping binding region. Kinetic analysis of single-channel currents in the presence of NPPB indicate drug-induced closed time constants averaging 2.2 msec at -100 mV. The affinity for NPPB calculated from single-channel block, K(D) = 35 microm, exceeds that for other arylaminobenzoates studied thus far. These drugs do not affect the rate of activation of wild-type (WT) channels expressed in oocytes, consistent with a simple mechanism of block by pore occlusion, and appear to have a single binding site in the pore. Block by NPPB and DPC were affected by pore-domain mutations in different ways. In contrast to its effects on block by DPC, mutation T1134F-CFTR decreased the affinity and reduced the voltage-dependence for block by NPPB. We also show that the alteration of macroscopic block by NPPB and DPC upon changes in bath pH is due to both direct effects (i.e., alteration of voltage-dependence) and indirect effects (alteration of cytoplasmic drug loading). These results indicate that both NPPB and DPC block CFTR by entering the pore from the cytoplasmic side and that the structural requirements for binding are not the same, although the binding regions within the pore are similar. The two drugs may be useful as probes for overlapping regions in the pore. PMID:10811966

  7. Waterpipe Tobacco Smoking and Cigarette Smoking: A Direct Comparison of Toxicant Exposure and Subjective Effects

    PubMed Central

    Cobb, Caroline O.; Shihadeh, Alan; Weaver, Michael F.

    2011-01-01

    Introduction: Waterpipe tobacco smoking is increasing worldwide and is believed by many users to be less harmful and addictive than cigarette smoking. In fact, waterpipe tobacco and cigarette smoke contain many of the same chemicals, and users are exposed to the dependence-producing drug nicotine as well as other smoke toxicants. The subjective effect profile of these 2 tobacco use methods has not been compared directly, though this information is relevant to understanding the risk of dependence development. Methods: Fifty-four participants who reported waterpipe and cigarette smoking completed 2, 45-min, counter-balanced sessions in which they completed a waterpipe use episode (mean smoking time = 43.3 min) or a cigarette (mean = 6.1 min). Outcome measures included plasma nicotine, carboxyhemoglobin (COHb), and subjective effects, including those relevant to predicting dependence potential. Results: Mean (±SEM) peak plasma nicotine concentration did not differ by session (waterpipe = 9.8 ± 1.0 ng/ml; cigarette = 9.4 ± 1.0 ng/ml). Mean peak COHb concentration differed significantly (waterpipe = 4.5% ± 0.3%; cigarette = 1.2% ± 0.1%). Subjective effect changes for waterpipe and cigarette were comparable in magnitude but often longer lived for waterpipe. Conclusions: Relative to a cigarette, waterpipe tobacco smoking was associated with similar peak nicotine exposure, 3.75-fold greater COHb, and 56-fold greater inhaled smoke volume. Waterpipe and cigarette influenced many of the same subjective effect measures. These findings are consistent with the conclusion that waterpipe tobacco smoking presents substantial risk of dependence, disease, and death, and they can be incorporated into prevention interventions that might help deter more adolescents and young adults from experimenting with an almost certainly lethal method of tobacco use. PMID:21127030

  8. Comparison of direct and alternating current vacuum ultraviolet lamps in atmospheric pressure photoionization.

    PubMed

    Vaikkinen, Anu; Haapala, Markus; Kersten, Hendrik; Benter, Thorsten; Kostiainen, Risto; Kauppila, Tiina J

    2012-02-01

    A direct current induced vacuum ultraviolet (dc-VUV) krypton discharge lamp and an alternating current, radio frequency (rf) induced VUV lamp that are essentially similar to lamps in commercial atmospheric pressure photoionization (APPI) ion sources were compared. The emission distributions along the diameter of the lamp exit window were measured, and they showed that the beam of the rf lamp is much wider than that of the dc lamp. Thus, the rf lamp has larger efficient ionization area, and it also emits more photons than the dc lamp. The ionization efficiencies of the lamps were compared using identical spray geometries with both lamps in microchip APPI mass spectrometry (μAPPI-MS) and desorption atmospheric pressure photoionization-mass spectrometry (DAPPI-MS). A comprehensive view on the ionization was gained by studying six different μAPPI solvent compositions, five DAPPI spray solvents, and completely solvent-free DAPPI. The observed reactant ions for each solvent composition were very similar with both lamps except for toluene, which showed a higher amount of solvent originating oxidation products with the rf lamp than with the dc lamp in μAPPI. Moreover, the same analyte ions were detected with both lamps, and thus, the ionization mechanisms with both lamps are similar. The rf lamp showed a higher ionization efficiency than the dc lamp in all experiments. The difference between the lamp ionization efficiencies was greatest when high ionization energy (IE) solvent compositions (IEs above 10 eV), i.e., hexane, methanol, and methanol/water, (1:1 v:v) were used. The higher ionization efficiency of the rf lamp is likely due to the larger area of high intensity light emission, and the resulting larger efficient ionization area and higher amount of photons emitted. These result in higher solvent reactant ion production, which in turn enables more efficient analyte ion production. PMID:22229729

  9. Direct comparisons of hand and mouth kinematics during grasping, feeding and fork-feeding actions

    PubMed Central

    Quinlan, D. J.; Culham, J. C.

    2015-01-01

    While a plethora of studies have examined the kinematics of human reach-to-grasp actions, few have investigated feeding, another ethologically important real-world action. Two seminal studies concluded that the kinematics of the mouth during feeding are comparable to those of the hand during grasping (Castiello, 1997; Churchill et al., 1999); however, feeding was done with a fork or spoon, not with the hand itself. Here, we directly compared grasping and feeding kinematics under equivalent conditions. Participants were presented with differently sized cubes of cheese (10-, 20- or 30-mm on each side) and asked to use the hand to grasp them or to use a fork to spear them and then bring them to the mouth to bite. We measured the apertures of the hand during grasping and the teeth during feeding, as well as reaching kinematics of the arm in both tasks. As in many past studies, we found that the hand oversized considerably larger (~11–27 mm) than the food item during grasping; moreover, the amount of oversizing scaled with food size. Surprisingly, regardless of whether the hand or fork was used to transport the food, the mouth oversized only slightly larger (~4–11 mm) than the food item during biting and the oversizing did not increase with food size. Total movement times were longer when using the fork compared to the hand, particularly when using the fork to bring food to the mouth. While reach velocity always peaked approximately halfway through the movement, relative to the reach the mouth opened more slowly than the hand, perhaps because less time was required for the smaller oversizing. Taken together, our results show that while many aspects of kinematics share some similarity between grasping and feeding, oversizing may reflect strategies unique to the hand vs. mouth (such as the need to have the digits approach the target surface perpendicularly for grip stability during lifting) and differences in the neural substrates of grasping and feeding. PMID

  10. 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

  11. Morphological comparison of the craniofacial phenotypes of mouse models expressing the Apert FGFR2 S252W mutation in neural crest- or mesoderm-derived tissues

    PubMed Central

    Heuzé, Yann; Singh, Nandini; Basilico, Claudio; Jabs, Ethylin Wang; Holmes, Greg; Richtsmeier, Joan T

    2014-01-01

    Bones of the craniofacial skeleton are derived from two distinct cell lineages, cranial neural crest and mesoderm, and articulate at sutures and synchondroses which represent major bone growth sites. Premature fusion of cranial suture(s) is associated with craniofacial dysmorphogenesis caused in part by alteration in the growth potential at sutures and can occur as an isolated birth defect or as part of a syndrome, such as Apert syndrome. Conditional expression of the Apert FGFR2 S252W mutation in mesoderm was previously shown to be necessary and sufficient to cause coronal craniosynostosis. Here we used micro computed tomography images of mice expressing the Apert mutation constitutively in either mesoderm or neural crest to quantify craniofacial shape variation and suture fusion patterns, and to identify shape changes in craniofacial bones derived from the lineage not expressing the mutation, referred to here as secondary shape changes. Our results show that at postnatal day 0: (i) conditional expression of the FGFR2 S252W mutation in neural crest-derived tissues causes a more severe craniofacial phenotype than when expressed in mesoderm-derived tissues; and (ii) both mesoderm- and neural crest-specific mouse models display secondary shape changes. We also show that premature suture fusion is not necessarily dependent on the expression of the FGFR2 S252W mutation in the sutural mesenchyme. More specifically, it appears that suture fusion patterns in both mouse models are suture-specific resulting from a complex combination of the influence of primary abnormalities of biogenesis or signaling within the sutures, and timing. PMID:24632501

  12. 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

  13. Comparison of the direct platelet immunofluorescence test (direct PIFT) with a modified direct monoclonal antibody-specific immobilization of platelet antigens (direct MAIPA) in detection of platelet-associated IgG.

    PubMed

    Joutsi, L; Kekomäki, R

    1997-01-01

    Glycoprotein (GP)-specific platelet-associated IgG (PA-IgG) may be demonstrable in autoimmune-mediated thrombocytopenia. We studied 159 consecutive patients with histories of thrombocytopenia by a modified direct monoclonal antibody-specific immobilization of platelet antigens (direct MAIPA) assay, which immobilizes GP IIb/ IIIa, GP Ib/IX and GP Ia/IIa simultaneously. This modification requires smaller quantities of platelets than standard measurements performed separately. PA-IgG was present in 84/159 (53%) patients, as shown by the direct platelet immunofluorescence test (PIFT) with flow cytometry as a reference. PA-IgG against GP IIb/IIIa and/or GP Ib/IX and/or GP Ia/IIa was noted in 46 patients (29%), of whom 93% (43/46)-were also PA-IgG positive. The amount of PA-IgG detected by PIFT correlated directly with that detected by direct MAIPA (r = 0.71; P < 0.001). Only three patients 12548 with negative direct PIFT had GP-specific PA-IgG. GPV-specific PA-IgG was detected in 13 (10%) of the 125 patients, in whom further studies could be performed. In the subgroup of patients with GP-specific PA-IgG, the median fluorescence intensities of direct PIFT were higher than in patients with no GP-specific PA-IgG (P < 0.001). Direct PIFT and direct MAIPA divided the patients into asymmetric subgroups. However, the relative roles of these tests in the diagnosis of autoimmune-mediated thrombocytopenia await further studies. PMID:9012711

  14. Phenotype MicroArrays for High-Throughput Phenotypic Testing and Assay of Gene Function

    PubMed Central

    Bochner, Barry R.; Gadzinski, Peter; Panomitros, Eugenia

    2001-01-01

    The bacterium Escherichia coli is used as a model cellular system to test and validate a new technology called Phenotype MicroArrays (PMs). PM technology is a high-throughput technology for simultaneous testing of a large number of cellular phenotypes. It consists of preconfigured well arrays in which each well tests a different cellular phenotype and an automated instrument that continuously monitors and records the response of the cells in all wells of the arrays. For example, nearly 700 phenotypes of E. coli can be assayed by merely pipetting a cell suspension into seven microplate arrays. PMs can be used to directly assay the effects of genetic changes on cells, especially gene knock-outs. Here, we provide data on phenotypic analysis of six strains and show that we can detect expected phenotypes as well as, in some cases, unexpected phenotypes. PMID:11435407

  15. Lp(a) glycoprotein phenotypes. Inheritance and relation to Lp(a)-lipoprotein concentrations in plasma.

    PubMed Central

    Utermann, G; Menzel, H J; Kraft, H G; Duba, H C; Kemmler, H G; Seitz, C

    1987-01-01

    The Lp(a) lipoprotein represents a quantitative genetic trait. It contains two different polypeptide chains, the Lp(a) glycoprotein and apo B-100. We have demonstrated the Lp(a) glycoprotein directly in human sera by sodium dodecyl sulfate-gel electrophoresis under reducing conditions after immunoblotting using anti-Lp(a) serum and have observed inter- and intraindividual size heterogeneity of the glycoprotein with apparent molecular weights ranging from approximately 400,000-700,000 D. According to their relative mobilities compared with apo B-100 Lp(a) patterns were categorized into phenotypes F (faster than apo B-100), B (similar to apo B-100), S1, S2, S3, and S4 (all slower than apo B-100), and into the respective double-band phenotypes. Results from neuraminidase treatment of isolated Lp(a) glycoprotein indicate that the phenotypic differences do not reside in the sialic acid moiety of the glycoprotein. Family studies are compatible with the concept that Lp(a) glycoprotein phenotypes are controlled by a series of autosomal alleles (Lp[a]F, Lp[a]B, Lp[a]S1, Lp[a]S2, Lp[a]S3, Lp[a]S4, and Lp[a]0) at a single locus. Comparison of Lp(a) plasma concentrations in different phenotypes revealed a highly significant association of phenotype with concentration. Phenotypes B, S1, and S2 are associated with high and phenotypes S3 and S4 with low Lp(a) concentrations. This suggests that the same gene locus is involved in determining Lp(a) glycoprotein phenotypes and Lp(a) lipoprotein concentrations in plasma and is the first indication for structural differences underlying the quantitative genetic Lp(a)-trait. Images PMID:2956279

  16. 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

  17. 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

  18. Citrullinemia: phenotypic variations.

    PubMed

    Whelan, D T; Brusso, T; Spate, M

    1976-06-01

    An 18-month-old female infant was found to have citrullinemia on routine plasma screening by the Scriver Method at 5 days of age. At 10 days of age, plasma citrulline concentration was 0.704mumol/ml (normal, 0.010 to 0.030mumol/ml) and has remained 60 to 80 times higher than normal. Urine citrulline concentration was markedly elevated. Hyperammonemia occurred at 1 month of age. The serum ammonia concentration was 473mug/100 ml (normal, 50 to 250 mug/100 ml) and rose to 770mug/100 ml at 4 months of age. Dietary protein was restricted to 1.6 gm/kg/day. Without further change in protein intake, the serum ammonia concentration decreased to 280mug/100 ml and, since then, it has returned to normal. The addition of three synthetic L-amino acids was required for a short time during dietary therapy. At 10 months of age, the infant was given a normal diet. At 18 months of age, her physical and mental development is normal. Activity of argininosuccinic acid synthetase measured in skin fibroblasts was 0.0037mumol of radioactive carbon dioxide per milligram of protein per hour. To demonstrate heterozygosity, fasting plasma citrulline concentrations were measured in five members of the family. Comparison of findings in this patient with those reported in the literature suggests phenotypical variation of the disease, probably due to genetic heterogeneity. PMID:934749

  19. Detecting virulence and drug resistance mycobacterial phenotypes in vivo

    PubMed Central

    Timmins, Graham

    2015-01-01

    Bacterial phenotypes are predominantly studied in culture because detection of their specific metabolic pathways in the host is challenging. Development of stable isotope breath tests allowing in situ phenotype analyses may endow diagnostics with new modalities based upon direct monitoring of in vivo microbial metabolism and host–pathogen phenotypic interactions. PMID:25800730

  20. Generation of mesenchymal stromal cells in the presence of platelet lysate: a phenotypic and functional comparison of umbilical cord blood- and bone marrow-derived progenitors

    PubMed Central

    Avanzini, Maria Antonietta; Bernardo, Maria Ester; Cometa, Angela Maria; Perotti, Cesare; Zaffaroni, Nadia; Novara, Francesca; Visai, Livia; Moretta, Antonia; Del Fante, Claudia; Villa, Raffaella; Ball, Lynne M.; Fibbe, Willem E.; Maccario, Rita; Locatelli, Franco

    2009-01-01

    Background Mesenchymal stromal cells are employed in various different clinical settings in order to modulate immune response. However, relatively little is known about the mechanisms responsible for their immunomodulatory effects, which could be influenced by both the cell source and culture conditions. Design and Methods We tested the ability of a 5% platelet lysate-supplemented medium to support isolation and ex vivo expansion of mesenchymal stromal cells from full-term umbilical-cord blood. We also investigated the biological/functional properties of umbilical cord blood mesenchymal stromal cells, in comparison with platelet lysate-expanded bone marrow mesenchymal stromal cells. Results The success rate of isolation of mesenchymal stromal cells from umbilical cord blood was in the order of 20%. These cells exhibited typical morphology, immunophenotype and differentiation capacity. Although they have a low clonogenic efficiency, umbilical cord blood mesenchymal stromal cells may possess high proliferative potential. The genetic stability of these cells from umbilical cord blood was demonstrated by a normal molecular karyotype; in addition, these cells do not express hTERT and telomerase activity, do express p16ink4a protein and do not show anchorage-independent cell growth. Concerning alloantigen-specific immune responses, umbilical cord blood mesenchymal stromal cells were able to: (i) suppress T- and NK-lymphocyte proliferation, (ii) decrease cytotoxic activity and (iii) only slightly increase interleukin-10, while decreasing interferon-γ secretion, in mixed lymphocyte culture supernatants. While an indoleamine 2,3-dioxygenase-specific inhibitor did not reverse mesenchymal stromal cell-induced suppressive effects, a prostaglandin E2-specific inhibitor hampered the suppressive effect of both umbilical cord blood- and bone marrow-mesenchymal stromal cells on alloantigen-induced cytotoxic activity. Mesenchymal stromal cells from both sources expressed HLA

  1. 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

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

    DOE PAGESBeta

    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. 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

  3. Expression of H-ras correlates with metastatic potential: evidence for direct regulation of the metastatic phenotype in 10T1/2 and NIH 3T3 cells.

    PubMed Central

    Egan, S E; McClarty, G A; Jarolim, L; Wright, J A; Spiro, I; Hager, G; Greenberg, A H

    1987-01-01

    Using three independent approaches, we studied the effects of H-ras on metastasis formation. Analysis of five in vitro-ras-transfected 10T1/2 clones with either flat or refractile morphologies revealed a relationship between metastatic potential, H-ras expression, and anchorage-independent growth. Four metastatic variants derived from a poorly metastatic, low-H-ras-expressing line all expressed high levels of H-ras RNA and grew efficiently in soft agar. Activation of H-ras expression in the metastatic tumors had occurred through amplification and rearrangement of H-ras sequences. In addition, preinduction of p21 synthesis in NIH 3T3 line 433, which contains v-H-ras under transcriptional control of the glucocorticoid-sensitive mouse mammary tumor virus long terminal repeat, significantly increased metastatic efficiency. Glucocorticoid treatment of normal or pEJ-transformed NIH 3T3 cells did not affect metastatic potential. These data reveal a direct relationship between ras expression and metastasis formation and suggest that metastatic and transformed phenotypes may be coregulated in ras-transformed 10T1/2 and NIH 3T3 cells. Images PMID:3102946

  4. Normal adult ramified microglia separated from other central nervous system macrophages by flow cytometric sorting: Phenotypic differences defined and direct ex vivo antigen presentation to myelin basic protein-reactive CD4{sup +} T cells compared

    SciTech Connect

    Ford, A.L.; Goodsall, A.L.; Sedgwick, J.D.

    1995-05-01

    Ramified microglia in the adult central nervous system (CNS) are the principal glial element up-regulating MHC class I and II expression in response to inflammatory events or neuronal damage. A proportion of these cells also express MHC class II constitutively in the normal CNS. The role of microglia as APCs for CD4{sup +} cells extravasating into the CNS remains undefined. In this study, using irradiation bone marrow chimeras in CD45-congenic rats, the phenotype CD45{sup low}CD11b/c{sup +} is shown to identify microglial cells specifically within the CNS. Highly purified populations of microglia and nonmicroglial but CNS-associated macrophages (CD45{sup high}CD11b/c{sup +}) have been obtained directly from the adult CNS, by using flow cytometric sorting. Morphologically, freshly isolated microglia vs other CNS macrophages are quite distinct. Of the two populations recovered from the normal CNS, it is the minority CD45{sup high}CD11 b/c{sup +} transitional macrophage population, and not microglia, that is the effective APC for experimental autoimmune encephalomyelitis-inducing CD4{sup +} myelin basic protein (MBP)-reactive T cells. CD45{sup high}CD11b/c{sup +} CNS macrophages also stimulate MBP-reactive T cells without addition of MBP to culture suggesting presentation of endogenous Ag. This is the first study in which microglia vs other CNS macrophages have been analyzed for APC ability directly from the CNS, with substantial cross-contamination between the two populations eliminated. The heterogeneity of these populations in terms of APC function is clearly demonstrated. Evidence is still lacking that adult CNS microglia have the capacity to interact with and stimulate CD4{sup +} T cells to proliferate or secrete IL-2. 60 refs., 6 figs., 1 tab.

