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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. 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.

  4. PhenoBlocks: Phenotype Comparison Visualizations.

    PubMed

    Glueck, Michael; Hamilton, Peter; Chevalier, Fanny; Breslav, Simon; Khan, Azam; Wigdor, Daniel; Brudno, Michael

    2016-01-01

    The differential diagnosis of hereditary disorders is a challenging task for clinicians due to the heterogeneity of phenotypes that can be observed in patients. Existing clinical tools are often text-based and do not emphasize consistency, completeness, or granularity of phenotype reporting. This can impede clinical diagnosis and limit their utility to genetics researchers. Herein, we present PhenoBlocks, a novel visual analytics tool that supports the comparison of phenotypes between patients, or between a patient and the hallmark features of a disorder. An informal evaluation of PhenoBlocks with expert clinicians suggested that the visualization effectively guides the process of differential diagnosis and could reinforce the importance of complete, granular phenotypic reporting.

  5. Do ants make direct comparisons?

    PubMed

    Robinson, Elva J H; Smith, Faith D; Sullivan, Kathryn M E; Franks, Nigel R

    2009-07-22

    Many individual decisions are informed by direct comparison of the alternatives. In collective decisions, however, only certain group members may have the opportunity to compare options. Emigrating ant colonies (Temnothorax albipennis) show sophisticated nest-site choice, selecting superior sites even when they are nine times further away than the alternative. How do they do this? We used radio-frequency identification-tagged ants to monitor individual behaviour. Here we show for the first time that switching between nests during the decision process can influence nest choice without requiring direct comparison of nests. Ants finding the poor nest were likely to switch and find the good nest, whereas ants finding the good nest were more likely to stay committed to that nest. When ants switched quickly between the two nests, colonies chose the good nest. Switching by ants that had the opportunity to compare nests had little effect on nest choice. We suggest a new mechanism of collective nest choice: individuals respond to nest quality by the decision either to commit or to seek alternatives. Previously proposed mechanisms, recruitment latency and nest comparison, can be explained as side effects of this simple rule. Colony-level comparison and choice can emerge, without direct comparison by individuals.

  6. Do ants make direct comparisons?

    PubMed Central

    Robinson, Elva J.H.; Smith, Faith D.; Sullivan, Kathryn M.E.; Franks, Nigel R.

    2009-01-01

    Many individual decisions are informed by direct comparison of the alternatives. In collective decisions, however, only certain group members may have the opportunity to compare options. Emigrating ant colonies (Temnothorax albipennis) show sophisticated nest-site choice, selecting superior sites even when they are nine times further away than the alternative. How do they do this? We used radio-frequency identification-tagged ants to monitor individual behaviour. Here we show for the first time that switching between nests during the decision process can influence nest choice without requiring direct comparison of nests. Ants finding the poor nest were likely to switch and find the good nest, whereas ants finding the good nest were more likely to stay committed to that nest. When ants switched quickly between the two nests, colonies chose the good nest. Switching by ants that had the opportunity to compare nests had little effect on nest choice. We suggest a new mechanism of collective nest choice: individuals respond to nest quality by the decision either to commit or to seek alternatives. Previously proposed mechanisms, recruitment latency and nest comparison, can be explained as side effects of this simple rule. Colony-level comparison and choice can emerge, without direct comparison by individuals. PMID:19386652

  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. Isolation and phenotypic characterization of mucosal nasal lymphocytes by direct ex vivo analysis.

    PubMed

    Wolfram, Christin; Rasche, Claudia; Audring, Heike; Wahls, Michael; Worm, Margitta