  5. Direct comparison of magnetic resonance imaging and conductance microcatheter in the evaluation of left ventricular function in mice.

    PubMed

    Jacoby, Christoph; Molojavyi, Andrei; Flögel, Ulrich; Merx, Marc W; Ding, Zhaoping; Schrader, Jürgen

    2006-01-01

    The aim of the present work was to study the reliability of conductance microcatheter volumetric measurements as compared to magnetic resonance imaging (MRI) in the same set of mice. Mice left ventricular (LV) volumes were monitored under basal conditions and in a hypertrophy model induced by transverse aortic constriction (TAC). Cardiac function was evaluated in isoflurane anesthetized mice (n = 8) by MRI followed by 1.4 F Millar microtip catheter measurements. The second group of mice with TAC-induced cardiac hypertrophy was studied eight weeks after surgery. Reliability of 3D-reconstructed MRI data was confirmed by comparison with autopsy masses (autopsy LV mass = 73.6 +/- 3.4 mg; MRI LV mass = 76.9 +/- 3.7 mg). Conduction catheter was found to greatly underestimate end-diastolic and end-systolic volumes and thus stroke volume as well as cardiac output in control mice (MRI: EDV = 79 +/- 8 microl, ESV = 27+/-9 microl, SV = 51 +/- 9 microl, CO = 25 +/- 6 ml/min; Catheter: EDV = 28 +/- 5 microl, ESV = 8 +/- 4 microl, SV = 19 +/- 4 microl, CO = 10 +/- 2 ml/min). However, values for ejection fraction showed no significant differences between the two methods. In the hypertrophy model, stroke volume and cardiac output were increased when measured with MRI (SV: +19 +/- 20%; CO: +28 +/- 27%), whereas catheter data showed opposite directional changes (SV: -22 +/- 37%; CO: -31 +/- 37%). Ejection fraction was found to be reduced only in catheter measurements (-31 +/- 26%). In summary, our data demonstrate that absolute volumetric values are strikingly underestimated by conduction catheter measurements and that even detection of directional changes with this method may not always be feasible. PMID:16132173

  6. Comparison of User-Directed and Automatic Mapping of the Planned Isocenter to Treatment Space for Prostate IGRT

    PubMed Central

    Wang, Andrew; Kress, Andrea; Qin, An; Cullip, Timothy; Tracton, Gregg; Yan, Di; Chaney, Edward

    2013-01-01

    Image-guided radiotherapy (IGRT), adaptive radiotherapy (ART), and online reoptimization rely on accurate mapping of the radiation beam isocenter(s) from planning to treatment space. This mapping involves rigid and/or nonrigid registration of planning (pCT) and intratreatment (tCT) CT images. The purpose of this study was to retrospectively compare a fully automatic approach, including a non-rigid step, against a user-directed rigid method implemented in a clinical IGRT protocol for prostate cancer. Isocenters resulting from automatic and clinical mappings were compared to reference isocenters carefully determined in each tCT. Comparison was based on displacements from the reference isocenters and prostate dose-volume histograms (DVHs). Ten patients with a total of 243 tCTs were investigated. Fully automatic registration was found to be as accurate as the clinical protocol but more precise for all patients. The average of the unsigned x, y, and z offsets and the standard deviations (σ) of the signed offsets computed over all images were (avg. ±  σ (mm)): 1.1 ± 1.4, 1.8 ± 2.3, 2.5 ± 3.5 for the clinical protocol and 0.6 ± 0.8, 1.1 ± 1.5 and 1.1 ± 1.4 for the automatic method. No failures or outliers from automatic mapping were observed, while 8 outliers occurred for the clinical protocol. PMID:24348526

  7. 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.

  8. Comparison of epoxy- and siloxane-based single-mode optical waveguides defined by direct-write lithography

    NASA Astrophysics Data System (ADS)

    Elmogi, Ahmed; Bosman, Erwin; Missinne, Jeroen; Van Steenberge, Geert

    2016-02-01

    This paper reports on the fabrication and characterization of single-mode polymer optical waveguides at telecom and SOI compatible wavelengths; by making a comparison between an epoxy and a siloxane polymer waveguide material system (both commercially-available). The proposed waveguides can be used in short-reach optical interconnects targeting chip-to-chip communication on the interposer level or providing a coupling interface between single-mode optical fibers and photonic integrated circuits (PICs). This technology enables the integration of optoelectronic chips for photonic packaging purposes. First, the single-mode dimensions (4 × 4 μm2 and 5 × 5 μm2) for both materials at selected wavelengths (1.31 μm and 1.55 μm) were determined based on the refractive index measurements. Then, the waveguides were patterned by a direct-write lithography method. The fabricated waveguides show a high-quality surface with smooth sidewalls. The optical propagation losses were measured using the cut-back method. For the siloxane-based waveguides, the propagation losses were found to be 0.34 dB/cm and 1.36 dB/cm at 1.31 μm and 1.55 μm respectively while for the epoxy-based waveguides the losses were 0.49 dB/cm and 2.23 dB/cm at 1.31 μm and 1.55 μm respectively.

  9. Density functional theory based direct comparison of coherent tunneling and electron hopping in redox-active single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Kastlunger, Georg; Stadler, Robert

    2015-03-01

    To define the conductance of single-molecule junctions with a redox functionality in an electrochemical cell, two conceptually different electron transport mechanisms, namely, coherent tunneling and vibrationally induced hopping, compete with each other, where implicit parameters of the setup such as the length of the molecule and the applied gate voltage decide which mechanism is the dominant one. Although coherent tunneling is most efficiently described within Landauer theory and the common theoretical treatment of electron hopping is based on Marcus theory, both theories are adequate for the processes they describe without introducing accuracy-limiting approximations. For a direct comparison, however, it has to be ensured that the crucial quantities obtained from electronic structure calculations, i.e., the transmission function T (E ) in Landauer theory and the transfer integral V , the reorganization energy λ , and the driving force Δ G0 in Marcus theory, are derived from similar grounds, as pointed out by Nitzan and coworkers in a series of publications. In this paper our framework is a single-particle picture, for which we perform density functional theory calculations for the conductance corresponding to both transport mechanisms for junctions with the central molecule containing one, two, or three Ruthenium centers, from which we extrapolate our results in order to define the critical length of the transition point of the two regimes which we identify at 5.76nm for this type of molecular wire. We also discuss trends in the dependence on an electrochemically induced gate potential.

  10. Comparison of one-dimensional probabilistic finite element method with direct numerical simulation of dynamically loaded heterogeneous materials

    NASA Astrophysics Data System (ADS)

    Robbins, Joshua; Voth, Thomas

    2011-06-01

    Material response to dynamic loading is often dominated by microstructure such as grain topology, porosity, inclusions, and defects; however, many models rely on assumptions of homogeneity. We use the probabilistic finite element method (WK Liu, IJNME, 1986) to introduce local uncertainty to account for material heterogeneity. The PFEM uses statistical information about the local material response (i.e., its expectation, coefficient of variation, and autocorrelation) drawn from knowledge of the microstructure, single crystal behavior, and direct numerical simulation (DNS) to determine the expectation and covariance of the system response (velocity, strain, stress, etc). This approach is compared to resolved grain-scale simulations of the equivalent system. The microstructures used for the DNS are produced using Monte Carlo simulations of grain growth, and a sufficient number of realizations are computed to ensure a meaningful comparison. Finally, comments are made regarding the suitability of one-dimensional PFEM for modeling material heterogeneity. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  11. 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.

  12. The Nature of Stable Insomnia Phenotypes

    PubMed Central

    Pillai, Vivek; Roth, Thomas; Drake, Christopher L.

    2015-01-01

    Study Objectives: We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Design: Longitudinal. Setting: Urban, community-based. Participants: Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). Interventions: None. Measurements and results: At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the “neither criterion” phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. Conclusions: By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With

  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. The Effect of Educational Modules Strategy on the Direct and Postponed Study's Achievement of Seventh Primary Grade Students in Science, in Comparison with the Conventional Approach

    ERIC Educational Resources Information Center

    Alelaimat, Abeer Rashed; Ghoneem, Khowla Abd Al Raheem

    2012-01-01

    This study aimed at revealing the effect of educational modules strategy on the direct and postponed study's achievement of seventh primary grade students in science, in comparison with the conventional approach. The sample of the study consists of (174) male and female students randomly chosen from schools in the city of Mafraq, students are…

  15. 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.

  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. PMID:23906572

  17. 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

  18. Novel phenotypes of prediabetes?

    PubMed

    Häring, Hans-Ulrich

    2016-09-01

    This article describes phenotypes observed in a prediabetic population (i.e. a population with increased risk for type 2 diabetes) from data collected at the University hospital of Tübingen. We discuss the impact of genetic variation on insulin secretion, in particular the effect on compensatory hypersecretion, and the incretin-resistant phenotype of carriers of the gene variant TCF7L2 is described. Imaging studies used to characterise subphenotypes of fat distribution, metabolically healthy obesity and metabolically unhealthy obesity are described. Also discussed are ectopic fat stores in liver and pancreas that determine the phenotype of metabolically healthy and unhealthy fatty liver and the recently recognised phenotype of fatty pancreas. The metabolic impact of perivascular adipose tissue and pancreatic fat is discussed. The role of hepatokines, particularly that of fetuin-A, in the crosstalk between these organs is described. Finally, the role of brain insulin resistance in the development of the different prediabetes phenotypes is discussed. PMID:27344314

  19. Phenotypic switching in bacteria

    NASA Astrophysics Data System (ADS)

    Merrin, Jack

    Living matter is a non-equilibrium system in which many components work in parallel to perpetuate themselves through a fluctuating environment. Physiological states or functionalities revealed by a particular environment are called phenotypes. Transitions between phenotypes may occur either spontaneously or via interaction with the environment. Even in the same environment, genetically identical bacteria can exhibit different phenotypes of a continuous or discrete nature. In this thesis, we pursued three lines of investigation into discrete phenotypic heterogeneity in bacterial populations: the quantitative characterization of the so-called bacterial persistence, a theoretical model of phenotypic switching based on those measurements, and the design of artificial genetic networks which implement this model. Persistence is the phenotype of a subpopulation of bacteria with a reduced sensitivity to antibiotics. We developed a microfluidic apparatus, which allowed us to monitor the growth rates of individual cells while applying repeated cycles of antibiotic treatments. We were able to identify distinct phenotypes (normal and persistent) and characterize the stochastic transitions between them. We also found that phenotypic heterogeneity was present prior to any environmental cue such as antibiotic exposure. Motivated by the experiments with persisters, we formulated a theoretical model describing the dynamic behavior of several discrete phenotypes in a periodically varying environment. This theoretical framework allowed us to quantitatively predict the fitness of dynamic populations and to compare survival strategies according to environmental time-symmetries. These calculations suggested that persistence is a strategy used by bacterial populations to adapt to fluctuating environments. Knowledge of the phenotypic transition rates for persistence may provide statistical information about the typical environments of bacteria. We also describe a design of artificial

  20. Comparison of unextruded air slip direct chill cast 6061 ingot with bar stock extruded from conventional direct chill cast 6061 ingot

    NASA Astrophysics Data System (ADS)

    Bergsma, S. C.; Kassner, M. E.

    1997-08-01

    Air Slip direct chill cast 6061 small diameter ingots (Direct Forge) were compared with 6061 extruded bar stock. The T6 mechanical properties were compared for both the Direct Forge ingot and the extruded bar stock, as well as cold impact extruded cylinders produced from Direct Forge small diameter ingot and extruded stock. It was found that the tensile and fatigue properties of Direct Forge ingot and cylinders from this ingot were significantly superior to those of extruded stock and cylinder produced from this stock. The improved properties are a result of higher solidification rates leading to smaller alloy-constituent dispersed particles and, thus, the production of smaller and more stable grain sizes. Direct Forge has the additional advantages of (a) not requiring hot or cold work prior to forming impacted extruded or forged parts, (b) being utilized in the T6 temper without any prior deformation, (c) having isotropic and consistent properties, (d) not requiring machining to remove surface segregation or defects, and (e) having more consistent and refined grain sizes.

  1. 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

  2. Direct Comparison of Virtual-Histology Intravascular Ultrasound and Optical Coherence Tomography Imaging for Identification of Thin-Cap Fibroatheroma

    PubMed Central

    Brown, Adam J.; Obaid, Daniel R.; Costopoulos, Charis; Parker, Richard A.; Calvert, Patrick A.; Teng, Zhongzhao; Hoole, Stephen P.; West, Nick E.J.; Goddard, Martin

    2015-01-01

    Background— Although rupture of thin-cap fibroatheroma (TCFA) underlies most myocardial infarctions, reliable TCFA identification remains challenging. Virtual-histology intravascular ultrasound (VH-IVUS) and optical coherence tomography (OCT) can assess tissue composition and classify plaques. However, direct comparisons between VH-IVUS and OCT are lacking and it remains unknown whether combining these modalities improves TCFA identification. Methods and Results— Two hundred fifty-eight regions-of-interest were obtained from autopsied human hearts, with plaque composition and classification assessed by histology and compared with coregistered ex vivo VH-IVUS and OCT. Sixty-seven regions-of-interest were classified as fibroatheroma on histology, with 22 meeting criteria for TCFA. On VH-IVUS, plaque (10.91±4.82 versus 8.42±4.57 mm2; P=0.01) and necrotic core areas (1.59±0.99 versus 1.03±0.85 mm2; P=0.02) were increased in TCFA versus other fibroatheroma. On OCT, although minimal fibrous cap thickness was similar (71.8±44.1 μm versus 72.6±32.4; P=0.30), the number of continuous frames with fibrous cap thickness ≤85 μm was higher in TCFA (6.5 [1.75–11.0] versus 2.0 [0.0–7.0]; P=0.03). Maximum lipid arc on OCT was an excellent discriminator of fibroatheroma (area under the curve, 0.92; 95% confidence interval, 0.87–0.97) and TCFA (area under the curve, 0.86; 95% confidence interval, 0.81–0.92), with lipid arc ≥80° the optimal cut-off value. Using existing criteria, the sensitivity, specificity, and diagnostic accuracy for TCFA identification was 63.6%, 78.1%, and 76.5% for VH-IVUS and 72.7%, 79.8%, and 79.0% for OCT. Combining VH-defined fibroatheroma and fibrous cap thickness ≤85 μm over 3 continuous frames improved TCFA identification, with diagnostic accuracy of 89.0%. Conclusions— Both VH-IVUS and OCT can reliably identify TCFA, although OCT accuracy may be improved using lipid arc ≥80° and fibrous cap thickness ≤85 μm over 3

  3. FYPO: the fission yeast phenotype ontology

    PubMed Central

    Harris, Midori A.; Lock, Antonia; Bähler, Jürg; Oliver, Stephen G.; Wood, Valerie

    2013-01-01

    Motivation: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast. Results: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species. Availability: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/). Contact: mah79@cam.ac.uk or vw253@cam.ac.uk PMID:23658422

  4. Direct comparison of the performance of a bio-inspired synthetic nickel catalyst and a [NiFe]-hydrogenase, both covalently attached to electrodes.

    PubMed

    Rodriguez-Maciá, Patricia; Dutta, Arnab; Lubitz, Wolfgang; Shaw, Wendy J; Rüdiger, 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 have come in mimicking the enzymatic performance. The catalytic properties of the [Ni(P(Cy) 2 N(Gly) 2 )2 ](2+) complex with the [NiFe]-hydrogenase from Desulfovibrio vulgaris immobilized on a functionalized electrode were compared under identical conditions. At pH 7, the enzyme shows higher activity and lower overpotential with better stability, while at low pH, the molecular catalyst outperforms the enzyme in all respects. 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 bio-inspired complexes in fuel cells. PMID:26140506

  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. PMID:25319333

  6. Practical limitations of superresolution imaging due to conventional sample preparation revealed by a direct comparison of CLSM, SIM and dSTORM.

    PubMed

    Bachmann, Michael; Fiederling, Felix; Bastmeyer, Martin

    2016-06-01

    We evaluate the suitability of conventional sample preparation and labelling methods for two superresolution techniques, structured illumination microscopy and direct stochastic optical reconstruction microscopy, by a comparison to established confocal laser scanning microscopy. We show that SIM is compatible with standard fixation procedures and immunofluorescence labelling protocols and improves resolution by a factor of two compared to confocal laser scanning microscopy. With direct stochastic optical reconstruction microscopy, fluorophores can theoretically be localized with much higher precision. However, in practice, with indirect immunofluorescence labelling density can be insufficient due to the bulky probes to reveal biological structures with high resolution. Fine structures like single actin fibres are in fact resolved with direct stochastic optical reconstruction microscopy when using small affinity probes, but require proper adjustment of the fixation protocol. Finally, by a direct comparison of immunofluorescent and genetic labelling with fluorescent proteins, we show that target morphology in direct stochastic optical reconstruction microscopy data sets can differ significantly depending on the labelling method and the molecular environment of the target. PMID:26694787

  7. Comparison of acceptance of background noise and speech reception threshold in quantifying the hearing aid directivity benefit

    NASA Astrophysics Data System (ADS)

    Freyaldenhoven, Melinda C.; Nabelek, Anna K.; Burchfield, Samuel B.

    2003-04-01

    Hearing aid directivity benefit was compared as improvement in acceptance of background noise and speech reception threshold (SRT). Forty adult subjects were tested wearing binaural hearing aids in omnidirectional and directional listening conditions. Acceptance of background noise was determined by having subjects select their most comfortable listening level (MCL) for a story delivered from a loudspeaker (0). Next, speech babble was added (180) and the subjects selected the maximum background noise level (BNL) which was acceptable while listening to and following the story. The MCL minus the BNL yielded the acceptable noise level (ANL), all in dB. The difference between the ANL for the omni-directional and directional conditions is the directivity benefit. The SRT was determined by delivering spondaic words (0) at the subjects MCL. Next, speech babble was delivered (180) and adjusted until the subject could repeat 50% of the spondees. The difference between the SRT for the omni-directional and directional conditions is the directivity benefit. Mean directional benefit, ANL=3.50 dB and SRT=3.60 dB, were not significantly different. The individual ANLs and SRTs were significantly correlated (r=-0.36, p=0.002). The ANL procedure appears to be a viable tool for quantifying hearing aid directivity benefit. [Work supported by NIDCD (NIH) 3 RO1 DC 05018-01S1.

  8. A direct comparison of Ge and Si(Li) detectors in the 2--20 keV range

    SciTech Connect

    Rossington, C.S.; Giauque, R.D.; Jaklevic, J.M.

    1991-10-01

    The spectral response of high purity Ge (HPGe) and lithium-drifted Si (Si(Li)) surface barrier detectors of similar geometry has been measured over a range of x-ray energies under identical experimental conditions. Detector characteristics such as spectral background, escape peak intensity, entrance window absorption, and energy resolution are presented and compared. Although these characteristic have been discussed in the literature previously, this paper represents an attempt to consolidate the information by making comparisons under equivalent experimental conditions for the two types of detectors. A primary goal of the study is a comparison of the two types of detectors for use in x-ray fluorescence applications.