    2009-05-01

    Cellular inflammation of the nasal mucosa demonstrates a local immune response which plays an important role in allergic rhinitis. The aim of the present study was to characterize nasal mucosal lymphocytes regarding their activation and differentiation state by direct ex vivo flowcytometric analysis. Lymphocytes from the inferior turbinates were isolated by a mechanical method of preparation and, for comparison, from peripheral blood by Ficoll gradient centrifugation. Patients suffering from rhinitis or difficulty in nasal breathing were divided into an allergic (pollen-allergy, n = 13) and non-allergic group (n = 24). Expression of different T- and B-cell markers was determined by flowcytometric analysis. CD4+ T-cells from the nasal mucosa exhibited a memory phenotype (CD45RO+, 97%), were highly activated (CD69+, 43-73%), and showed low expression of the cutaneous lymphocyte antigen (CLA+, 5%). Nasal CD20+ B-lymphocytes expressed significantly higher levels of mIgE and lower levels of CD23 and CD80 than peripheral B-cells. Subsets of CD80+ (4%) and CD86+ (6%) CD20+ B-lymphocytes were identified in the nasal mucosa. No significant differences between allergic and non-allergic individuals were determined. As expected, the data show profound phenotypical differences between circulating peripheral blood and nasal mucosal lymphocytes. Activated memory lymphocytes are present in the nasal mucosa from allergic, but also non-allergic patients and may indicate to a significant role of a local inflammatory state without systemic criteria for allergy. In our study, we show that direct ex vivo isolation of lymphocytes is practicable method and offers a new technique to examine the local nasal allergic immune response using a multiparametric phenotypical analysis. PMID:18766360

  10. Candida nivariensis in comparison to different phenotypes of Candida glabrata.

    PubMed

    Swoboda-Kopeć, Ewa; Sikora, Magdalena; Golas, Marlena; Piskorska, Katarzyna; Gozdowski, Dariusz; Netsvyetayeva, Irina

    2014-12-01

    The purpose of the study was to establish the prevalence of new Candida glabrata complex species: Candida nivariensis and Candida bracarensis isolated from clinical material, evaluate their phenotypes and the prevalence of gene family encoding extracellular glycosylphosphatidylinositol-linked aspartyl proteases, crucial for C. glabrata virulence. Study material included 224 C. glabrata clinical strains. Candida glabrata phenotypes were identified using CHROMagar Candida medium. Strains were analysed by using C. glabrata-specific PCR for the internal transcribed spacer region to confirmed the identification. To identify C. nivariensis and C. bracarensis strains, the D1/D2 region of 26S rRNA was sequenced. The prevalence of YPS-family proteases genes was detected using standard PCR method. Candida nivariensis amounted about 6% among the total number of C. glabrata strains. Candida nivariensis strains had a white phenotype on chromogenic agar media and assimilated two sugars - trehalose and glucose. Among the 13 C. nivariensis strains, 10 did not present any YPS-family protease genes. Coexistence of all detected YPS-family protease genes was specific for C. glabrata species. This study identified C. nivariensis strains; however, no C. bracarensis strains were identified. The white phenotype of C. nivariensis was confirmed. Most strains of the new species do not present any of the tested YPS genes.

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

    PubMed

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

    2008-12-01

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

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

    PubMed Central

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

    2014-01-01

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

  13. Direct Field and Reverberant Chamber Acoustic Test Comparisons

    NASA Technical Reports Server (NTRS)

    OConnell, Michael

    2007-01-01

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

  14. Social Comparison Processes in an Organizational Context: New Directions

    ERIC Educational Resources Information Center

    Goodman, Paul S.; Haisley, Emily

    2007-01-01

    The goal of this article is to frame some new directions to social comparison research in organizational settings. Four themes are developed. First, we examine the role of organizational variables in shaping the basic sub processes in social comparison, such as the selection of referents. The second theme focuses on the meaning of level of…

  15. 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

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

    PubMed Central

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

    2013-01-01

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

  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.

  19. 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

  20. Comparison of phenotype of gammadelta T cells generated using various cultivation methods.

    PubMed

    Mehrle, Stefan; Watzl, Carsten; von Lilienfeld-Toal, Marie; Amoroso, Alfredo; Schmidt, Jan; Märten, Angela

    2009-06-30

    It has been demonstrated, that gammadelta T cells play an important role in the development of immune responses to many pathogens. gammadelta T cells play a role in the clearance of viral and microbiological infections, anti-tumor responses, but also in autoimmune diseases. Many different protocols for the isolation and cultivation of gammadelta T cells can be found in the literature. Here we compare three common cultivation protocols for gammadelta T cells derived from peripheral blood with a newly developed protocol depending on SLAM (Signaling Lymphocyte Activation Molecule) stimulation. We demonstrate that the cultivation protocol chosen to raise gammadelta T cells has direct impact on the resulting gammadelta T cell phenotype. We show differences in gammadelta TCR composition, memory phenotype formation, CD8 receptor expression and the expression of NK cell markers depending on the stimulation protocol used. As such, the cultivation protocol chosen for a series of experiments might have significant impact on the outcome of the experiments and should be considered carefully.

  1. 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

  2. Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information

    PubMed Central

    2010-01-01

    Background The genetic contributions to human common disorders and mouse genetic models of disease are complex and often overlapping. In common human diseases, unlike classical Mendelian disorders, genetic factors generally have small effect sizes, are multifactorial, and are highly pleiotropic. Likewise, mouse genetic models of disease often have pleiotropic and overlapping phenotypes. Moreover, phenotypic descriptions in the literature in both human and mouse are often poorly characterized and difficult to compare directly. Methods In this report, human genetic association results from the literature are summarized with regard to replication, disease phenotype, and gene specific results; and organized in the context of a systematic disease ontology. Similarly summarized mouse genetic disease models are organized within the Mammalian Phenotype ontology. Human and mouse disease and phenotype based gene sets are identified. These disease gene sets are then compared individually and in large groups through dendrogram analysis and hierarchical clustering analysis. Results Human disease and mouse phenotype gene sets are shown to group into disease and phenotypically relevant groups at both a coarse and fine level based on gene sharing. Conclusion This analysis provides a systematic and global perspective on the genetics of common human disease as compared to itself and in the context of mouse genetic models of disease. PMID:20092628

  3. 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

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

    PubMed

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

    2014-12-01

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

  5. Identification of Pathogenic Rare Yeast Species in Clinical Samples: Comparison between Phenotypical and Molecular Methods▿

    PubMed Central

    Cendejas-Bueno, Emilio; Gomez-Lopez, Alicia; Mellado, Emilia; Rodriguez-Tudela, Juan L.; Cuenca-Estrella, Manuel

    2010-01-01

    Species identification using both phenotypic and molecular methods and antifungal susceptibility tests was carried out with 60 uncommon clinical yeasts. Our data show that phenotypic methods were insufficient for correct identification (only 25%) and that most of the wrongly identified strains showed a resistant antifungal profile. PMID:20237094

  6. 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

  7. 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.

  8. Neurons generated by direct conversion of fibroblasts reproduce synaptic phenotype caused by autism-associated neuroligin-3 mutation.

    PubMed

    Chanda, Soham; Marro, Samuele; Wernig, Marius; Südhof, Thomas C

    2013-10-01

    Recent studies suggest that induced neuronal (iN) cells that are directly transdifferentiated from nonneuronal cells provide a powerful opportunity to examine neuropsychiatric diseases. However, the validity of using this approach to examine disease-specific changes has not been demonstrated. Here, we analyze the phenotypes of iN cells that were derived from murine embryonic fibroblasts cultured from littermate wild-type and mutant mice carrying the autism-associated R704C substitution in neuroligin-3. We show that neuroligin-3 R704C-mutant iN cells exhibit a large and selective decrease in AMPA-type glutamate receptor-mediated synaptic transmission without changes in NMDA-type glutamate receptor- or in GABAA receptor-mediated synaptic transmission. Thus, the synaptic phenotype observed in R704C-mutant iN cells replicates the previously observed phenotype of R704C-mutant neurons. Our data show that the effect of the R704C mutation is applicable even to neurons transdifferentiated from fibroblasts and constitute a proof-of-concept demonstration that iN cells can be used for cellular disease modeling.

  9. Predation risk as a driving force for phenotypic assortment: a cross-population comparison.

    PubMed

    Croft, D P; Darden, S K; Ruxton, G D

    2009-05-22

    Frequency-dependent predation has been proposed as a general mechanism driving the phenotypic assortment of social groups via the 'oddity effect', which occurs when the presence of odd individuals in a group allows a predator to fixate on a single prey item, increasing the predator's attack-to-kill ratio. However, the generality of the oddity effect has been debated and, previously, there has not been an ecological assessment of the role of predation risk in driving the phenotypic assortment of social groups. Here, we compare the levels of body length assortment of social groups between populations of the Trinidadian guppy (Poecilia reticulata) that experience differences in predation risk. As predicted by the oddity effect hypothesis, we observe phenotypic assortment by body length to be greater under high predation risk. However, we found that a number of low-predation populations were also significantly assorted by body length, suggesting that other mechanisms may have a role to play.

  10. Brief Report: Broader Autism Phenotype Predicts Spontaneous Reciprocity of Direct Gaze

    ERIC Educational Resources Information Center

    Chen, Frances S.; Yoon, Jennifer M. D.