  9. Direct Comparison of Monazite Ages Obtained By in situ Techniques: Ion-Probe Isotopic Ages Versus Electron Microprobe Chemical Ages

    NASA Astrophysics Data System (ADS)

    Tracy, R. J.; Loehn, C. W.; Dahl, P. S.; Aleinikoff, J. N.; Wooden, J. L.; Hamilton, M.; Mazdab, F.; Jones, C.

    2005-12-01

    that the improved spatial resolution of the EMP has better sampled the core domain. Other direct comparison of IMP and EMP ages include: (1) a grain of Wendell mnz; 3 IMP ages of 311 (+/-42), 280 (+/-20) and 294 (+/-20); the weighted mean EMP age is 318 (+/-4). (2) Former USGS IMP standard TM-1: ID-TIMS age of 1768 (+/-1.4); weighted mean EMP age of 1736 (+/-10). (3) 3 grains of Black Mountain (VT) Granite: grain 5, IMP age of 368 (+/-12) and EMP age of 358 (+/-5) ; grain 6, IMP age of 376 (+/-12), EMP age of 365 (+/-6); and grain 12, IMP age of 386 (+/-12), EMP age of 382 (+/-2).

  10. Comparison of Directigen FLU-A with viral isolation and direct immunofluorescence for the rapid detection and identification of influenza A virus.

    PubMed Central

    Waner, J L; Todd, S J; Shalaby, H; Murphy, P; Wall, L V

    1991-01-01

    Directigen FLU-A, an enzyme immunoassay membrane test, was compared prospectively to isolation in cell culture and direct immunofluorescence (IF) for the detection of influenza A virus. One hundred ninety specimens were evaluated by Directigen FLU-A and cell culture; 184 of these specimens were also tested by direct IF. The sensitivity of Directigen FLU-A compared to isolation in cell culture and direct IF was 100%. The specificities of Directigen FLU-A compared to isolation and direct IF were identical, 91.6%. Fourteen specimens that were positive by Directigen FLU-A did not yield virus in culture; two of the specimens, however, were positive by direct IF, and four other specimens were not specimens of choice for the test. A positive Directigen result had positive predictive values of 62.6 and 75.0% compared to isolation and direct IF, respectively; a positive Directigen result with an intensity reading of 2+ or greater, however, had positive predictive values of 85 and 100% compared to isolation and direct IF, respectively. In all comparisons, the negative predictive value was 100%. There was no evidence that cross-reactivity occurred with non-influenza A antigens. Directigen FLU-A should serve as a convenient screening test for influenza A and as a rapid test supported by isolation in cell culture during an influenza outbreak. PMID:2037665

  11. Comparison of predicted susceptibility between genotype and virtual phenotype HIV drug resistance interpretation systems among treatment-naive HIV-infected patients in Asia: TASER-M cohort analysis

    PubMed Central

    2012-01-01

    Background Accurate interpretation of HIV drug resistance (HIVDR) testing is challenging, yet important for patient care. We compared genotyping interpretation, based on the Stanford University HIV Drug Resistance Database (Stanford HIVdb), and virtual phenotyping, based on the Janssen Diagnostics BVBA’s vircoTYPE™ HIV-1, and investigated their level of agreement in antiretroviral (ARV) naive patients in Asia, where non-B subtypes predominate. Methods Sequences from 1301 ARV-naive patients enrolled in the TREAT Asia Studies to Evaluate Resistance – Monitoring Study (TASER-M) were analysed by both interpreting systems. Interpretations from both Stanford HIVdb and vircoTYPE™ HIV-1 were initially grouped into 2 levels: susceptible and non-susceptible. Discrepancy was defined as a discordant result between the susceptible and non-susceptible interpretations from the two systems for the same ARV. Further analysis was performed when interpretations from both systems were categorised into 3 levels: susceptible, intermediate and resistant; whereby discrepancies could be categorised as major discrepancies and minor discrepancies. Major discrepancy was defined as having a susceptible result from one system and resistant from the other. Minor discrepancy corresponded to having an intermediate interpretation in one system, with a susceptible or resistant result in the other. The level of agreement was analysed using the prevalence adjusted bias adjusted kappa (PABAK). Results Overall, the agreement was high, with each ARV being in “almost perfect agreement”, using Landis and Koch’s categorisation. Highest discordance was observed for efavirenz (75/1301, 5.8%), all arising from susceptible Stanford HIVdb versus non-susceptible vircoTYPE™ HIV-1 predictions. Protease Inhibitors had highest level of concordance with PABAKs all above 0.99, followed by Nucleoside Reverse Transcriptase Inhibitors with PABAKs above 0.97 and non-NRTIs with the lowest PABAK of 0.88. The

  12. 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.

  13. Direct Aerosol Radiative Forcing from Combined A-Train Observations - Preliminary Comparisons with AeroCom Models and Pathways to Observationally Based All-sky Estimates

    NASA Astrophysics Data System (ADS)

    Redemann, J.; Livingston, J. M.; Shinozuka, Y.; Kacenelenbogen, M. S.; Russell, P. B.; LeBlanc, S. E.; Vaughan, M.; Ferrare, R. A.; Hostetler, C. A.; Rogers, R. R.; Burton, S. P.; Torres, O.; Remer, L. A.; Stier, P.; Schutgens, N.

    2014-12-01

    We describe a technique for combining CALIOP aerosol backscatter, MODIS spectral AOD (aerosol optical depth), and OMI AAOD (absorption aerosol optical depth) retrievals for the purpose of estimating full spectral sets of aerosol radiative properties, and ultimately for calculating the 3-D distribution of direct aerosol radiative forcing. We present results using one year of data collected in 2007 and show comparisons of the aerosol radiative property estimates to collocated AERONET retrievals. Use of the recently released MODIS Collection 6 data for aerosol optical depths derived with the dark target and deep blue algorithms has extended the coverage of the multi-sensor estimates towards higher latitudes. Initial calculations of seasonal clear-sky aerosol radiative forcing based on our multi-sensor aerosol retrievals compare well with over-ocean and top of the atmosphere IPCC-2007 model-based results, and with more recent assessments in the "Climate Change Science Program Report: Atmospheric Aerosol Properties and Climate Impacts" (2009). For the first time, we present comparisons of our multi-sensor aerosol direct radiative forcing estimates to values derived from a subset of models that participated in the latest AeroCom initiative. We discuss the major challenges that exist in extending our clear-sky results to all-sky conditions. On the basis of comparisons to suborbital measurements, we present some of the limitations of the MODIS and CALIOP retrievals in the presence of adjacent or underlying clouds. Strategies for meeting these challenges are discussed.

  14. Comparison of laser-assisted damage in soft tissue using bi-directional and forward-firing optical fiber

    NASA Astrophysics Data System (ADS)

    Kim, Changhwan; Sohn, Ik-Bu; Park, Hoyong; Lee, Yong Joong; Lee, Ho

    2014-03-01

    Laser-assisted endoscopic surgery is made possible by employing optical devices such as fiber optics and hollow wave-guides. In some applications of laser-assisted endoscopic surgery, it is necessary to change the direction of the light emission. Our group reported a new fabrication method for bi-directional firing fibers. The conical surface of the fiber tip made the bi-directional emission of the laser light at the distal end of the fiber. In this study, we employed the bi-directional firing fiber for laser-assisted coagulation of soft tissue. The developed fiber and the normal forward-firing fiber are used for the endoscopic delivery system of a continuous IR laser into an in vitro porcine liver. The ablation and coagulation pattern were compared for two distinctive fiber systems. Regardless of the laser's parameters, the bi-directional firing fiber produced a cavity and coagulation zone with more or less a circular shape, while the forward fiber produced an elongated cavity and coagulation region. The bi-directional firing fiber produced wider and shorter coagulation and cavity zones compared to that of the forward-firing fiber. We expect the bi-directional firing fiber to be an excellent optical delivery system for endoscopic laser-hyperthermia when used against various tumors in the liver, breast and thyroid.

  15. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

    PubMed

    Doan, Son; Lin, Ko-Wei; Conway, Mike; Ohno-Machado, Lucila; Hsieh, Alex; Feupe, Stephanie Feudjio; Garland, Asher; Ross, Mindy K; Jiang, Xiaoqian; Farzaneh, Seena; Walker, Rebecca; Alipanah, Neda; Zhang, Jing; Xu, Hua; Kim, Hyeon-Eui

    2014-01-01

    The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net. PMID:23989082

  16. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes

    PubMed Central

    Doan, Son; Lin, Ko-Wei; Conway, Mike; Ohno-Machado, Lucila; Hsieh, Alex; Feupe, Stephanie Feudjio; Garland, Asher; Ross, Mindy K; Jiang, Xiaoqian; Farzaneh, Seena; Walker, Rebecca; Alipanah, Neda; Zhang, Jing; Xu, Hua; Kim, Hyeon-Eui

    2014-01-01

    The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net. PMID:23989082

  17. Efficacy of α-blocker in improving ureteral stent-related symptoms: a meta-analysis of both direct and indirect comparison

    PubMed Central

    He, Feng; Man, Li-bo; Li, Gui-zhong; Liu, Ning

    2016-01-01

    Objective To critically evaluate the efficacy of an α-blocker in improving ureteral-stent-related symptoms and preliminarily investigate the difference between different types of α-blockers. Methods Relevant randomized controlled trials were identified through searching PubMed, the Cochrane Library, Embase, and other sources. After quality assessment and data abstraction, direct comparison based on the Ureteral Stent-related Symptom Questionnaire (USSQ) between α-blockers and control was performed by RevMan 5.3. Indirect comparison between different types of α-blockers was performed by ITC 1.0. Sensitive and subgroup analyses were used to handle important clinical factors. Results Sixteen randomized controlled trials containing 1,489 cases were included. Compared with control, α-blockers significantly reduced the overall urinary symptom, pain index, general health index, and scores related to sexual matters, while no significant difference was found in work performance and additional problem scores. Subgroup analysis showed that the duration of stent insertion, patient’s age, stent size, and the type of α-blocker had the potential to influence the outcomes. Through indirect comparison, we found alfuzosin and terazosin to be better than tamsulosin in pain relief and general health improvement. Conclusion α-Blocker was effective in treating ureteral stent-related symptoms, as it improved the major indexes of USSQ post-insertion or post-removal. Alfuzosin and terazosin seemed to be better than tamsulosin, which needs further verification because of the lack of direct comparison currently. PMID:27307709

  18. 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.

  19. Resolution of rupture directivity in weak events (Mw ~ 5): a comparison of 1D and 2D source parameterizations

    NASA Astrophysics Data System (ADS)

    Ángel López Comino, José; Stich, Daniel; Morales, José; Ferreira, Ana M. G.

    2016-04-01

    Rupture directivity of small to moderate magnitude earthquakes may resolve the fault plane ambiguity and explain the disproportionate damage caused by some events. However, it is challenging to robustly resolve characteristic parameters such as direction, length, asymmetry and speed of rupture of weak events with short source durations. Here we infer directivity from apparent source time functions (ASTF) at regional distance and quantify the associated uncertainties. First, we use ASTF durations to model a propagating 1D line source with general asymmetry. Second, we use the full ASTF signals to invert for the 2D distribution of fault slip. Slip inversion is performed through a Popperian scheme, where random trial models are either falsified on account of large misfit, or else become member of the solution set of the inverse problem. We assess the resolution of rupture directivity representing centroid shifts from the solution set in a rose diagram. Using as example an event with well-studied rupture directivity, the 2011 Mw 5.2 Lorca (Spain) earthquake, 1D and 2D parameterizations yield similar estimates for direction (N213°E and N220°E respectively) and asymmetry (67:33, 65:35) of rupture propagation, as well as rupture length (2.1 km, 2.7 km) and speed (3.5 km/s, 3.25 km/s). The asymmetry of rupture is moderate, and the high rupture velocity ≥ 90% vS may be held primarily responsible for the strong directivity effect of this earthquake. Formal uncertainties of rupture extent and speed are large in the 1D model, while the more general 2D model produces larger uncertainties in rupture directivity and asymmetry. We show that inversion of apparent source durations is intrinsically unable to resolve highly asymmetric bilateral ruptures, while inversion of full ASTFs misses part of the signal's complexity, suggesting the presence of deconvolution artifacts. We extend the analysis to the Mw 4.6 foreshock of the Lorca earthquake, inferring similar directivity

  20. Genetic resources for phenotyping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotyping of structured populations, along with molecular genotyping, will be essential for marker development in peanut. This research is essential for making the peanut genome sequence and genomic tools useful to breeders because it makes the connection between genes, gene markers, genetic maps...

  1. 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…

  2. Selection against Aerial Dispersal in Ants: Two Non-Flying Queen Phenotypes in Pogonomyrmex laticeps

    PubMed Central

    Peeters, Christian; Keller, Roberto A.; Johnson, Robert A.

    2012-01-01

    The South American seed-harvester ant Pogonomyrmex laticeps has dimorphic queens: ergatoid (permanently wingless) and brachypterous (short, non-functional wings). Surveys in western Argentina indicated that colonies near Chilecito, La Rioja Province, produced only ergatoid queens, while those near Punta Balasto, Catamarca Province (263 km away), produced only brachypterous queens. Brachypterous queens were significantly larger than ergatoid queens for 10 of 11 external characters, but both phenotypes had comparable reproductive potential, i.e., a spermatheca and a similar number of ovarioles. Using normal winged queens of the closely related P. uruguayensis for comparison, we determined that both queen phenotypes in P. laticeps had a full set of dorsal thoracic sclerites, albeit each sclerite was much reduced, whereas workers had a thorax without distinct dorsal sclerites. Sclerites were fused and immobile in ergatoid queens, while they were separable and fully articulated in brachypterous queens. Both phenotypes lacked the big indirect flight muscles, but brachypterous queens retained the tiny direct flight muscles. Overall, this dimorphism across populations indicates that there are alternative solutions to selective pressures against flying queens. We lack field data about colony founding strategy (independent or dependent) for either queen phenotype, but colonies at both sites produced numerous gynes, and we infer that all foundresses initiate colonies independently and are obligate foragers. PMID:23110094

  3. The QDREC web server: determining dose–response characteristics of complex macroparasites in phenotypic drug screens

    PubMed Central

    Asarnow, Daniel; Rojo-Arreola, Liliana; Suzuki, Brian M.; Caffrey, Conor R.; Singh, Rahul

    2015-01-01

    Summary: Neglected tropical diseases (NTDs) caused by helminths constitute some of the most common infections of the world’s poorest people. The etiological agents are complex and recalcitrant to standard techniques of molecular biology. Drug screening against helminths has often been phenotypic and typically involves manual description of drug effect and efficacy. A key challenge is to develop automated, quantitative approaches to drug screening against helminth diseases. The quantal dose–response calculator (QDREC) constitutes a significant step in this direction. It can be used to automatically determine quantitative dose–response characteristics and half-maximal effective concentration (EC50) values using image-based readouts from phenotypic screens, thereby allowing rigorous comparisons of the efficacies of drug compounds. QDREC has been developed and validated in the context of drug screening for schistosomiasis, one of the most important NTDs. However, it is equally applicable to general phenotypic screening involving helminths and other complex parasites. Availability and implementation: QDREC is publically available at: http://haddock4.sfsu.edu/qdrec2/. Source code and datasets are at: http://tintin.sfsu.edu/projects/phenotypicAssays.html. Contact: rahul@sfsu.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25540182

  4. Advance Directives in Some Western European Countries: A Legal and Ethical Comparison between Spain, France, England, and Germany.

    PubMed

    Veshi, Denard; Neitzke, Gerald

    2015-09-01

    We have studied national laws on advance directives in various Western European countries: Romance-speaking countries (Italy, France, Portugal, and Spain), English-speaking countries (Ireland and the United Kingdom), and German-speaking countries (Austria, Germany, and Switzerland). We distinguish two potentially complementary types of advance medical declaration: the 'living will' and the nomination of a legal proxy. After examining the similarities and differences between countries, we analyse in detail the legislation of four countries (Spain, France, England, and Germany), since the other countries in this survey have similar legal principles and/or a similar political approach. In conclusion, we note that in all the countries examined, advance directives have been seen as an instrument to enable the patient's right to self-determination. Notwithstanding, in Romance-speaking countries, the involvement of physicians in the end-of-life process and risks arising from the execution of advance directives were also considered. PMID:26427271

  5. Comparison of direct and quasi-static methods for neutron kinetic calculations with the EDF R and D COCAGNE code

    SciTech Connect

    Girardi, E.; Guerin, P.; Dulla, S.; Nervo, M.; Ravetto, P.

    2012-07-01

    Quasi-Static (QS) methods are quite popular in the reactor physics community and they exhibit two main advantages. First, these methods overcome both the limits of the Point Kinetic (PK) approach and the issues of the computational effort related to the direct discretization of the time-dependent neutron transport equation. Second, QS methods can be implemented in such a way that they can be easily coupled to very different external spatial solvers. In this paper, the results of the coupling between the QS methods developed by Politecnico di Torino and the EDF R and D core code COCAGNE are presented. The goal of these activities is to evaluate the performances of QS methods (in term of computational cost and precision) with respect to the direct kinetic solver (e.g. {theta}-scheme) already available in COCAGNE. Additionally, they allow to perform an extensive cross-validation of different kinetic models (QS and direct methods). (authors)

  6. [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. PMID:187512

  7. The Direct Assessment of Functional Abilities (DAFA): a comparison to an indirect measure of instrumental activities of daily living.

    PubMed

    Karagiozis, H; Gray, S; Sacco, J; Shapiro, M; Kawas, C

    1998-02-01

    The Direct Assessment of Functional Abilities (DAFA) was designed as a direct measure of instrumental activities of daily living (IADLs) that could be compared with an indirect assessment of IADLs by the Pfeffer Functional Activities Questionnaire (PFAQ). The DAFA (28 demented and 15 control subjects) and PFAQ (subjects and informants) were administered twice, together with a brief cognitive battery. Demented subjects performed significantly worse on direct assessment (DAFA) than predicted by self-report (PFAQ), and overestimation of abilities increased with severity of dementia. In contrast, informants tended to underestimate abilities of demented subjects, but not to a significant degree. Control (nondemented) subjects had comparable results with the two methods. The DAFA may provide a more objective measure of functional status in demented subjects than do indirect methods of assessment. PMID:9499659

  8. 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.

  9. 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

  10. 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

  11. 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). PMID:26857378

  12. 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

  13. 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…

  14. Patterns of Co-Occurring Non-Verbal Behaviour and Self-Directed Speech; a Comparison of Three Methodological Approaches

    ERIC Educational Resources Information Center

    Kuvalja, Martina; Verma, Mohini; Whitebread, David

    2014-01-01

    "Self-directed speech"--the audible or partially whispered self-talk that children engage in during their daily activities, was proposed by Vygotsky to have a mediating role in the emerging self-regulatory behaviour of young children. Studies with correlational findings tend to lend support to this hypothesis but fail to delineate the…

  15. 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...

  16. 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...

  17. 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…

  18. The Direct Assessment of Functional Abilities (DAFA): A Comparison to an Indirect Measure of Instrumental Activities of Daily Living.

    ERIC Educational Resources Information Center

    Karagiozis, Helen; Gray, Sarah; Sacco, Jane; Shapiro, Martha; Kawas, Claudia

    1998-01-01

    Presents the results of administering the Direct Awareness of Functional Abilities (DAFA) and the Pfeefer Activities Questionnaire to 28 demented, and 15 control subjects. Results show that the DAFA may provide a more objective measure of functional status in demented subjects than is provided by indirect methods of assessment. (MKA)

  19. Comparison of model- and design-based sampling strategies for characterizing spatial variablity with ECa-directed soil sampling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spatial variability has a profound influence on solute transport in the vadose zone, soil quality assessment, and site-specific crop management. Directed soil sampling based on geospatial measurements of apparent soil electrical conductivity (ECa) is a potential means of characterizing the spatial ...

  20. A Comparison of Factors Related to University Students' Learning: College-Transfer and Direct-Entry from High School Students

    ERIC Educational Resources Information Center

    Acai, Anita; Newton, Genevieve

    2015-01-01

    Articulation agreements between colleges and universities, whereby students with two-year college diplomas can receive advancement toward a four-year university degree, are provincially mandated in some Canadian provinces and highly encouraged in others. In this study, we compared learning in college transfer and direct-entry from high school…

  1. GaAs quantum structures: comparison between direct pseudopotential and single-band truncated-crystal calculations

    NASA Astrophysics Data System (ADS)

    Franceschetti, Alberto; Zunger, Alex

    1996-03-01

    We compare the results of a single-band truncated-crystal (SBTC) approximation with direct pseudopotential calculations for free-standing, hydrogen-passivated GaAs quantum films, wires and dots. While the non parabolicity of the bulk energy bands is taken into account by the SBTC approximation, the interband coupling introduced by the lack of translational invariance is ignored. We find that (i) the confinement energy of the valence-band maximum is overestimated by the SBTC method, because the ``zero-confinement'' character of this state is neglected; (ii) the confinement energy of the Γ-derived conduction-band minimum (direct gap) is slightly overestimated by the SBTC approximation, mainly because of the assumption of infinite potential barriers at the boundaries; (iii) the confinement energy of the X-derived conduction-band minimum (indirect gap) is severely underestimated by the SBTC method in quantum wires and dots; (iv) while the SBTC approximation predicts ``quantum deconfinement'' (i.e. reduction of gap as size is reduced) for the direct gap of quantum wires, such effect is not present in the direct pseudopotential calculation.

  2. 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

  3. 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

  4. Plant phenotypic plasticity in a changing climate.

    PubMed

    Nicotra, A B; Atkin, O K; Bonser, S P; Davidson, A M; Finnegan, E J; Mathesius, U; Poot, P; Purugganan, M D; Richards, C L; Valladares, F; van Kleunen, M

    2010-12-01

    Climate change is altering the availability of resources and the conditions that are crucial to plant performance. One way plants will respond to these changes is through environmentally induced shifts in phenotype (phenotypic plasticity). Understanding plastic responses is crucial for predicting and managing the effects of climate change on native species as well as crop plants. Here, we provide a toolbox with definitions of key theoretical elements and a synthesis of the current understanding of the molecular and genetic mechanisms underlying plasticity relevant to climate change. By bringing ecological, evolutionary, physiological and molecular perspectives together, we hope to provide clear directives for future research and stimulate cross-disciplinary dialogue on the relevance of phenotypic plasticity under climate change. PMID:20970368

  5. Regulatory mechanisms link phenotypic plasticity to evolvability.

    PubMed

    van Gestel, Jordi; Weissing, Franz J

    2016-01-01

    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. PMID:27087393

  6. Root phenotyping: from component trait in the lab to breeding.

    PubMed

    Kuijken, René C P; van Eeuwijk, Fred A; Marcelis, Leo F M; Bouwmeester, Harro J

    2015-09-01

    In the last decade cheaper and faster sequencing methods have resulted in an enormous increase in genomic data. High throughput genotyping, genotyping by sequencing and genomic breeding are becoming a standard in plant breeding. As a result, the collection of phenotypic data is increasingly becoming a limiting factor in plant breeding. Genetic studies on root traits are being hampered by the complexity of these traits and the inaccessibility of the rhizosphere. With an increasing interest in phenotyping, breeders and scientists try to overcome these limitations, resulting in impressive developments in automated phenotyping platforms. Recently, many such platforms have been thoroughly described, yet their efficiency to increase genetic gain often remains undiscussed. This efficiency depends on the heritability of the phenotyped traits as well as the correlation of these traits with agronomically relevant breeding targets. This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability. It also intends to give direction to future phenotyping and breeding strategies for optimizing root system functioning. A quantitative framework to determine the efficiency of phenotyping platforms for genetic gain is described. By increasing heritability, managing effects caused by interactions between genotype and environment and by quantifying the genetic relation between traits phenotyped in platforms and ultimate breeding targets, phenotyping platforms can be utilized to their maximum potential. PMID:26071534

  7. A Direct Comparison of Alloderm-Ready to Use (RTU) and DermACELL in Immediate Breast Implant Reconstruction

    PubMed Central

    Salzberg, C. Andrew

    2016-01-01

    The objective of this study was to compare the 2 leading human acellular dermal matrices in breast reconstruction with implants. This retrospective study draws on the experience of 2 expert surgeons with a history of long-standing use of the Alloderm-RTU (LifeCell Corporation, Branchburg, NJ) product who switched to the DermACELL acellular dermal matrix (LifeNet Health, Virgina Beach, Va) product. The consecutive nature of these data over this change allowed comparison between the 2 products without the confounding effects of patient selection or change in technique. The postoperative complications of seroma, infection, implant loss, and unplanned return to the operating room were studied, and no statistical differences were noted between these 2 products. The overall complications rates were low, with implant loss and infection less than 2% in 249 cases. Recommendations are for continued use of acellular dermal matrix in breast reconstruction and product selection based on price and availability.

  8. A direct comparison of MELCOR 1.8.3 and MAAP4 results for several PWR & BWR accident sequences

    SciTech Connect

    Leonard, M.T.; Ashbaugh, S.G.; Cole, R.K.; Bergeron, K.D.; Nagashima, K.

    1996-08-01

    This paper presents a comparison of calculations of severe accident progression for several postulated accident sequences for representative Pressurized Water Reactors (PWR) and Boiling Water Reactors (BWR) nuclear power plants performed with the MELCOR 1.8.3 and the MAAP4 computer codes. The PWR system examined in this study is a 1100 MWe system similar in design to a Westinghouse 3-loop plant with a large dry containment; the BWR is a 1100 MWe system similar in design to General Electric BWR/4 with a Mark I containment. A total of nine accident sequences were studied with both codes. Results of these calculations are compared to identify major differences in the timing of key events in the calculated accident progression or other important aspects of severe accident behavior, and to identify specific sources of the observed differences.

  9. A Direct Comparison of Alloderm-Ready to Use (RTU) and DermACELL in Immediate Breast Implant Reconstruction.

    PubMed

    Zenn, Michael R; Salzberg, C Andrew

    2016-01-01

    The objective of this study was to compare the 2 leading human acellular dermal matrices in breast reconstruction with implants. This retrospective study draws on the experience of 2 expert surgeons with a history of long-standing use of the Alloderm-RTU (LifeCell Corporation, Branchburg, NJ) product who switched to the DermACELL acellular dermal matrix (LifeNet Health, Virgina Beach, Va) product. The consecutive nature of these data over this change allowed comparison between the 2 products without the confounding effects of patient selection or change in technique. The postoperative complications of seroma, infection, implant loss, and unplanned return to the operating room were studied, and no statistical differences were noted between these 2 products. The overall complications rates were low, with implant loss and infection less than 2% in 249 cases. Recommendations are for continued use of acellular dermal matrix in breast reconstruction and product selection based on price and availability. PMID:27602176

  10. Clinical interpretation of CNVs with cross-species phenotype data

    PubMed Central

    Czeschik, Johanna Christina; Doelken, Sandra C; Hehir-Kwa, Jayne Y; Ibn-Salem, Jonas; Mungall, Christopher J; Smedley, Damian; Haendel, Melissa A; Robinson, Peter N

    2015-01-01

    Background Clinical evaluation of CNVs identified via techniques such as array comparative genome hybridisation (aCGH) involves the inspection of lists of known and unknown duplications and deletions with the goal of distinguishing pathogenic from benign CNVs. A key step in this process is the comparison of the individual's phenotypic abnormalities with those associated with Mendelian disorders of the genes affected by the CNV. However, because often there is not much known about these human genes, an additional source of data that could be used is model organism phenotype data. Currently, almost 6000 genes in mouse and zebrafish are, when knocked out, associated with a phenotype in the model organism, but no disease is known to be caused by mutations in the human ortholog. Yet, searching model organism databases and comparing model organism phenotypes with patient phenotypes for identifying novel disease genes and medical evaluation of CNVs is hindered by the difficulty in integrating phenotype information across species and the lack of appropriate software tools. Methods Here, we present an integrated ranking scheme based on phenotypic matching, degree of overlap with known benign or pathogenic CNVs and the haploinsufficiency score for the prioritisation of CNVs responsible for a patient's clinical findings. Results We show that this scheme leads to significant improvements compared with rankings that do not exploit phenotypic information. We provide a software tool called PhenogramViz, which supports phenotype-driven interpretation of aCGH findings based on multiple data sources, including the integrated cross-species phenotype ontology Uberpheno, in order to visualise gene-to-phenotype relations. Conclusions Integrating and visualising cross-species phenotype information on the affected genes may help in routine diagnostics of CNVs. PMID:25280750

  11. Comparison of residual stresses in Inconel 718 simple parts made by electron beam melting and direct laser metal sintering

    DOE PAGESBeta

    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 hasmore » shown that residual stresses in electron beam melting parts are much smaller than that of direct laser metal sintering parts.« less

  12. 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.

  13. 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.

  14. Estimating the prevalence of xenophobia and anti-Semitism in Germany: A comparison of randomized response and direct questioning.

    PubMed

    Krumpal, Ivar

    2012-11-01

    An experimental CATI-survey (N=2041), asking sensitive questions about xenophobia and anti-Semitism in Germany, was conducted to compare the randomized response technique (RRT) and the direct questioning technique. Unlike the vast majority of RRT surveys measuring the prevalence of socially undesirable behaviors, only few studies have explored the effectiveness of the RRT with respect to the disclosure of socially undesirable opinions. Results suggest that the RRT is an effective method eliciting more socially undesirable opinions and yielding more valid prevalence estimates of xenophobia and anti-Semitism than direct questioning ('more-is-better' assumption). Furthermore, the results indicate that with increasing topic sensitivity, the benefits of using the RRT also increase. Finally, adapted logistic regression analyses show that several covariates such as education and generalized trust are related to the likelihood of being prejudiced towards foreigners and Jews. PMID:23017963

  15. Comparison of Diagnostic Ability of Storage Phosphor Plate in Detecting Proximal Caries with Direct Measurement by Stereomicroscope: A Pilot Study

    PubMed Central

    Thomas, Sunila; Nair, Bindu J.; Vineet, Alex Daniel; Thomas, Jincy; Ranimol, Prasanna; Vijayan, Aswathy K.

    2015-01-01

    Radiography plays an important role in detection of interproximal caries. The aim of study is to compare diagnostic ability of photo stimulable phosphor (PSP) with direct measurement using stereomicroscope in detecting proximal caries. Hundred proximal surfaces of 50 extracted human posterior teeth were radiographed with dental X-ray unit. The image receptors used was storage phosphor plate Vista scan (size 2), (time of exposure 0.4 s). Radiographs were interpreted and caries lesions were classified on a 4-point scale suggested by Abesi et al. The teeth were sectioned with diamond disc and were examined under a stereomicroscope with 20x magnification. Diagnostic accuracy of digital image is similar to that observed with stereomicroscope. The PSP plate digital X ray system can effectively be employed for detecting proximal caries as compared to direct observation by stereomicro-scope. Further study with more number of observer/evaluator and large sample size is recommended. PMID:26664712

  16. Comparison of Diagnostic Ability of Storage Phosphor Plate in Detecting Proximal Caries with Direct Measurement by Stereomicroscope: A Pilot Study.

    PubMed

    Vivek, Velayudhannair; Thomas, Sunila; Nair, Bindu J; Vineet, Alex Daniel; Thomas, Jincy; Ranimol, Prasanna; Vijayan, Aswathy K

    2015-09-28

    Radiography plays an important role in detection of interproximal caries. The aim of study is to compare diagnostic ability of photo stimulable phosphor (PSP) with direct measurement using stereomicroscope in detecting proximal caries. Hundred proximal surfaces of 50 extracted human posterior teeth were radiographed with dental X-ray unit. The image receptors used was storage phosphor plate Vista scan (size 2), (time of exposure 0.4 s). Radiographs were interpreted and caries lesions were classified on a 4-point scale suggested by Abesi et al. The teeth were sectioned with diamond disc and were examined under a stereomicroscope with 20x magnification. Diagnostic accuracy of digital image is similar to that observed with stereomicroscope. The PSP plate digital X ray system can effectively be employed for detecting proximal caries as compared to direct observation by stereomicro-scope. Further study with more number of observer/evaluator and large sample size is recommended. PMID:26664712

  17. Comparison of direct, indirect, and ecosystem engineering effects of an earthworm on the red-backed salamander.

    PubMed

    Ransom, Tami S

    2012-10-01

    In addition to creating or modifying habitat, ecosystem engineers interact with other species as predators, prey, or competitors. The earthworm, Lumbricus terrestris, interacts with the common woodland salamander, Plethodon cinereus, via: (1) ecosystem engineering, by providing burrows that are used as a refuge, (2) direct effects as a prey item, and (3) indirectly, by competing with microinvertebrates, another prey item for P. cinereus. Using enclosures in the forest, I examined the relative strengths of these component pathways between seasons and salamander age classes. I found that the relative strength (partial eta2) of the positive direct (trophic) effect of L. terrestris on the change in mass of P. cineresus was greater than that of the negative indirect effect, but only in summer. Positive effects of ecosystem engineering were only evident over the winter as increased adult survival. This research has implications for how habitat provisioning complements more well-studied species interactions, such as competition and predation, within communities. PMID:23185881

  18. Direction of interstellar hydrogen flow in the heliosphere: theoretical modelling and comparison with SOHO/SWAN data

    NASA Astrophysics Data System (ADS)

    Katushkina, O. A.; Izmodenov, V. V.; Alexashov, D. B.

    2015-01-01

    The analysis of SOlar and Heliospheric Observatory (SOHO) Solar Wind ANisotropies (SWAN) data for backscattered solar Lyman α radiation performed by Lallement et al. showed for the first time that the average direction of interstellar hydrogen flow in the heliosphere is deflected by several degrees relative to the original direction of the interstellar wind outside the heliosphere. This deflection is caused by the indirect influence of the interstellar magnetic field (IsMF) through charge exchange between hydrogen atoms and interstellar protons deflected by the IsMF in the region of interaction between the solar wind and the local interstellar medium (LISM). Thus, measurements of the backscattered Lyman α radiation at the Earth's orbit can be used as a remote IsMF diagnostic. However, the direction of interstellar hydrogen flow in the vicinity of the Sun may be influenced by other effects such as the solar radiation pressure, gravitation and ionization and kinetic non-Maxwellian properties of the hydrogen distribution and also may depend on other LISM parameters besides IsMF. In this work, we perform a theoretical modelling of the backscattered solar Lyman α radiation seen at 1 au from the Sun and analyse the direction of hydrogen flow in the heliosphere, which can be obtained from the spectral properties of the backscattered radiation. The influence of different effects mentioned above is investigated. Also we compare our results obtained by means of a state-of-art 3D time-dependent kinetic model of the hydrogen distribution with the SWAN data of 1996.

  19. Measurement of plasma momentum exerted on target by a small helicon plasma thruster and comparison with direct thrust measurement

    NASA Astrophysics Data System (ADS)

    Takahashi, Kazunori; Komuro, Atsushi; Ando, Akira

    2015-02-01

    Momentum, i.e., force, exerted from a small helicon plasma thruster to a target plate is measured simultaneously with a direct thrust measurement using a thrust balance. The calibration coefficient relating a target displacement to a steady-state force is obtained by supplying a dc to a calibration coil mounted on the target, where a force acting to a small permanent magnet located near the coil is directly measured by using a load cell. As the force exerted by the plasma flow to the target plate is in good agreement with the directly measured thrust, the validity of the target technique is demonstrated under the present operating conditions, where the thruster is operated in steady-state. Furthermore, a calibration coefficient relating a swing amplitude of the target to an impulse bit is also obtained by pulsing the calibration coil current. The force exerted by the pulsed plasma, which is estimated from the measured impulse bit and the pulse width, is also in good agreement with that obtained for the steady-state operation; hence, the thrust assessment of the helicon plasma thruster by the target is validated for both the steady-state and pulsed operations.

  20. Measurement of plasma momentum exerted on target by a small helicon plasma thruster and comparison with direct thrust measurement.

    PubMed

    Takahashi, Kazunori; Komuro, Atsushi; Ando, Akira

    2015-02-01

    Momentum, i.e., force, exerted from a small helicon plasma thruster to a target plate is measured simultaneously with a direct thrust measurement using a thrust balance. The calibration coefficient relating a target displacement to a steady-state force is obtained by supplying a dc to a calibration coil mounted on the target, where a force acting to a small permanent magnet located near the coil is directly measured by using a load cell. As the force exerted by the plasma flow to the target plate is in good agreement with the directly measured thrust, the validity of the target technique is demonstrated under the present operating conditions, where the thruster is operated in steady-state. Furthermore, a calibration coefficient relating a swing amplitude of the target to an impulse bit is also obtained by pulsing the calibration coil current. The force exerted by the pulsed plasma, which is estimated from the measured impulse bit and the pulse width, is also in good agreement with that obtained for the steady-state operation; hence, the thrust assessment of the helicon plasma thruster by the target is validated for both the steady-state and pulsed operations. PMID:25725840

  1. Cognitive Correlates of Functional Performance in Older Adults: Comparison of Self-Report, Direct Observation, and Performance-Based Measures

    PubMed Central

    Schmitter-Edgecombe, Maureen; Parsey, Carolyn; Cook, Diane J.