    2011-01-01

    We report evidence for a relationship in the general population between self-reported autism-associated traits and the spontaneous reciprocation of direct gaze, a behavior that we propose may reflect a tendency to synchronize with social partners. Adults viewed videos of actors whose gaze was either directed towards or averted from them.…

  11. Phenotypic and transcriptional plasticity directed by a yeast mitogen-activated protein kinase network.

    PubMed

    Breitkreutz, Ashton; Boucher, Lorrie; Breitkreutz, Bobby-Joe; Sultan, Mujahid; Jurisica, Igor; Tyers, Mike

    2003-11-01

    The yeast pheromone/filamentous growth MAPK pathway mediates both mating and invasive-growth responses. The interface between this MAPK module and the transcriptional machinery consists of a network of two MAPKs, Fus3 and Kss1; two regulators, Rst1 and Rst2 (a.k.a. Dig1 and Dig2); and two transcription factors, Ste12 and Tec1. Of 16 possible combinations of gene deletions in FUS3, KSS1, RST1, and RST2 in the sigma1278 background, 10 display constitutive invasive growth. Rst1 was the primary negative regulator of invasive growth, while other components either attenuated or enhanced invasive growth, depending on the genetic context. Despite activation of the invasive response by lesions at the same level in the MAPK pathway, transcriptional profiles of different invasive mutant combinations did not exhibit a unified program of gene expression. The distal MAPK regulatory network is thus capable of generating phenotypically similar invasive-growth states (an attractor) from different molecular architectures (trajectories) that can functionally compensate for one another. This systems-level robustness may also account for the observed diversity of signals that trigger invasive growth. PMID:14668360

  12. 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

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

    PubMed

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

    2004-07-01

    Caffeine and dextromethorphan have been used successfully both alone and in combination to assess phenotype and enzyme activity in children of various ages. Previous pediatric phenotyping studies with these agents have used varying durations of urine collection. However, the minimum duration required for accurate phenotypic assessment with these compounds in children remains unknown. We calculated the cumulative metabolite recoveries and molar ratios in urine collected from children for 2, 4, 6, and 8 hours after caffeine and dextromethorphan administration to determine when respective urinary molar ratios stabilize and thus likely accurately reflect enzyme activity. Subjects (n = 24, ages 3-8 years) were given 4 oz of Coca-Cola(R) ( approximately 11.5 mg caffeine) and a single oral dose of dextromethorphan (0.5 mg/kg). Urine was collected at discrete intervals (0-2, 2-4, 4-6, and 6-8 h) during an 8-hour period, and the cumulative metabolite recoveries and urinary molar ratios were calculated. CYP2D6 genotyping was also performed in 21 of 24 subjects. In CYP2D6 extensive metabolizers, the extent of recovery for relevant metabolites was equivalent by 4 hours and represented 45% to 60% of the total amount recovered in the 8-hour period. The 2-hour CYP1A2 ratio was significantly different from those of longer collection intervals. Metabolite ratios for all other enzymes (i.e., NAT-2, XO, and CYP2D6) were independent of the duration of urine collection. These data suggest that a 4-hour urine collection is adequate for the concurrent assessment of hepatic CYP1A2, NAT-2, XO, and CYP2D6 activity in children ages 3 to 8 years who are CYP2D6 extensive metabolizers, using standard caffeine and dextromethorphan phenotyping methods. Longer collection periods may be required, however, in younger children or CYP2D6 poor metabolizers. PMID:15199075

  14. Comparison of three phenotypic and deoxyribonucleic acid extraction methods for isolation and Identification of Nocardia spp

    PubMed Central

    Faghri, Jamshid; Bourbour, Samane; Moghim, Sharare; Meidani, Mohsen; Safaei, Hajiye Ghasemian; Hosseini, Nafise; Esfahani, Bahram Nasr; Fazeli, Hussein; Sedighi, Mansour