    2013-01-01

    Neuropsychologists are often asked to answer questions about the effects of cognitive deficits on everyday functioning. This study examined the relationship between and the cognitive correlates of self-report, performance-based, and direct observation measures commonly used as proxy measures for everyday functioning. Participants were 88 community-dwelling, cognitively healthy older adults (age 50–86 years). Participants completed standardized neuropsychological tests and questionnaires, and performed eight activities of daily living (e.g., water plants, fill a medication dispenser) while under direct observation in a campus apartment. All proxy measures of everyday function were sensitive to the effects of healthy cognitive aging. After controlling for age, cognitive predictors explained a unique amount of the variance for only the performance-based behavioral simulation measure (i.e., Revised Observed Tasks of Daily Living). The self-report instrumental activities of daily living (IADL) and the performance-based everyday problem-solving test (i.e., EPT) did not correlate with each other; however, both were unique predictors of the direct observation measure. These findings suggest that neuropsychologists must be cautious in making predictions about the quality of everyday activity completion in cognitively healthy older adults from specific cognitive functions. The findings further suggest that a self-report of IADLs and the performance-based EPT may be useful measures for assessing everyday functional status in cognitively healthy older adults. PMID:21729400

  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. A Comparison of the C-MAC Video Laryngoscope to the Macintosh Direct Laryngoscope for Intubation in the Emergency Department

    PubMed Central

    Sakles, John C.; Mosier, Jarrod; Chiu, Stephen; Cosentino, Mari; Kalin, Leah

    2015-01-01

    Study objective We determine the proportion of successful intubations with the C-MAC video laryngoscope (C-MAC) compared with the direct laryngoscope in emergency department (ED) intubations. Methods This was a retrospective analysis of prospectively collected data entered into a continuous quality improvement database during a 28-month period in an academic ED. After each intubation, the operator completed a standardized data form evaluating multiple aspects of the intubation, including patient demographics, indication for intubation, device(s) used, reason for device selection, difficult airway characteristics, number of attempts, and outcome of each attempt. Intubation was considered ultimately successful if the endotracheal tube was correctly inserted into the trachea with the initial device. An attempt was defined as insertion of the device into the mouth regardless of whether there was an attempt to pass the tube. The primary outcome measure was ultimate success. Secondary outcome measures were first-attempt success, Cormack-Lehane view, and esophageal intubation. Multivariate logistic regression analyses, with the inclusion of a propensity score, were performed for the outcome variables ultimate success and first-attempt success. Results During the 28-month study period, 750 intubations were performed with either the C-MAC with a size 3 or 4 blade or a direct laryngoscope with a Macintosh size 3 or 4 blade. Of these, 255 were performed with the C-MAC as the initial device and 495 with a Macintosh direct laryngoscope as the initial device. The C-MAC resulted in successful intubation in 248 of 255 cases (97.3%; 95% confidence interval [CI] 94.4% to 98.9%). A direct laryngoscope resulted in successful intubation in 418 of 495 cases (84.4%; 95% CI 81.0% to 87.5%). In the multivariate regression model, with a propensity score included, the C-MAC was positively predictive of ultimate success (odds ratio 12.7; 95% CI 4.1 to 38.8) and first-attempt success (odds

  4. Phenotypic plasticity in two marine snails: constraints superseding life history.

    PubMed

    Hollander, J; Collyer, M L; Adams, D C; Johannesson, K

    2006-11-01

    In organisms encountering predictable environments, fixed development is expected, whereas in organisms that cannot predict their future environment, phenotypic plasticity would be optimal to increase local adaptation. To test this prediction we experimentally compared phenotypic plasticity in two rocky-shore snail species; Littorina saxatilis releasing miniature snails on the shore, and Littorina littorea releasing drifting larvae settling on various shores, expecting L. littorea to show more phenotypic plasticity than L. saxatilis. We compared magnitude and direction of vectors of phenotypic difference in juvenile shell traits after 3 months exposure to different stimuli simulating sheltered and crab-rich shores, or wave-exposed and crab-free shores. Both species showed similar direction and magnitude of vectors of phenotypic difference with minor differences only between ecotypes of the nondispersing species, indicating that plasticity is an evolving trait in L. saxatilis. The lack of a strong plastic response in L. littorea might be explained by limits rather than costs to plasticity. PMID:17040383

  5. Detection of direct-acting mutagens in ambient air: A comparison of two highly sensitive mutagenicity assays

    SciTech Connect

    Houk, V.S.; Goto, S.; Endo, O.; Claxton, L.D.; Lewtas, J.; Matsushita, H. )

    1992-01-01

    Ambient air has been shown to contain numerous hazardous pollutants, many of which are known or suspected carcinogens and mutagens. Bioassays play a prominent role in the characterization of these genotoxic pollutants, and as new test methods are developed, it is incumbent upon researchers to evaluate assay performance and report relative merits. In this study, two Salmonella test methods (the spiral and preincubation assays) were assessed to determine their usefulness as screening methods for monitoring direct-acting mutagens in ambient air. The spiral assay automates the conventional plate-incorporation assay and has been shown to reduce the labor, materials, and sample mass required to perform mutagenicity testing. The preincubation assay has been shown to enhance test sensitivity for certain classes of compound, thereby reducing the amount of sample required for dose-response analysis. Both assays were used to test organic extracts of airborne particulate matter collected in Tokyo during the winters of 1988 and 1990. In addition to the conventional tester strains TA98 and TA100, two newly developed YG strains were evaluated. Strains YG1024 and YG1029-derived from TA98 and TA100, respectively-contain an acetyltransferase plasmid that confers upon the strains greater sensitivity towards nitroarenes. Results from this study indicated that both assays were able to detect direct-acting mutagens in the Tokyo air samples. The mutagenic activity associated with the samples was directly related to the particle mass present in a given volume of air. Mutagenic response was greater in the spiral assay relative to the preincubation assay, especially when YG tester strains were used. The YG strains were significantly more sensitive to mutation than the TA strains in both assays, which suggests that nitroaromatics are an important class of genotoxic contaminant present in Tokyo air.

  6. Phase contrast X-ray microtomography of the Rhodnius prolixus head: Comparison of direct reconstruction and phase retrieval approach

    NASA Astrophysics Data System (ADS)

    Almeida, A. P.; Braz, D.; Nogueira, L. P.; Colaço, M. V.; Soares, J.; Cardoso, S. C.; Garcia, E. S.; Azambuja, P.; Gonzalez, M. S.; Mohammadi, S.; Tromba, G.; Barroso, R. C.

    2014-02-01

    We have used phase-contrast X-ray microtomography (PPC-μCT) to study the head of the blood-feeding bug, Rhodnius prolixus, which is one of the most important insect vector of Trypanosoma cruzi, ethiologic agent of Chagas disease in Latin America. Images reconstructed from phase-retrieved projections processed by ANKA phase are compared to those obtained through direct tomographic reconstruction of the flat-field-corrected transmission radiographs. It should be noted that the relative locations of the important morphological internal structures are observable with a precision that is difficult to obtain without the phase retrieval approach.

  7. 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.

  8. Viability of Actinobacillus pleuropneumoniae in frozen pig lung samples and comparison of different methods of direct diagnosis in fresh samples.

    PubMed

    Gutierrez, C B; Rodriguez Barbosa, J I; Gonzalez, O R; Tascon, R I; Rodriguez Ferri, E F

    1992-04-01

    A comparative study on different methods of diagnosis of Actinobacillus pleuropneumoniae from both fresh and frozen pig lungs is described. A total of 196 lung tissues with pneumonic lesions were examined for culture isolation on chocolate blood agar, as well as for antigen detection by means of the coagglutination test, the immunodiffusion test and the indirect ELISA. These samples were subsequently frozen for 1 yr and then they were recultured. A. pleuropneumoniae was recovered from fresh lung specimens in 30 cases (15.3%) and from frozen samples in only two cases (0.9%). Such a different degree of isolation demonstrates that long freezing had an adverse effect on the viability of this organism in lung samples. A pleuropneumoniae detection was positive in 134 samples (68.4%) by at least one of the immunological techniques examined. The indirect ELISA was the most sensitive and specific test, with antigen detected in 125 lungs (63.8%). In comparison with the coagglutination and immunodiffusion tests, the sensitivities of the indirect ELISA were 95.8 and 93.7%, and the specificities were 67.0 and 63.4%, respectively. PMID:1563263

  9. A COMPARISON OF MODEL BASED AND DIRECT OPTIMIZATION BASED FILTERING ALGORITHMS FOR SHEARWAVE VELOCITY RECONSTRUCTION FOR ELECTRODE VIBRATION ELASTOGRAPHY

    PubMed Central

    Ingle, Atul; Varghese, Tomy

    2014-01-01

    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. PMID:25285187

  10. Comparison of directly compressed vitamin B12 tablets prepared from micronized rotary-spun microfibers and cast films.

    PubMed

    Sebe, István; Bodai, Zsolt; Eke, Zsuzsanna; Kállai-Szabó, Barnabás; Szabó, Péter; Zelkó, Romána

    2015-01-01

    Fiber-based dosage forms are potential alternatives of conventional dosage forms from the point of the improved extent and rate of drug dissolution. Rotary-spun polymer fibers and cast films were prepared and micronized in order to direct compress after homogenization with tabletting excipients. Particle size distribution of powder mixtures of micronized fibers and films homogenized with tabletting excipients were determined by laser scattering particle size distribution analyzer. Powder rheological behavior of the mixtures containing micronized fibers and cast films was also compared. Positron annihilation lifetime spectroscopy was applied for the microstructural characterization of micronized fibers and films. The water-soluble vitamin B12 release from the compressed tablets was determined. It was confirmed that the rotary spinning method resulted in homogeneous supramolecularly ordered powder mixture, which was successfully compressed after homogenization with conventional tabletting excipients. The obtained directly compressed tablets showed uniform drug release of low variations. The results highlight the novel application of micronized rotary-spun fibers as intermediate for further processing reserving the original favorable powder characteristics of fibrous systems. PMID:25190153

  11. Comparison of Total Evaporation (TE) and Direct Total Evaporation (DTE) methods in TIMS by using NBL CRMs

    NASA Astrophysics Data System (ADS)

    Hasözbek, Altug; Mathew, Kattathu; Wegener, Michael

    2013-04-01

    The total evaporation (TE) is a well-established analytical method for safeguards measurement of uranium and plutonium isotope-amount ratios using the thermal ionization mass spectrometry (TIMS). High accuracy and precision isotopic measurements find many applications in nuclear safeguards, for e.g. assay measurements using isotope dilution mass spectrometry. To achieve high accuracy and precision in TIMS measurements, mass dependent fractionation effects are minimized by either the measurement technique or changes in the hardware components that are used to control sample heating and evaporation process. At NBL, direct total evaporation (DTE) method on the modified MAT261 instrument, uses the data system to read the ion signal intensity and its difference from a pre-determined target intensity, is used to control the incremental step at which the evaporation filament is heated. The feedback and control is achieved by proprietary hardware from SPECTROMAT that uses an analog regulator in the filament power supply with direct feedback of the detector intensity. Compared to traditional TE method on this instrument, DTE provides better precision (relative standard deviation, expressed as a percent) and accuracy (relative difference, expressed as a percent) of 0.05 to 0.08 % for low enriched and high enriched NBL uranium certified reference materials.

  12. Continuity of parenting practices across generations in an at-risk sample: a prospective comparison of direct and mediated associations.

    PubMed

    Capaldi, Deborah M; Pears, Katherine C; Patterson, Gerald R; Owen, Lee D

    2003-04-01

    A prospective model of parenting and externalizing behavior spanning 3 generations (G1, G2, and G3) was examined for young men from an at-risk sample of young adult men (G2) who were in approximately the youngest one third of their cohort to become fathers. It was first predicted that the young men in G2 who had children the earliest would show high levels of antisocial behavior. Second, it was predicted that G1 poor parenting practices would show both a direct association with the G2 son's subsequent parenting and a mediated effect via his development of antisocial and delinquent behavior by adolescence. The young fathers had more arrests and were less likely to have graduated from high school than the other young men in the sample. Findings were most consistent with the interpretation that there was some direct effect of parenting from G1 to G2 and some mediated effect via antisocial behavior in G2. PMID:12735396

  13. A Direct Comparison Between EUV Coronal Flux and Helium Resonance Line Photon Flux from SOHO/CDS Data

    NASA Technical Reports Server (NTRS)

    Andretta, V.; Landi, Enrico; DelZanna, Giulio; Jordan, Stuart D.

    1999-01-01

    In the wealth of EUV spectroscopic and imaging data gathered by the SOHO and TRACE missions, a prominent role is played by the helium resonance emission. For example, He I lines are among the most intense features in CDS/NIS spectra, while the EIT 304 waveband (dominated by He II emission) is routinely employed to map the structure of the solar chromosphere and transition region. However, no 'standard' model has emerged so far that is able to interpret observed He spectra/images to a satisfactory degree of self-consistency. Recent research on the problem of the formation of the solar helium spectrum tends to rule out a dominant role of coronal radiation in exciting He resonance lines. However, while evidence for this result is strong, it is based on indirect tests. Here we present a preliminary assessment of this issue based on a more direct approach, which involves a measure with CDS/GIS of the photoionizing EUV radiation. This measure can be directly compared with the observed flux in the main He I and He II resonance lines observed with CDS/NIS2.

  14. KSHV Induction of Angiogenic and Lymphangiogenic Phenotypes

    PubMed Central

    DiMaio, Terri A.; Lagunoff, Michael

    2012-01-01

    Kaposi’s sarcoma (KS) is a highly vascularized tumor supporting large amounts of neo-angiogenesis. The major cell type in KS tumors is the spindle cell, a cell that expresses markers of lymphatic endothelium. KSHV, the etiologic agent of KS, is found in the spindle cells of all KS tumors. Considering the extreme extent of angiogenesis in KS tumors at all stages it has been proposed that KSHV directly induces angiogenesis in a paracrine fashion. In accordance with this theory, KSHV infection of endothelial cells in culture induces a number of host pathways involved in activation of angiogenesis and a number of KSHV genes themselves can induce pathways involved in angiogenesis. Spindle cells are phenotypically endothelial in nature, and therefore, activation through the induction of angiogenic and/or lymphangiogenic phenotypes by the virus may also be directly involved in spindle cell growth and tumor induction. Accordingly, KSHV infection of endothelial cells induces cell autonomous angiogenic phenotypes to activate host cells. KSHV infection can also reprogram blood endothelial cells to lymphatic endothelium. However, KSHV induces some blood endothelial specific genes upon infection of lymphatic endothelial cells creating a phenotypic intermediate between blood and lymphatic endothelium. Induction of pathways involved in angiogenesis and lymphangiogenesis are likely to be critical for tumor cell growth and spread. Thus, induction of both cell autonomous and non-autonomous changes in angiogenic and lymphangiogenic pathways by KSHV likely plays a key role in the formation of KS tumors. PMID:22479258

  15. Comparison of Measured Direct Normal Irradiance Data to Calculated Using the Disc Model for the Texas Panhandle

    SciTech Connect

    Vick, B. D.; Myers, D.

    2011-01-01

    It is important that we convert from fossil energy to wind and solar energy. Wind energy is currently the cheapest form of renewable energy, but it is usually a poor match to utility electrical generation in the Great Plains of the United States. Concentrating solar power (CSP) plants are a better match to utility electrical loading, but so far none of these plants have been constructed in the Great Plains. Part of the reason no CSP plants have been constructed is lack of confidence in the solar resource data required (direct normal irradiance or DNI for short). There are several models for converting global solar radiation to DNI, and one of them is the DISC model. Both DNI data and global radiation data were collected at the USDA-Agricultural Research Laboratory at Bushland, Texas, for the years 2009 and 2010. Using the DISC model and measured global radiation data, DNI was calculated and compared to measured DNI data. The total annual solar energy estimated with the model was 5% greater than what was actually measured which was fairly close. However, on a monthly or hourly basis, the percentage difference could be as high as 25%. Analysis of individual months and days resulted in some recommendations for improving the DISC model. Some of the poor correlations between measured solar energy and calculated solar energy using the DISC model implied that another model (DIRINDEX) might be better. Therefore, additional work is planned to investigate the DIRINDEX model with the same data set to see if the correlation improves. This work may potentially lead to the increased use of solar energy for electrical generation, which will decrease the use of fossil fuels and the environmental pollution from fossil fuel power plants. 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

  16. Cerebral blood flow quantification in the rat: a direct comparison of arterial spin labeling MRI with radioactive microsphere PET

    PubMed Central

    2012-01-01

    Background Arterial spin labeling magnetic resonance imaging (ASL-MRI) has been recognised as a valuable method for non-invasive assessment of cerebral blood flow but validation studies regarding quantification accuracy by comparison against an accepted gold standard are scarce, especially in small animals. We have conducted the present study with the aim of comparing ASL flow-sensitive alternating inversion recovery (FAIR)-derived unidirectional water uptake (K1) and 68Ga/64Cu microsphere (MS)-derived blood flow (f) in the rat brain. Methods In 15 animals, K1and f were determined successively in dedicated small animal positron emission tomography and MR scanners. The Renkin-Crone model modified by a scaling factor was used for the quantification of f and K1. Results Below about 1 mL/min/mL, we obtain an approximately linear relationship between f and K1. At higher flow values, the limited permeability of water at the blood brain barrier becomes apparent. Within the accessed dynamic flow range (0.2 to 1.9 mL/min/mL), the data are adequately described by the Renkin-Crone model yielding a permeability surface area product of (1.53±0.46) mL/min/mL. Conclusion The ASL-FAIR technique is suitable for absolute blood flow quantification in the rat brain when using a one-compartment model including a suitable extraction correction for data evaluation. Trial registration 24-9168.21-4/2004-1 (registered in Freistadt Sachsen, Landesdirektion Dresden) PMID:22978819

  17. A Dual Source Ion Mobility-Mass Spectrometer for Direct Comparison of ESI and MALDI Collision Cross Section Measurements

    PubMed Central

    Sundarapandian, Sevugarajan; May, Jody C.; McLean, John A.

    2010-01-01

    In this report, we describe a dual ionization source ion mobility-mass spectrometer (IM-MS) instrument platform for investigations that critically compare ion mobility collision cross section (CCS) measurements obtained from different ionization methods. The instrument incorporates both matrix-assisted laser desorption ionization (MALDI) and nano-electrospray ionization (nESI) sources. The nESI source incorporates a keyhole geometry ion funnel design which facilitates axial ion focusing, accumulation, and generation of short duration (10–30 µs) ion pulses for use with the IM-MS. The IM-MS instrument operation is independent of which ionization source is used. This allows comparisons of collision cross section measurements to be made between both ion sources with minimal differences in the instrumental arrangement. The performance of the nESI ion source is evaluated by measuring the collision cross section values of the charge states of equine cytochrome c (z = 9 to 16) and values are in good agreement (<2% deviation) with those previously reported in the literature. Several charge states (z = 8 to 11) of cytochrome c exhibit multiple cross sectional features in the ion mobility analysis. An analysis of the tryptic peptides of cytochrome c formed by both ESI and MALDI demonstrate that on average, +1 MALDI ions are similar in CCS to +1 ESI ions and are smaller than +2 ESI ions. The ion mobility resolving power with ESI (30–35) is comparable to that obtained by using MALDI (35–40), which suggests that both sources produce sufficiently narrow ion pulses for the measurement to be predominately diffusion rather than gate pulse width limited. PMID:20329759

  18. Wavelength-scanning calibration of detection efficiency of single photon detectors by direct comparison with a photodiode

    NASA Astrophysics Data System (ADS)

    Lee, Hee Jung; Park, Seongchong; Park, Hee Su; Hong, Kee Suk; Lee, Dong-Hoon; Kim, Heonoh; Cha, Myoungsik; Seb Moon, Han

    2016-04-01

    We present a practical calibration method of the detection efficiency (DE) of single photon detectors (SPDs) in a wide wavelength range from 480 nm to 840 nm. The setup consists of a GaN laser diode emitting a broadband luminescence, a tunable bandpass filter, a beam splitter, and a switched integrating amplifier which can measure the photocurrent down to the 100 fA level. The SPD under test with a fibre-coupled beam input is directly compared with a reference photodiode without using any calibrated attenuator. The relative standard uncertainty of the DE of the SPD is evaluated to be from 0.8% to 2.2% varying with wavelength (k  =  1).

  19. A comparison of the other-directed stigmatization produced by legal and illegal forms of affirmative action.

    PubMed

    Evans, David C

    2003-02-01

    Recent studies have begun to show that the stigma of incompetence sometimes directed toward the beneficiaries of affirmative action may be significantly reduced as the preferences granted to women and minorities become more moderate. The author examined whether the stigmatization of African Americans would differ under hiring policies that represented legal and illegal levels of racial preference according to federal regulations. Participants were 178 students and 161 corporate employees who rated fictitious Black and White target employees working under (a) an illegal policy of selection of unequal candidates, (b) a legal policy of selection of comparable candidates, or (c) equal opportunity. Participants rated Black targets' achievement-related traits lower than White targets only under the illegal policy. Under the legal policy, no such stigmatization was observed. Additional dependent measures and theoretical implications were explored. PMID:12675400

  20. Comparison of performance capabilities of spread spectrum coherent and direct detection CO2 DIAL systems and associated hardware fielding implications

    NASA Astrophysics Data System (ADS)

    Hasson, Victor H.; Dryden, Gordon L.

    2002-07-01

    This paper reviews the performance of a conventional direct detection CO2 Differential Absorption Lidar (DIAL) system with the coherent spread spectrum approach developed, validated and patented by Textron. The analysis shows that the coherent approach is far superior in terms of maximum attainable standoff range at a specified transmitter average power and substantially reduced system power and associated size and weight at a predetermined range. The requirements on local oscillator stability are fairly relaxed and the spread spectrum/coherent DIAL concept is fairly easy to implement. Performance parameter maps are presented for ground-based, low-altitude and high-altitude airborne systems with a range of aperture sizes and pulse formats.

  1. Validation of a New Minimally Invasive Intracranial Pressure Monitoring Method by Direct Comparison with an Invasive Technique.

    PubMed

    Vilela, Gustavo Henrique Frigieri; Cabella, Brenno; Mascarenhas, Sérgio; Czosnyka, Marek; Smielewski, Peter; Dias, Celeste; Cardim, Danilo Augusto; Mascarenhas, Yvonne Maria; Wang, Charles Chenwei; Andrade, Rodrigo; Tanaka, Koji; Lopes, Luiza Silva; Colli, Benedicto Oscar

    2016-01-01

    In this chapter we present in vivo experiments with a new minimally invasive method of monitoring intracranial pressure (ICP). Strain gauge deformation sensors are externally glued onto the exposed skull. The signal from these sensors is amplified, filtered, and sent to a computer with appropriate software for analysis and data storage. Saline infusions into the spinal channel of rats were performed to produce ICP changes, and minimally invasive ICP and direct Codman intraparenchymal ICP were simultaneously acquired in six animals. The similarity between the invasive and minimally invasive methods in response to ICP increase was assessed using Pearson's correlation coefficient. It demonstrated good agreement between the two measures < r > = 0.8 ± 0.2, with a range of 0.31-0.99. PMID:27165885

  2. 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.

  3. A comparison of direct fluorescent antibody and Giemsa staining for the post-mortem diagnosis of anaplasmosis.

    PubMed

    Johnston, L A; Trueman, K F; Leatch, G; Wilson, A J

    1980-03-01

    Direct fluorescent antibody (DFA) and Giemsa staining of Anaplasma marginale were compared in smears collected serially at post-mortem (PM) from 11 experimentally infected calves. Once smears had been prepared and air-dried they could be held for at least 5 days before staining with either technique with no noticeable change in staining quality. DFA staining was more sensitive in detecting anaplasms in smears than Giemsa staining. Anaplasma spp could be differentiated from Babesia bovis and B. bigemina by DFA staining but there were cross reactions between A. marginale and A. centrale. Blood smears prepared from subcutaneous vessels in the legs provided better diagnostic material than kidney, heart and lung smears. Brain smears were not suitable for PM diagnosis using either staining technique. PMID:7002139

  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. Mapping membrane protein backbone dynamics: a comparison of site-directed spin labeling with NMR 15N-relaxation measurements.

    PubMed

    Lo, Ryan H; Kroncke, Brett M; Solomon, Tsega L; Columbus, Linda

    2014-10-01

    The ability to detect nanosecond backbone dynamics with site-directed spin labeling (SDSL) in soluble proteins has been well established. However, for membrane proteins, the nitroxide appears to have more interactions with the protein surface, potentially hindering the sensitivity to backbone motions. To determine whether membrane protein backbone dynamics could be mapped with SDSL, a nitroxide was introduced at 55 independent sites in a model polytopic membrane protein, TM0026. Electron paramagnetic resonance spectral parameters were compared with NMR (15)N-relaxation data. Sequential scans revealed backbone dynamics with the same trends observed for the R1 relaxation rate, suggesting that nitroxide dynamics remain coupled to the backbone on membrane proteins. PMID:25296323

  6. Noradrenaline and dopamine neurons in the reward/effort trade-off: a direct electrophysiological comparison in behaving monkeys.

    PubMed

    Varazzani, Chiara; San-Galli, Aurore; Gilardeau, Sophie; Bouret, Sebastien

    2015-05-20

    Motivation determines multiple aspects of behavior, including action selection and energization of behavior. Several components of the underlying neural systems have been examined closely, but the specific role of the different neuromodulatory systems in motivation remains unclear. Here, we compare directly the activity of dopaminergic neurons from the substantia nigra pars compacta and noradrenergic neurons from the locus coeruleus in monkeys performing a task manipulating the reward/effort trade-off. Consistent with previous reports, dopaminergic neurons encoded the expected reward, but we found that they also anticipated the upcoming effort cost in connection with its negative influence on action selection. Conversely, the firing of noradrenergic neurons increased with both pupil dilation and effort production in relation to the energization of behavior. Therefore, this work underlines the contribution of dopamine to effort-based decision making and uncovers a specific role of noradrenaline in energizing behavior to face challenges. PMID:25995472

  7. Comparison of direct and indirect alcohol markers with PEth in blood and urine in alcohol dependent inpatients during detoxication.

    PubMed

    Winkler, M; Skopp, G; Alt, A; Miltner, E; Jochum, Th; Daenhardt, C; Sporkert, F; Gnann, H; Weinmann, W; Thierauf, A

    2013-07-01

    The importance of direct and indirect alcohol markers to evaluate alcohol consumption in clinical and forensic settings is increasingly recognized. While some markers are used to prove abstinence from ethanol, other markers are suitable for detection of alcohol misuse. Phosphatidyl ethanol (PEth) is ranked among the latter. There is only little information about the correlation between PEth and other currently used markers (ethyl glucuronide, ethyl sulfate, carbohydrate deficient transferrin, gamma-glutamyl transpeptidase, and methanol) and about their decline during detoxification. To get more information, 18 alcohol-dependent patients in withdrawal therapy were monitored for these parameters in blood and urine for up to 19 days. There was no correlation between the different markers. PEth showed a rapid decrease at the beginning of the intervention, a slow decline after the first few days, and could still be detected after 19 days of abstinence from ethanol. PMID:23274938

  8. 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.

  9. A comparison of sodium borohydride as a fuel for proton exchange membrane fuel cells and for direct borohydride fuel cells

    NASA Astrophysics Data System (ADS)

    Wee, Jung-Ho

    Two types of fuel cell systems using NaBH 4 aqueous solution as a fuel are possible: the hydrogen/air proton exchange membrane fuel cell (PEMFC) which uses onsite H 2 generated via the NaBH 4 hydrolysis reaction (B-PEMFC) at the anode and the direct borohydride fuel cell (DBFC) system which directly uses NaBH 4 aqueous solution at the anode and air at the cathode. Recently, research on these two types of fuel cells has begun to attract interest due to the various benefits of this liquid fuel for fuel cell systems for portable applications. It might therefore be relevant at this stage to evaluate the relative competitiveness of the two fuel cells. Considering their current technologies and the high price of NaBH 4, this paper evaluated and analyzed the factors influencing the relative favorability of each type of fuel cell. Their relative competitiveness was strongly dependent on the extent of the NaBH 4 crossover. When considering the crossover in DBFC systems, the total costs of the B-PEMFC system were the most competitive among the fuel cell systems. On the other hand, if the crossover problem were to be completely overcome, the total cost of the DBFC system generating six electrons (6e-DBFC) would be very similar to that of the B-PEMFC system. The DBFC system generating eight electrons (8e-DBFC) became even more competitive if the problem of crossover can be overcome. However, in this case, the volume of NaBH 4 aqueous solution consumed by the DBFC was larger than that consumed by the B-PEMFC.

  10. 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

  11. 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. PMID:26186122

  12. A comparison of direction finding results from an FFT peak identification technique with those from the music algorithm

    NASA Astrophysics Data System (ADS)

    Montbriand, L. E.

    1991-07-01

    A peak identification technique which uses the fast Fourier transform (FFT) algorithm is presented for unambiguously identifying up to three sources in signals received by the sampled aperture receiving array (SARA) of the Communications Research Center. The technique involves removing phase rotations resulting from the FFT and the data configuration and interpreting this result as the direction cosine distribution of the received signal. The locations and amplitudes of all peaks for one array arm are matched with those in a master list for a single source in order to identify actual sources. The identification of actual sources was found to be subject to the limitations of the FFT in that there was an inherent bias for the secondary and tertiary sources to appear at the side-lobe positions of the strongest source. There appears to be a limit in the ratio of the magnitude of a weaker source to that of the strongest source, below which it becomes too difficult to reliably identify true sources. For the SARA array this ratio is near-10 dB. Some of the data were also analyzed using the more complex MUSIC algorithm which yields a narrower directional peak for the sources than the FFT. For the SARA array, using ungroomed data, the largest side and grating lobes that the MUSIC algorithm produces are some 10 dB below the largest side and grating lobes that are produced using the FFT algorithm. Consequently the source-separation problem is less than that encountered using the FFT algorithm, but is not eliminated.

  13. 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. PMID:26850283

  14. Prediction of microbial phenotypes based on comparative genomics

    PubMed Central

    2015-01-01

    The accessibility of almost complete genome sequences of uncultivable microbial species from metagenomes necessitates computational methods predicting microbial phenotypes solely based on genomic data. Here we investigate how comparative genomics can be utilized for the prediction of microbial phenotypes. The PICA framework facilitates application and comparison of different machine learning techniques for phenotypic trait prediction. We have improved and extended PICA's support vector machine plug-in and suggest its applicability to large-scale genome databases and incomplete genome sequences. We have demonstrated the stability of the predictive power for phenotypic traits, not perturbed by the rapid growth of genome databases. A new software tool facilitates the in-depth analysis of phenotype models, which associate expected and unexpected protein functions with particular traits. Most of the traits can be reliably predicted in only 60-70% complete genomes. We have established a new phenotypic model that predicts intracellular microorganisms. Thereby we could demonstrate that also independently evolved phenotypic traits, characterized by genome reduction, can be reliably predicted based on comparative genomics. Our results suggest that the extended PICA framework can be used to automatically annotate phenotypes in near-complete microbial genome sequences, as generated in large numbers in current metagenomics studies. PMID:26451672

  15. 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

  16. 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

  17. Contrasting Association Results between Existing PheWAS Phenotype Definition Methods and Five Validated Electronic Phenotypes

    PubMed Central

    Leader, Joseph B; Pendergrass, Sarah A; Verma, Anurag; Carey, David J; Hartzel, Dustin N; Ritchie, Marylyn D; Kirchner, H. Lester

    2015-01-01

    Phenome-Wide Association Studies (PheWAS) comprehensively investigate the association between genetic variation and a wide array of outcome traits. Electronic health record (EHR) based PheWAS uses various abstractions of International Classification of Diseases, Ninth Revision (ICD-9) codes to identify case/control status for diagnoses that are used as the phenotypic variables. However, there have not been comparisons within a PheWAS between results from high quality derived phenotypes and high-throughput but potentially inaccurate use of ICD-9 codes for case/control definition. For this study we first developed a group of high quality algorithms for five phenotypes. Next we evaluated the association of these “gold standard” phenotypes and 4,636,178 genetic variants with minor allele frequency > 0.01 and compared the results from high-throughput associations at the 3 digit, 5 digit, and PheWAS codes for defining case/control status. We found that certain diseases contained similar patient populations across phenotyping methods but had differences in PheWAS. PMID:26958218

  18. 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

  19. A comparison of microstructure, texture and formability of direct chill cast versus continuous cast aluminum-magnesium alloys

    NASA Astrophysics Data System (ADS)

    Zhao, Yumin

    In this dissertation, microstructure and texture evolution of Al-Mg alloys produced by direct chill (DC) cast and continuous cast processes (CC) during thermo-mechanical processing were compared and the differences in formability between DC and CC alloys were identified. At the same time, the underlining mechanisms that cause the difference in structure, texture and formability between DC and CC alloys were analyzed. The recrystallization temperature of the DC AA5052 hot band was about 55°C lower than that of the CC AA5052 hot band. After complete recrystallization, DC AA5052 hot band possessed a stronger cube component than the CC AA5052 hot band. This result was associated with the particle structures of DC and CC AA5052 hot bands. Two different phase particles, Al6((Mn,Fe) and Mg2Si, existed in the DC and CC AA5052 hot bands. CC AA5052 hot band contained more Mg2Si particles than did the DC AA5052 hot band due to the absence of homogenization of the CC material before hot rolling. Mg2Si particles were easily dissolved at high treatment temperatures. After preheating at 454°C for 4 hours, the particle density in the preheated CC AA5052 hot band is closer to that in DC AA5052 alloy due to the dissolution of the Mg2Si particles. Therefore, the differences on recrystallization behaviors of the 80% cold rolled materials decreased, if the DC and CC materials were preheated at 454°C for 4 hours before cold rolling. If the as-received DC and CC AA5052 hot bands were directly cold rolled to 80% reduction, the cold rolled CC AA5052 alloy had a higher recrystallization temperature and a weaker cube recrystallization texture than the cold rolled DC AA5052 alloy. There still existed differences in texture evolution during cold rolling and isothermal annealing between DC and CC AA5052 and AA5182 materials, although the preheat treatment decreased the differences in particle structures and recrystallization temperature between DC and CC materials. Texture evolution during

  20. 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

  1. 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. PMID

  2. Comparison of Diagnostic Accuracy of Conventional Intraoral Periapical and Direct Digital Radiographs in Detecting Interdental Bone Loss

    PubMed Central

    Suragimath, Girish; Jaishankar, H.P.; Kulkarni, Prasad; Bijjaragi, Shobha C.; Sangle, Varsha Ajit

    2015-01-01

    Background: Periodontitis is an inflammatory disease of the supporting tissues of the teeth caused by specific microorganisms, resulting in destruction of the periodontal ligament and alveolar bone. Progressive loss of alveolar bone is the salient feature of periodontal disease. Accurate detection of periodontal disease with the use of radiographs helps in diagnosis, treatment and prognosis. Aims: The present study aims to compare the efficacy of conventional intraoral periapical (IOPA) and direct digital radiographs (RVG) in detecting interdental alveolar bone loss using intrasurgical (IS) measurements as the gold standard. Materials and Methods: Thirty patients elected to undergo periodontal flap surgery with periodontitis computing to 60 interdental alveolar defects on mandibular first molars were considered. IOPA and RVG were captured using standardized techniques. Bone loss measurements in IOPA and RVG were compared to the IS measurements. Statistical Analysis: Statistical analysis was carried out using student t test and ANOVA with the help of SPSS software and p-value <0.05 was considered as significant. Results: Both IOPA and RVG underestimated the bone loss measurements when compared to IS measurements which was statistically significant (p<0.0001). Bone loss measurements in RVG were closer to IS measurements than IOPA. Conclusion: Both the radiographic techniques IOPA and RVG underestimated bone loss by 1.5–2.5 mm. RVG was superior to IOPA for the detection of interdental bone loss due to reduced time and radiation exposure to obtain the same diagnostic information. PMID:25859522

  3. Quantitative morphological comparison of axon-targeting strategies for gene therapies directed to the nigro-striatal projection.

    PubMed

    Padmanabhan, S; Kareva, T; Kholodilov, N; Burke, R E

    2014-02-01

    Cellular targeting of mRNAs and proteins to axons is essential for axon growth during development and is likely to be important for adult maintenance as well. Given the importance and potency of these axon-targeting motifs to the biology of axons, it seems possible that they can be used in the design of transgenes that are intended to enhance axon growth or maintenance, so as to improve potency and minimize off-target effects. To investigate this possibility, it is first essential to assess known motifs for their efficacy. We have therefore evaluated four axon-targeting motifs, using adeno-associated viral vector-mediated gene delivery in the nigro-striatal dopaminergic system, a projection that is predominantly affected in Parkinson's disease. We have tested two mRNA axonal zipcodes, the 3' untranslated region (UTR) of β-actin and 3' UTR of tau, and two axonal-targeting protein motifs, the palmitoylation signal sequence in GAP-43 and the last 15 amino acids in the amyloid precursor protein, to direct the expression of the fluorescent protein Tomato in axons. These sequences, fused to Tomato, were able to target its expression to dopaminergic axons. Based on quantification of Tomato-positive axons, and the density of striatal innervation, we conclude that the C-terminal of the amyloid precursor protein is the most effective axon-targeting motif. PMID:24305419

  4. Comparison of chemical modifiers for direct determination of Cd, Cu and Zn in food stuffs by solid-sampling-ETAAS.

    PubMed

    Török, Peter; Žemberyová, Mária

    2012-05-01

    In this work, the capability of different chemical modifiers (Pd, Pd/Mg(NO3)2, Pd/NH4NO3, NH4H2PO4, NH4H2PO4/Mg(NO3)2) to eliminate the matrix effects in the direct determination of Cd, Cu and Zn in food-stuffs by solid sampling-electrothermal atomic absorption spectrometry was compared. The alternative analytical lines were used for determination of Cu (327.4nm) and Zn (307.6nm) in order to allow the introduction of reasonably high sample mass into the furnace. Mixed modifiers containing palladium were useful to eliminate the matrix effect in Cd determination. For Cu and Zn determination the application of Pd shows satisfactory analytical performance. In the determinations of Cd and Zn the phosphate containing modifiers shows elimination of matrix effects only when applying them to a partially pyrolysed sample (at 400°C). The achievable limits of detection for Cd, Cu and Zn in solid samples were 0.279ngg(-1); 0.020μgg(-1) and 2.04μgg(-1), respectively. PMID:26434331

  5. Observation of early shell-dopant mix in OMEGA direct-drive implosions and comparisons with radiation-hydrodynamic simulations

    SciTech Connect

    Baumgaertel, J. A.; Bradley, P. A.; Hsu, S. C.; Cobble, J. A.; Hakel, P.; Tregillis, I. L.; Krasheninnikova, N. S.; Murphy, T. J.; Schmitt, M. J.; Shah, R. C.; Obrey, K. D.; Batha, S.; Johns, H.; Joshi, T.; Mayes, D.; Mancini, R. C.; Nagayama, T.

    2014-05-15

    Temporally, spatially, and spectrally resolved x-ray image data from direct-drive implosions on OMEGA were interpreted with the aid of radiation-hydrodynamic simulations. Neither clean calculations nor those using a turbulent mix model can explain fully the observed migration of shell-dopant material (titanium) into the core. Shell-dopant migration was observed via time-dependent, spatially integrated spectra, and spatially and spectrally resolved x-ray images of capsule implosions and resultant dopant emissions. The titanium emission was centrally peaked in narrowband x-ray images. In post-processed clean simulations, the peak titanium emission forms in a ring in self-emission images as the capsule implodes. Post-processed simulations with mix reproduce trends in time-dependent, spatially integrated spectra, as well having centrally peaked Ti emission in synthetic multiple monochromatic imager. However, mix simulations still do not transport Ti to the core as is observed in the experiment. This suggests that phenomena in addition to the turbulent mix must be responsible for the transport of Ti. Simple diffusion estimates are unable to explain the early Ti mix into the core. Mechanisms suggested for further study are capsule surface roughness, illumination non-uniformity, and shock entrainment.

  6. 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). PMID:26928354

  7. The dimensional nature of eating pathology: Evidence from a direct comparison of categorical, dimensional, and hybrid models.