    2014-01-01

    Background: The aerobic Actinomycetes are a large group of soil-indwelling bacteria that are distributed in world-wide. These Gram-positive bacteria are most commonly associated with opportunistic infections in both immunocompromised and immunocompetent hosts. Materials and Methods: In this study, three phenotypic and deoxyribonucleic acid (DNA) extraction methods for isolation and identification of Nocardia genus were compared. Samples were taken in five different locations of Isfahan's suburb from hospitals area, parks, agricultural lands, gardens, arid lands with different soil temperature and pH. Results: In this study, showed that slip-buried-method was better than two other phenotypic methods; 14 out of 70 soil samples (20%) were positive for Nocardia spp. DNA of positive samples were extracted with three techniques and DNA extraction by microwave technique was better than others. This technique was confirmed with observation of DNA bands on 1% agarose gel. Conclusions: These bacteria are important in immune deficient patients such as cancer patients, transplant recipients, tuberculosis; acquired immunodeficiency syndrome etc., Their affluence is unsteady in different zones of the world. In this study, among the three phenotypic methods for the isolation of Nocardia slip-buried method was better than other methods. Among DNA extraction techniques, DNA extraction by microwave method would be selective method for DNA extraction of Nocardia spp. compared with others techniques. PMID:25221754

  15. 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

  16. 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.

  17. 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 p21(WAF1/CIP1) induction and the inactivation of JNK. Here, we have used microarray-derived transcriptional profiling to identify PE5 regulated genes on the NCI/ADR-RES ovarian cancer cell line. RT-qPCR analyses have confirmed the expression microarray findings. The results show that PE5 cause pleiotropic effects. Among them, it is remarkable the down-regulation of multiple genes that code for enzymes involved in deregulated metabolic pathways in cancer cells.

  18. 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

  19. 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.

  20. 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

  1. Distal 15q trisomy: phenotypic comparison of nine cases in an extended family.

    PubMed Central

    Schnatterly, P; Bono, K L; Robinow, M; Wyandt, H E; Kardon, N; Kelly, T E

    1984-01-01

    Nine related individuals have been identified as being trisomic for the distal part of the long arm of chromosome 15 (15q23 to 15qter). The physical characteristics, especially the facial features, of these nine cases are similar and distinctive. These include: facial asymmetry, down-slanting palpebral fissures, ptosis, prominent nose, long philtrum, down-turned mouth, midline crease in the lower lip, puffy cheeks, and micrognathia. By comparing related individuals with the same translocation, the variability due to different breakpoints can be eliminated. Clinical similarities between unrelated individuals with similar duplicated 15q material, but differing second chromosomes, suggest that the phenotype is due to the extra distal 15q chromosomal material. We conclude that distal 15q trisomy produces a clinically recognizable syndrome. Images Fig. 2 Fig. 4 PMID:6711563

  2. Distal 15q trisomy: phenotypic comparison of nine cases in an extended family.

    PubMed

    Schnatterly, P; Bono, K L; Robinow, M; Wyandt, H E; Kardon, N; Kelly, T E

    1984-03-01

    Nine related individuals have been identified as being trisomic for the distal part of the long arm of chromosome 15 (15q23 to 15qter). The physical characteristics, especially the facial features, of these nine cases are similar and distinctive. These include: facial asymmetry, down-slanting palpebral fissures, ptosis, prominent nose, long philtrum, down-turned mouth, midline crease in the lower lip, puffy cheeks, and micrognathia. By comparing related individuals with the same translocation, the variability due to different breakpoints can be eliminated. Clinical similarities between unrelated individuals with similar duplicated 15q material, but differing second chromosomes, suggest that the phenotype is due to the extra distal 15q chromosomal material. We conclude that distal 15q trisomy produces a clinically recognizable syndrome.

  3. 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

  4. 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.

  5. Autosomal recessive hypercholesterolemia (ARH) and homozygous familial hypercholesterolemia (FH): a phenotypic comparison.

    PubMed

    Pisciotta, Livia; Priore Oliva, Claudio; Pes, Giovanni Mario; Di Scala, Lilla; Bellocchio, Antonella; Fresa, Raffaele; Cantafora, Alfredo; Arca, Marcello; Calandra, Sebastiano; Bertolini, Stefano

    2006-10-01

    Autosomal recessive hypercholesterolemia (ARH) is a rare disorder, due to complete loss of function of an adaptor protein (ARH protein) required for receptor-mediated hepatic uptake of LDL. ARH is a phenocopy of homozygous familial hypercholesterolemia (HoFH) due to mutations in LDL receptor (LDLR) gene; however, previous studies suggested that ARH phenotype is less severe than that of HoFH. To test this hypothesis we compared 42 HoFH and 42 ARH patients. LDLR and ARH genes were analysed by Southern blotting and sequencing. LDLR activity was measured in cultured fibroblasts. In ARH plasma LDL cholestrol (LDL-C) level (14.25+/-2.29 mmol/L) was lower than in receptor-negative HoFH (21.38+/-3.56 mmol/L) but similar to that found in receptor-defective HoFH (15.52+/-2.39 mmol/L). The risk of coronary artery disease (CAD) was 9-fold lower in ARH patients. No ARH patients phenotype of ARH is milder than that of receptor-negative HoFH and resembles that observed in receptor-defective HoFH. PMID:16343504