    PubMed

    Luo, Xiaochen; Donnellan, M Brent; Burt, S Alexandra; Klump, Kelly L

    2016-07-01

    Eating disorders are conceptualized as categorical rather than dimensional in the current major diagnostic system (Diagnostic and Statistical Manual of Mental Disorders; 5th ed.; American Psychiatric Association, 2013) and in many previous studies. However, previous research has not critically evaluated this assumption or tested hybrid models (e.g., modeling latent variables with both dimensional and categorical features). Accordingly, the current study directly compared categorical, dimensional, and hybrid models for eating pathology in a large, population-based sample. Participants included 3,032 female and male twins (ages 9-30 years) from the Michigan State University Twin Registry. The Minnesota Eating Behaviors Survey was used to assess disordered eating symptoms including body dissatisfaction, weight preoccupation, binge eating, and compensatory behaviors. Results showed that dimensional models best fit the data in the overall sample as well as across subgroups divided by sex and pubertal status (e.g., prepubertal vs. postpubertal). It is interesting to note that the results favored more categorical models when using a case-control subset of our sample with participants who either endorsed substantial eating pathology or no/little eating pathology. Overall, findings provide support for a dimensional conceptualization of eating pathology and underscore the importance of using community samples to capture the full range of severity of eating pathology when investigating questions about taxonomy. (PsycINFO Database Record PMID:27214062

  8. A comparison of weight average and direct boundary fitting of sedimentation velocity data for indefinite polymerizing systems.

    PubMed

    Sontag, C A; Stafford, W F; Correia, J J

    2004-03-01

    Analysis of sedimentation velocity data for indefinite self-associating systems is often achieved by fitting of weight average sedimentation coefficients (s(20,w)) However, this method discriminates poorly between alternative models of association and is biased by the presence of inactive monomers and irreversible aggregates. Therefore, a more robust method for extracting the binding constants for indefinite self-associating systems has been developed. This approach utilizes a set of fitting routines (SedAnal) that perform global non-linear least squares fits of up to 10 sedimentation velocity experiments, corresponding to different loading concentrations, by a combination of finite element simulations and a fitting algorithm that uses a simplex convergence routine to search parameter space. Indefinite self-association is analyzed with the software program isodesfitter, which incorporates user provided functions for sedimentation coefficients as a function of the degree of polymerization for spherical, linear and helical polymer models. The computer program hydro was used to generate the sedimentation coefficient values for the linear and helical polymer assembly mechanisms. Since this curve fitting method directly fits the shape of the sedimenting boundary, it is in principle very sensitive to alternative models and the presence of species not participating in the reaction. This approach is compared with traditional fitting of weight average data and applied to the initial stages of Mg(2+)-induced tubulin self-associating into small curved polymers, and vinblastine-induced tubulin spiral formation. The appropriate use and limitations of the methods are discussed. PMID:15043931

  9. Hall effect in a strong magnetic field: Direct comparisons of compressible magnetohydrodynamics and the reduced Hall magnetohydrodynamic equations

    SciTech Connect

    Martin, L. N.; Dmitruk, P.; Gomez, D. O.

    2010-11-15

    In this work we numerically test a model of Hall magnetohydrodynamics in the presence of a strong mean magnetic field: the reduced Hall magnetohydrodynamic model (RHMHD) derived by [Gomez et al., Phys. Plasmas 15, 102303 (2008)] with the addition of weak compressible effects. The main advantage of this model lies in the reduction of computational cost. Nevertheless, up until now the degree of agreement with the original Hall MHD system and the range of validity in a regime of turbulence were not established. In this work direct numerical simulations of three-dimensional Hall MHD turbulence in the presence of a strong mean magnetic field are compared with simulations of the weak compressible RHMHD model. The results show that the degree of agreement is very high (when the different assumptions of RHMHD, such as spectral anisotropy, are satisfied). Nevertheless, when the initial conditions are isotropic but the mean magnetic field is maintained strong, the results differ at the beginning but asymptotically reach a good agreement at relatively short times. We also found evidence that the compressibility still plays a role in the dynamics of these systems, and the weak compressible RHMHD model is able to capture these effects. In conclusion the weak compressible RHMHD model is a valid approximation of the Hall MHD turbulence in the relevant physical context.

  10. 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.

  11. Direct Comparison of Full-Scale Vlasov-Fokker-Planck and Classical Modeling of Megagauss Magnetic Field Generation in Plasma Near Hohlraum Walls From Nanosecond Laser Pulses

    NASA Astrophysics Data System (ADS)

    Joglekar, Archis; Thomas, Alexander; Read, Martin; Kingham, Robert

    2014-10-01

    Here, we present 2D numerical modeling of near critical density plasma using a fully implicit Vlasov-Fokker-Planck (VFP) code, IMPACTA, with the addition of a ray tracing package. In certain situations, such as those at the critical surface at the walls of a hohlraum, magnetic fields are generated through the crossed temperature and electron density gradients. Modeling shows 0.3 MG fields and the strong heating also results in magnetization of the plasma up to ωτ ~ 5 . In the case without magnetic field generation, the heat flows from the laser heating region are isotropic. Including magnetic fields causes the heat flow to form jets along the wall due to the Righi-Leduc effect. The heating of the wall region causes steeper temperature gradients. This serves as a positive feedback mechanism for the field generation rate resulting in nearly twice the amount of field generated in comparison to the case without magnetic fields over 1 ns. The heat conduction, field generation, and the calculation of other transport quantities, is performed ab-initio due to the nature of the VFP equation set. In order to determine the importance of the kinetic effects from IMPACTA, we perform direct comparison with a classical (Braginskii) transport code with hydrodynamic motion (CTC+). The authors would like to acknowledge DOE Grant #DESC0010621 and Advanced Research Computing, UM-AA.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. Direct comparisons of 2D and 3D dental microwear proxies in extant herbivorous and carnivorous mammals.

    PubMed

    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

  17. 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

  18. Determination of free insulin-like growth factor-I in human serum: comparison of ultrafiltration and direct immunoradiometric assay.

    PubMed

    Frystyk, J; Ivarsen, P; Støving, R K; Dall, R; Bek, T; Hagen, C; Ørskov, H

    2001-04-01

    Two fundamentally different methods are currently used for the determination of free insulin-like growth factor-I (IGF-I): ultrafiltration by centrifugation (UF) and direct immunoradiometric assay (IRMA). The aim was to evaluate a commercial IRMA (DSL, Webster, TX, USA) and to compare it with UF. In the IRMA it is recommended that samples be incubated for 2 h at 5;C. When comparing samples (n = 8) incubated for 1 and 2 h, levels increased by 27 +/- 5% (P< 0.0001). When incubating samples at 22;C instead of 5;C, levels increased by 192 +/- 32% (P< 0.0001). Addition of IGF-binding protein-1 (IGFBP-1) to normal sera (n = 6) dose-dependently decreased ultrafiltered free IGF-I only (P< 0.0007). Similarly, UF was more sensitive than IRMA to addition of IGFBP-2 (P< 0.05). In healthy subjects (n = 35) IRMA yielded 20% higher levels than UF (1.09 +/- 0.09 vs 0.91 +/- 0.12 microg/L; P< 0.0001). IRMA and UF yielded similar results in healthy subjects treated with IGF-I (n = 5) or growth hormone (n = 7) and in acromegalic patients (n = 6) before and after somatostatin analogue treatment. However, marked differences were observed in conditions with elevated IGFBP-1 and -2. In type-1 diabetics (n = 23) ultrafiltered free IGF-I was more reduced than IRMA free IGF-I (38 +/- 9 vs 76 +/- 7% of matched controls (n = 13); P< 0.0001). In patients with chronic renal failure (n = 25), IRMA free IGF-I was identical to control levels (n = 13), whereas ultrafiltered free IGF-I was decreased by 51 +/- 7% (P< 0.0001). Similarly, women with anorexia nervosa (n = 9) studied before and after weight gain showed significant changes in ultrafiltered free IGF-I only (P< 0.03). In conclusion, IRMA was not very robust with respect to variations in sample incubation and this may bias results. IRMA generally yielded higher levels than UF, in accordance with the knowledge that IRMA measures free plus readily dissociable IGF-I. IRMA was less affected than UF by added IGFBP-1 and -2, and reductions in free

  19. 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

  20. Direct comparison of the generalized Visual Analog Scale (gVAS) and general Labeled Magnitude Scale (gLMS).

    PubMed

    Hayes, John E; Allen, Alissa L; Bennett, Samantha M

    2013-04-01

    Hundreds of studies have used the generalized Labeled Magnitude Scale (gLMS) to collect intensity data. Recent work on generalized affective scales like the Labeled Affective Magnitude (LAM) scale and Labeled Hedonic Scale (LHS) suggest a substantial proportion of participants fail to use the entire range of generalized scales, marking only at the adjective labels. This categorical behavior (i.e., clustering) is not limited to affective ratings, as it is well known anecdotally among users of the gLMS. One way to stop this behavior would be to retain a generalized top anchor and cross modal orientation procedure while stripping away the internal adjectives. Several published studies have already used this variant, the generalized Visual Analog Scale (gVAS). Because there are no reports directly comparing the gVAS and gLMS head to head, we did so in two experiments. In Experiment 1, participants (n=87) were randomized to 1 of 3 conditions to test effects of scaling instructions and scale structure. In Experiment 2, participants (n=58) assessed perceived ease of use and resolving power for each scale in a two-session crossover design. gLMS data showed evidence of categorical behavior, while gVAS data did not. Explicitly instructing participants to rate between adjectives did not reduce this behavior. The gLMS was easier to use according to participants, but resulted in non-normal data due to clustering near the adjective labels. gVAS data did not show categorical behavior, as there are no adjectives to cluster around, but the gVAS sacrifices semantic information about the magnitude of response. Regardless of scale type, participants felt the cross-modal orientation procedure helped them understand how to use the scale. Both scales were able to discriminate between sucrose samples in a concentration series. Relative tradeoffs between the two methods suggest the choice of one scale over the other depends on the specific goals and context of the project. PMID:23175601

  1. 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

  2. Direct comparison of antigen production and induction of apoptosis by canarypox virus- and modified vaccinia virus ankara-human immunodeficiency virus vaccine vectors.

    PubMed

    Zhang, Xiugen; Cassis-Ghavami, Farah; Eller, Mike; Currier, Jeff; Slike, Bonnie M; Chen, Xuemin; Tartaglia, James; Marovich, Mary; Spearman, Paul

    2007-07-01

    Recombinant poxvirus vectors are undergoing intensive evaluation as vaccine candidates for a variety of infectious pathogens. Avipoxviruses, such as canarypox virus, are replication deficient in mammalian cells by virtue of a poorly understood species-specific restriction. Highly attenuated vaccinia virus strains such as modified vaccinia virus Ankara (MVA) are similarly unable to complete replication in most mammalian cells but have an abortive-late phenotype, in that the block to replication occurs post-virus-specific DNA replication. In this study, an identical expression cassette for human immunodeficiency virus gag, pro, and env coding sequences was placed in canarypox virus and MVA vector backbones in order to directly compare vector-borne expression and to analyze differences in vector-host cell interactions. Antigen production by recombinant MVA was shown to be greater than that from recombinant canarypox virus in the mammalian cell lines and in the primary human cells tested. This observation was primarily due to a longer duration of antigen production in recombinant MVA-infected cells. Apoptosis induction was found to be more profound with the empty canarypox virus vector than with MVA. Remarkably, however, the inclusion of a gag/pro/env expression cassette altered the kinetics of apoptosis induction in recombinant MVA-infected cells to levels equal to those found in canarypox virus-infected cells. Antigen production by MVA was noted to be greater in human dendritic cells and resulted in enhanced T-cell stimulation in an in vitro antigen presentation assay. These results reveal differences in poxvirus vector-host cell interactions that should be relevant to their use as immunization vehicles. PMID:17409140

  3. Direct Comparison of Antigen Production and Induction of Apoptosis by Canarypox Virus- and Modified Vaccinia Virus Ankara-Human Immunodeficiency Virus Vaccine Vectors▿

    PubMed Central

    Zhang, Xiugen; Cassis-Ghavami, Farah; Eller, Mike; Currier, Jeff; Slike, Bonnie M.; Chen, Xuemin; Tartaglia, James; Marovich, Mary; Spearman, Paul

    2007-01-01

    Recombinant poxvirus vectors are undergoing intensive evaluation as vaccine candidates for a variety of infectious pathogens. Avipoxviruses, such as canarypox virus, are replication deficient in mammalian cells by virtue of a poorly understood species-specific restriction. Highly attenuated vaccinia virus strains such as modified vaccinia virus Ankara (MVA) are similarly unable to complete replication in most mammalian cells but have an abortive-late phenotype, in that the block to replication occurs post-virus-specific DNA replication. In this study, an identical expression cassette for human immunodeficiency virus gag, pro, and env coding sequences was placed in canarypox virus and MVA vector backbones in order to directly compare vector-borne expression and to analyze differences in vector-host cell interactions. Antigen production by recombinant MVA was shown to be greater than that from recombinant canarypox virus in the mammalian cell lines and in the primary human cells tested. This observation was primarily due to a longer duration of antigen production in recombinant MVA-infected cells. Apoptosis induction was found to be more profound with the empty canarypox virus vector than with MVA. Remarkably, however, the inclusion of a gag/pro/env expression cassette altered the kinetics of apoptosis induction in recombinant MVA-infected cells to levels equal to those found in canarypox virus-infected cells. Antigen production by MVA was noted to be greater in human dendritic cells and resulted in enhanced T-cell stimulation in an in vitro antigen presentation assay. These results reveal differences in poxvirus vector-host cell interactions that should be relevant to their use as immunization vehicles. PMID:17409140

  4. 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. PMID:23965820

  5. Phenotype as Agent for Epigenetic Inheritance.

    PubMed

    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. Optimization of Droplet Digital PCR from RNA and DNA extracts with direct comparison to RT-qPCR: Clinical implications for quantification of Oseltamivir-resistant subpopulations.

    PubMed

    Taylor, Sean C; Carbonneau, Julie; Shelton, Dawne N; Boivin, Guy

    2015-11-01

    The recent introduction of Droplet Digital PCR (ddPCR) has provided researchers with a tool that permits direct quantification of nucleic acids from a wide range of samples with increased precision and sensitivity versus RT-qPCR. The sample interdependence of RT-qPCR stemming from the measurement of Cq and ΔCq values is eliminated with ddPCR which provides an independent measure of the absolute nucleic acid concentration for each sample without standard curves thereby reducing inter-well and inter-plate variability. Well-characterized RNA purified from H275-wild type (WT) and H275Y-point mutated (MUT) neuraminidase of influenza A (H1N1) pandemic 2009 virus was used to demonstrate a ddPCR optimization workflow to assure robust data for downstream analysis. The ddPCR reaction mix was also tested with RT-qPCR and gave excellent reaction efficiency (between 90% and 100%) with the optimized MUT/WT duplexed assay thus enabling the direct comparison of the two platforms from the same reaction mix and thermal cycling protocol. ddPCR gave a marked improvement in sensitivity (>30-fold) for mutation abundance using a mixture of purified MUT and WT RNA and increased precision (>10 fold, p<0.05 for both inter- and intra-assay variability) versus RT-qPCR from patient samples to accurately identify residual mutant viral population during recovery. PMID:26315318

  7. A comparison of GPS solutions for strain and SKS fast directions: Implications for modes of shear in the mantle of a plate boundary zone

    NASA Astrophysics Data System (ADS)

    houlie, nicolas; Stern, Tim

    2014-05-01

    We study the strain rate field computed using the GPS GEONET dataset collected during the last decade. We show that we can infer the amount of simple shear accumulated in the mantle by comparing the compression strain orientation with the SKS fast directions. We suggest the mantle beneath the southern part of the south island is under pure shear while to the north the amount of distributed shear is larger. At last, we confirm that, in that context, the strike of New Zealand fault systems make a 60 degree angle with the compression strain rate axis. We compute the strain rate field and the vectors for the principal axis of strain in within New Zealand based on 10 years of data from the Geonet network. A comparison of the principal axis of extension with the fast directions from SKS splitting shows a consistent 20 degree divergence in the northern south Island with the two sets of vectors becoming parallel in central South Island. We firstly interpret these data as confirmation of mantle flow driving crustal kinematics. In addition we suggest the data are consistent with a mode of predominately simple and pure shear in northern and central South Island respectively.

  8. [18F]DPA-714: Direct Comparison with [11C]PK11195 in a Model of Cerebral Ischemia in Rats

    PubMed Central

    Boutin, Hervé; Prenant, Christian; Maroy, Renaud; Galea, James; Greenhalgh, Andrew D.; Smigova, Alison; Cawthorne, Christopher; Julyan, Peter; Wilkinson, Shane M.; Banister, Samuel D.; Brown, Gavin; Herholz, Karl; Kassiou, Michael; Rothwell, Nancy J.

    2013-01-01

    Purpose Neuroinflammation is involved in several brain disorders and can be monitored through expression of the translocator protein 18 kDa (TSPO) on activated microglia. In recent years, several new PET radioligands for TSPO have been evaluated in disease models. [18F]DPA-714 is a TSPO radiotracer with great promise; however results vary between different experimental models of neuroinflammation. To further examine the potential of [18F]DPA-714, it was compared directly to [11C]PK11195 in experimental cerebral ischaemia in rats. Methods Under anaesthesia, the middle cerebral artery of adult rats was occluded for 60 min using the filament model. Rats were allowed recovery for 5 to 7 days before one hour dynamic PET scans with [11C]PK11195 and/or [18F]DPA-714 under anaesthesia. Results Uptake of [11C]PK11195 vs [18F]DPA-714 in the ischemic lesion was similar (core/contralateral ratio: 2.84±0.67 vs 2.28±0.34 respectively), but severity of the brain ischemia and hence ligand uptake in the lesion appeared to vary greatly between animals scanned with [11C]PK11195 or with [18F]DPA-714. To solve this issue of inter-individual variability, we performed a direct comparison of [11C]PK11195 and [18F]DPA-714 by scanning the same animals sequentially with both tracers within 24 h. In this direct comparison, the core/contralateral ratio (3.35±1.21 vs 4.66±2.50 for [11C]PK11195 vs [18F]DPA-714 respectively) showed a significantly better signal-to-noise ratio (1.6 (1.3–1.9, 95%CI) fold by linear regression) for [18F]DPA-714. Conclusions In a clinically relevant model of neuroinflammation, uptake for both radiotracers appeared to be similar at first, but a high variability was observed in our model. Therefore, to truly compare tracers in such models, we performed scans with both tracers in the same animals. By doing so, our result demonstrated that [18F]DPA-714 displayed a higher signal-to-noise ratio than [11C]PK11195. Our results suggest that, with the longer half-life of

  9. 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

  10. 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

  11. Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes.

    PubMed

    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

    2016-02-01

    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

  12. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

    PubMed Central

    Chong, Jessica X.; Buckingham, Kati J.; Jhangiani, Shalini N.; Boehm, Corinne; Sobreira, Nara; Smith, Joshua D.; Harrell, Tanya M.; McMillin, Margaret J.; Wiszniewski, Wojciech; Gambin, Tomasz; Coban Akdemir, Zeynep H.; Doheny, Kimberly; Scott, Alan F.; Avramopoulos, Dimitri; Chakravarti, Aravinda; Hoover-Fong, Julie; Mathews, Debra; Witmer, P. Dane; Ling, Hua; Hetrick, Kurt; Watkins, Lee; Patterson, Karynne E.; Reinier, Frederic; Blue, Elizabeth; Muzny, Donna; Kircher, Martin; Bilguvar, Kaya; López-Giráldez, Francesc; Sutton, V. Reid; Tabor, Holly K.; Leal, Suzanne M.; Gunel, Murat; Mane, Shrikant; Gibbs, Richard A.; Boerwinkle, Eric; Hamosh, Ada; Shendure, Jay; Lupski, James R.; Lifton, Richard P.; Valle, David; Nickerson, Deborah A.; Bamshad, Michael J.

    2015-01-01

    Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families. PMID:26166479

  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. PMID:27581484

  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. PMID:27196636

  16. Pseudomonas Aeruginosa Resistance Phenotypes and Phenotypic Highlighting Methods

    PubMed Central

    BĂLĂŞOIU, MARIA; BĂLĂŞOIU, A.T.; MĂNESCU, RODICA; AVRAMESCU, CARMEN; IONETE, OANA

    2014-01-01

    Pseudomonas aeruginosa genus bacteria are well known for their increased drug resistance (phenotypic ang genotypic resistance). The most important resistance mechanisms are: enzyme production, reduction of pore expression, reduction of the external membrane proteins expression, efflux systems, topoisomerase mutations. These mechanisms often accumulate and lead to multidrug ressitance strains emergence. The most frequent acquired resistance mechanisms are betalactamase-type enzyme production (ESBLs, AmpC, carbapenemases), which determine variable phenotypes of betalactamines resistance, phenotypes which are associated with aminoglycosides and quinolones resistance. The nonenzymatic drug resistance mechanisms are caused by efflux systems, pore reduction and penicillin-binding proteins (PBP) modification, which are often associated to other resistance mechanisms. Phenotypic methods used for testing these mechanisms are based on highlighting these phenotypes using Kirby Bauer antibiogram, clinical breakpoints, and “cut off” values recommended by EUCAST 2013 standard, version 3.1. PMID:25729587

  17. Phenotypical diversity of patients with LEOPARD syndrome carrying the worldwide recurrent p.Tyr279Cys PTPN11 mutation.

    PubMed

    Nemes, Edina; Farkas, Katalin; Kocsis-Deák, Barbara; Drubi, Andrea; Sulák, Adrienn; Tripolszki, Kornélia; Dósa, Piroska; Ferenc, Lakatos; Nagy, Nikoletta; Széll, Márta

    2015-12-01

    LEOPARD syndrome (LS, OMIM 151100) is a rare monogenic disorder. The name is an acronym of its major features such as multiple lentigines, electrocardiographic conduction defects, ocular hypertelorism, pulmonary stenosis, abnormalities of genitalia, retardation of growth and sensorineural deafness. LS develops due to mutations in the protein-tyrosine phosphatase nonreceptor-type 11, PTPN11. Here, we have investigated a 51-year-old Hungarian male patient affected by LS. Direct sequencing of the PTPN11 gene revealed a worldwide recurrent missense mutation (c.836A/G; p.Tyr279Cys), which has been previously identified in 47 LS patients. Comparison of the clinical phenotypes of our patient and the ones reported in the literature demonstrates great phenotypic diversity despite the same genotype. PMID:26377839

  18. Expanding the phenotype of mosaic trisomy 20.

    PubMed

    Willis, Mary J H; Bird, Lynne M; Dell'Aquilla, Marie; Jones, Marilyn C

    2008-02-01

    Mosaic trisomy 20 is one of the more common cytogenetic abnormalities found on amniocentesis or chorionic villus sampling. Studies have shown that outcome is normal in 90-93% of prenatally diagnosed cases. There are however, reports in the literature of children with mosaic trisomy 20 described as having an assortment of dysmorphic features and varying levels of developmental delay. Unfortunately, the literature has not defined a specific phenotype for this entity. Here we report on three patients with mosaic trisomy 20, two of whom were identified prenatally. Over a number of years of follow-up it has become apparent that there are some striking similarities among the three. Comparison between our patients and the literature cases indicates a more consistent phenotype than has previously been suggested. Recurring features include; spinal abnormalities (including spinal stenosis, vertebral fusion, and kyphosis), hypotonia, lifelong constipation, sloped shoulders, and significant learning disabilities despite normal intelligence. These findings may be overlooked on routine history and physical exam or assumed to be standard pediatric problems. It is not our intention to suggest that there is a distinctive face for this entity but to suggest that a subtle phenotype does exist. We have attempted to identify a set of findings for which any child diagnosed with mosaic trisomy 20 should be assessed or followed even in the presence of an apparently normal physical exam at birth. PMID:18203170

  19. 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.

  20. 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

  1. A comparison of direct measurement and model simulation of total flux of volatile organic compounds from the subsurface to the atmosphere under natural field conditions

    NASA Astrophysics Data System (ADS)

    Tillman, Fred D.; Choi, Jee-Won; Smith, James A.

    2003-10-01

    Accurate quantification of natural attenuation of volatile organic compounds (VOCs) in groundwater requires an accounting of all VOC mass-loss processes, including volatilization into soil gas with ultimate transport to land surface and the atmosphere. This paper compares two methods of estimating VOC flux to the atmosphere. The first method measures VOC flux at land surface using a vertical flux chamber (VFC). The VFC has been shown in a previous laboratory study to reliably measure organic vapor fluxes from soil to the atmosphere that are caused by either gas phase diffusion or a combination of advection plus diffusion [, 2003]. The second method simulates VOC flux using a transient, one-dimensional gas flow and transport model incorporating the effects of gas phase diffusion, equilibrium air-water partitioning of organic vapors, and unsaturated zone airflow caused by atmospheric pressure changes (i.e., barometric pumping). Flux chamber measurements were made concurrently with field data measurements required for the flow and transport model at a trichloroethene (TCE)-contaminated field site. The two methods of VOC flux estimation provided comparable results in nine sets of field comparisons with the flux chamber estimating a lower flux during most of the time periods. Sensitivity analyses of model input parameters produce upper and lower bounds on best estimate flux simulations. Average VFC measurements fall within these upper and lower bounds of combined parameter values for all nine comparison events. The ease of use, lack of a priori site knowledge and accuracy of the VFC compared with the data-intensive flow and transport model suggests that direct measurement of VOC flux from the subsurface to the atmosphere at contaminated sites could become routine practice, providing important information to decision makers about the progress of monitored natural attenuation.

  2. 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.

  3. Determining which phenotypes underlie a pleiotropic signal

    PubMed Central

    Majumdar, Arunabha; Haldar, Tanushree; Witte, John S.

    2016-01-01

    Discovering pleiotropic loci is important to understand the biological basis of seemingly distinct phenotypes. Most methods for assessing pleiotropy only test for the overall association between genetic variants and multiple phenotypes. To determine which specific traits are pleiotropic, we evaluate via simulation and application three different strategies. The first is model selection techniques based on the inverse regression of genotype on phenotypes. The second is a subset-based meta-analysis ASSET [Bhattacharjee et al., 2012], which provides an optimal subset of non-null traits. And the third is a modified Benjamini-Hochberg (B-H) procedure of controlling the expected false discovery rate [Benjamini and Hochberg, 1995] in the framework of phenome-wide association study. From our simulations we see that an inverse regression based approach MultiPhen [O’Reilly et al., 2012] is more powerful than ASSET for detecting overall pleiotropic association, except for when all the phenotypes are associated and have genetic effects in the same direction. For determining which specific traits are pleiotropic, the modified B-H procedure performs consistently better than the other two methods. The inverse regression based selection methods perform competitively with the modified B-H procedure only when the phenotypes are weakly correlated. The efficiency of ASSET is observed to lie below and in between the efficiency of the other two methods when the traits are weakly and strongly correlated, respectively. In our application to a large GWAS, we find that the modified B-H procedure also performs well, indicating that this may be an optimal approach for determining the traits underlying a pleiotropic signal. PMID:27238845

  4. Determining Which Phenotypes Underlie a Pleiotropic Signal.

    PubMed

    Majumdar, Arunabha; Haldar, Tanushree; Witte, John S

    2016-07-01

    Discovering pleiotropic loci is important to understand the biological basis of seemingly distinct phenotypes. Most methods for assessing pleiotropy only test for the overall association between genetic variants and multiple phenotypes. To determine which specific traits are pleiotropic, we evaluate via simulation and application three different strategies. The first is model selection techniques based on the inverse regression of genotype on phenotypes. The second is a subset-based meta analysis ASSET [Bhattacharjee et al., ], which provides an optimal subset of nonnull traits. And the third is a modified Benjamini-Hochberg (B-H) procedure of controlling the expected false discovery rate [Benjamini and Hochberg, ] in the framework of phenome-wide association study. From our simulations we see that an inverse regression-based approach MultiPhen [O'Reilly et al., ] is more powerful than ASSET for detecting overall pleiotropic association, except for when all the phenotypes are associated and have genetic effects in the same direction. For determining which specific traits are pleiotropic, the modified B-H procedure performs consistently better than the other two methods. The inverse regression-based selection methods perform competitively with the modified B-H procedure only when the phenotypes are weakly correlated. The efficiency of ASSET is observed to lie below and in between the efficiency of the other two methods when the traits are weakly and strongly correlated, respectively. In our application to a large GWAS, we find that the modified B-H procedure also performs well, indicating that this may be an optimal approach for determining the traits underlying a pleiotropic signal. PMID:27238845

  5. 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

  6. Virtual environments for the transfer of navigation skills in the blind: a comparison of directed instruction vs. video game based learning approaches

    PubMed Central

    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. Emerging molecular phenotypes of asthma.

    PubMed

    Ray, Anuradha; Oriss, Timothy B; Wenzel, Sally E

    2015-01-15

    Although asthma has long been considered a heterogeneous disease, attempts to define subgroups of asthma have been limited. In recent years, both clinical and statistical approaches have been utilized to better merge clinical characteristics, biology, and genetics. These combined characteristics have been used to define phenotypes of asthma, the observable characteristics of a patient determined by the interaction of genes and environment. Identification of consistent clinical phenotypes has now been reported across studies. Now the addition of various 'omics and identification of specific molecular pathways have moved the concept of clinical phenotypes toward the concept of molecular phenotypes. The importance of these molecular phenotypes is being confirmed through the integration of molecularly targeted biological therapies. Thus the global term asthma is poised to become obsolete, being replaced by terms that more specifically identify the pathology associated with the disease. PMID:25326577

  8. Plant Phenotype Characterization System

    SciTech Connect

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  9. Bi-Directional Isolated DC-DC Converter for Next-Generation Power Distribution—Comparison of Converters Using Si and SiC Devices

    NASA Astrophysics Data System (ADS)

    Biela, Juergen; Aggeler, Daniel; Inoue, Shigenori; Akagi, Hirofumi; Kolar, Johann W.

    In this paper two bi-directional DC-DC converters for a 1MW next-generation BTB system of a distribution system, as it is applied in Japan, are presented and compared with respect to design, efficiency and power density. One DC-DC converter applies commercially available Si-devices and the other one high voltage SiC switch, which consists of a SiC JFET cascode (MOSFET+1 JFET) in series with five SiC JFETs. In the comparison also the high frequency, high voltage transformer, which ensures galvanic isolation and which is a core element of the DC-DC converter, is examined in detail by analytic calculations and FEM simulations. For validating the analytical considerations a 20kW SiC DC-DC converter has been designed in detail. Measurement results for the switching and conduction losses have been acquired from the SiC and also for a Si system for calculating the losses of the scaled 1MW system.

  10. 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).

  11. Direct comparison of 210Po, 234Th and POC particle-size distributions and export fluxes at the Bermuda Atlantic Time-series Study (BATS) site.

    PubMed

    Stewart, Gillian; Moran, S Bradley; Lomas, Michael W; Kelly, Roger P

    2011-05-01

    Particle-reactive, naturally occurring radionuclides are useful tracers of the sinking flux of organic matter from the surface to the deep ocean. Since the Joint Global Ocean Flux Study (JGOFS) began in 1987, the disequilibrium between (234)Th and its parent (238)U has become widely used as a technique to measure particle export fluxes from surface ocean waters. Another radionuclide pair, (210)Po and (210)Pb, can be used for the same purpose but has not been as widely adopted due to difficulty with accurately constraining the (210)Po/(210)Pb radiochemical balance in the ocean and because of the more time-consuming radiochemical procedures. Direct comparison of particle flux estimated in different ocean regions using these short-lived radionuclides is important in evaluating their utility and accuracy as tracers of particle flux. In this paper, we present paired (234)Th/(238)U and (210)Po/(210)Pb data from oligotrophic surface waters of the subtropical Northwest Atlantic and discuss their advantages and limitations. Vertical profiles of total and particle size-fractionated (210)Po and (234)Th activities, together with particulate organic carbon (POC) concentrations, were measured during three seasons at the Bermuda Atlantic Time-series Study (BATS) site. Both (210)Po and (234)Th reasonably predict sinking POC flux caught in sediment traps, and each tracer provides unique information about the magnitude and efficiency of the ocean's biological pump. PMID:21055851

  12. A comparison of the fixed bin method with the floating bin and direct count methods: effect of VNTR profile frequency estimation and reference population.

    PubMed

    Monson, K L; Budowle, B

    1993-09-01

    When the results of a forensic comparison of highly polymorphic variable number tandem repeat (VNTR) loci fail to exclude a suspect as a possible contributor of biological evidence, it is desirable to convey to the trier of fact the significance of the match. Furthermore, in a forensic context, it is desirable that the estimated frequency of occurrence be conservative, that is, that any uncertainty in the estimate will favor the accused. Using an empirical approach with a data base of 2046 individuals belonging to one of four population groups, this study examined the effect of the method used to estimate frequency of occurrence of a VNTR profile from a reference data base, and the consequences of using a data base that may not represent the circumstances of the crime. The fixed bin method was at least as conservative as the floating bin and genotype counting (direct counting) methods. Secondly, for forensic purposes, profile frequency estimates from different reference populations do not deviate greatly. VNTR profiles are rare in any of the data bases. PMID:8228875

  13. Direct Electron Transfer Kinetics of Peroxidase at Edge Plane Sites of Cup-Stacked Carbon Nanofibers and Their Comparison with Single-Walled Carbon Nanotubes.

    PubMed

    Komori, Kikuo; Tatsuma, Tetsu; Sakai, Yasuyuki

    2016-09-13

    Electron transfer kinetics at the graphene edge site is of great interest from the viewpoints of application to sensing and energy conversion and storage. Here we analyzed kinetics of direct electron transfer of horseradish peroxidase (HRP) adsorbed through surfactant sodium dodecyl sulfate at cup-stacked carbon nanofibers (CSCNFs), which provide highly ordered graphene edges, and compared it with that at single-walled carbon nanotubes (SWCNTs), which consist of a rolled-up basal plane graphene. The heterogeneous electron transfer rate constant of the Fe(2+/3+) couple of the HRP reaction center at CSCNFs (ca. 34.8 s(-1)) was an order of magnitude larger than that at SWCNTs (ca. 4.7 s(-1)). In addition, the overall rate constant of the electron transfer reaction from CSCNFs to HRP oxidized by H2O2 was higher than that from SWCNTs by a factor of 3. CSCNFs also allowed enhancement of the complex-formation reaction rate of HRP with H2O2, in comparison with that at SWCNTs. CSCNFs would therefore be applied to not only biosensors but also biofuel cells with enhanced performance. PMID:27529505

  14. Direct comparison between a two-dimensional magneto-optical trap and a Zeeman slower as sources of cold sodium atoms

    NASA Astrophysics Data System (ADS)

    Pedrozo-Peñafiel, E.; Vivanco, F.; Castilho, P.; Paiva, R. R.; Farias, K. M.; Bagnato, V. S.

    2016-06-01

    The atom source is a relevant component in many atomic molecular optics experiments. The compactness and efficiency of the source are fundamental issues, acquiring more importance as the complexity of the experiments increases. Characterizing new techniques to produce high atom flux is necessary to know the efficiency and peculiarities of each one. This allows choosing the most suitable source for a specific experiment. In this work, we show a direct comparison between a two-dimensional magneto-optical trap (2D-MOT) and a Zeeman slower (ZS) as source of cold sodium atoms to load a standard three-dimensional magneto-optical trap. The optimum parameters for each case are obtained by observing the loading rate and the final number of atoms in the 3D-MOT. We conclude that the 2D-MOT provides a high flux of atoms comparable with that produced by the ZS, but with an enormous advantage with respect to the size of the apparatus.

  15. 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.

  16. Ionophore-containing siloprene membranes: direct comparison between conventional ion-selective electrodes and silicon nanowire-based field-effect transistors.

    PubMed

    Cao, Anping; Mescher, Marleen; Bosma, Duco; Klootwijk, Johan H; Sudhölter, Ernst J R; de Smet, Louis C P M

    2015-01-20

    Siloprene-based, ion-selective membranes (ISMs) were drop-casted onto a field-effect transistor device that consisted of a single-chip array of top-down prepared silicon nanowires (SiNWs). Within one array, two sets of SiNWs were covered with ISMs, each containing two different ionophores, allowing the simultaneous sensing of K and Na ions using a flow cell. It is shown that both ions can be effectively detected in the same solution over a wide concentration range from 10(-4) to 10(-1) M without interference. The ISMs were also analyzed in a conventional ISE configuration, allowing a direct comparison. While the responses for K(+) were similar for both sensor configurations, remarkably, the Na(+) response of the ISM-covered SiNW device was found to be higher than the one of the ISE configuration. The addition of a Na(+) buffering hydrogel layer between the SiO2 of the SiNW and the ISM reduced the response, showing the importance of keeping the boundary potential at the SiO2/ISM interface constant. The responses of the siloprene-covered SiNW devices were found to be stable over a period of at least 6 weeks, showing their potential as a multichannel sensor device. PMID:25487713

  17. Distinct phenotypes in zebrafish models of human startle disease☆

    PubMed Central

    Ganser, Lisa R.; Yan, Qing; James, Victoria M.; Kozol, Robert; Topf, Maya; Harvey, Robert J.; Dallman, Julia E.

    2013-01-01

    Startle disease is an inherited neurological disorder that causes affected individuals to suffer noise- or touch-induced non-epileptic seizures, excessive muscle stiffness and neonatal apnea episodes. Mutations known to cause startle disease have been identified in glycine receptor subunit (GLRA1 and GLRB) and glycine transporter (SLC6A5) genes, which serve essential functions at glycinergic synapses. Despite the significant successes in identifying startle disease mutations, many idiopathic cases remain unresolved. Exome sequencing in these individuals will identify new candidate genes. To validate these candidate disease genes, zebrafish is an ideal choice due to rapid knockdown strategies, accessible embryonic stages, and stereotyped behaviors. The only existing zebrafish model of startle disease, bandoneon (beo), harbors point mutations in glrbb (one of two zebrafish orthologs of human GLRB) that cause compromised glycinergic transmission and touch-induced bilateral muscle contractions. In order to further develop zebrafish as a model for startle disease, we sought to identify common phenotypic outcomes of knocking down zebrafish orthologs of two known startle disease genes, GLRA1 and GLRB, using splice site-targeted morpholinos. Although both morphants were expected to result in phenotypes similar to the zebrafish beo mutant, our direct comparison demonstrated that while both glra1 and glrbb morphants exhibited embryonic spasticity, only glrbb morphants exhibited bilateral contractions characteristic of beo mutants. Likewise, zebrafish over-expressing a dominant startle disease mutation (GlyR α1R271Q) exhibited spasticity but not bilateral contractions. Since GlyR βb can interact with GlyR α subunits 2–4 in addition to GlyR α1, loss of the GlyR βb subunit may produce more severe phenotypes by affecting multiple GlyR subtypes. Indeed, immunohistochemistry of glra1 morphants sugges