  6. A Comparison of Transcriptional Patterns and Mycological Phenotypes following Infection of Fusarium graminearum by Four Mycoviruses

    PubMed Central

    Lee, Kyung-Mi; Cho, Won Kyong; Yu, Jisuk; Son, Moonil; Choi, Hoseong; Min, Kyunghun; Lee, Yin-Won; Kim, Kook-Hyung

    2014-01-01

    Many fungi-infecting viruses, which are termed mycoviruses, have been identified, and most do not cause any visible symptoms. Some mycoviruses, however, can attenuate the virulence of the infected fungi, a phenomenon referred to as hypovirulence. To study fungus responses to virus infection, we established a model system composed of Fusarium graminearum and four mycoviruses including FgV1 (Fusarium graminearum virus 1), FgV2, FgV3, and FgV4. FgV1 and FgV2 infections caused several phenotypic alterations in F. graminearum including abnormal colony morphology, defects in perithecium development, and reductions in growth rate, conidiation, and virulence. In contrast, FgV3 and FgV4 infections did not cause any phenotypic change. An RNA-Seq-based analysis of the host transcriptome identified four unique Fusarium transcriptomes, one for each of the four mycoviruses. Unexpectedly, the fungal host transcriptome was more affected by FgV1 and FgV4 infections than by FgV2 and FgV3 infections. Gene ontology (GO) enrichment analysis revealed that FgV1 and FgV3 infections resulted in down-regulation of host genes required for cellular transport systems. FgV4 infection reduced the expression of genes involved in RNA processing and ribosome assembly. We also found 12 genes that were differentially expressed in response to all four mycovirus infections. Unfortunately, functions of most of these genes are still unknown. Taken together, our analysis provides further detailed insights into the interactions between mycoviruses and F. graminearum. PMID:24964178

  7. Glycine receptor knock-in mice and hyperekplexia-like phenotypes: comparisons with the null mutant.

    PubMed

    Findlay, Geoffrey S; Phelan, Rachel; Roberts, Michael T; Homanics, Gregg E; Bergeson, Susan E; Lopreato, Gregory F; Mihic, S John; Blednov, Yuri A; Harris, R Adron

    2003-09-01

    Strychnine-sensitive glycine receptors (GlyRs) inhibit neurotransmission in the spinal cord and brainstem. To better define the function of this receptor in vivo, we constructed a point mutation that impairs receptor function in the alpha1-subunit and compared these knock-in mice to oscillator (spdot) mice lacking functional GlyR alpha1-subunits. Mutation of the serine residue at amino acid 267 to glutamine (alpha1S267Q) results in a GlyR with normal glycine potency but decreased maximal currents, as shown by electrophysiological recordings using Xenopus oocytes. In addition, single-channel recordings using human embryonic kidney 293 cells indicated profoundly altered properties of the mutated GlyR. We produced knock-in mice bearing the GlyR alpha1 S267Q mutation to assess the in vivo consequences of selectively decreasing GlyR efficacy. Chloride uptake into brain synaptoneurosomes from knock-in mice revealed decreased responses to maximally effective glycine concentrations, although wild-type levels of GlyR expression were observed using 3H-strychnine binding and immunoblotting. A profound increase in the acoustic startle response was observed in knock-in mice as well as a "limb clenching" phenotype. In contrast, no changes in coordination or pain perception were observed using the rotarod or hot-plate tests, and there was no change in GABA(A)-receptor-mediated chloride uptake. Homozygous S267Q knock-in mice, like homozygous spdot mice, exhibited seizures and died within 3 weeks of birth. In heterozygous spdot mice, both decreased 3H-strychnine binding and chloride flux were observed; however, neither enhanced acoustic startle responses nor limb clenching were seen. These data demonstrate that a dominant-negative point mutation in GlyR disrupting normal function can produce a more dramatic phenotype than the corresponding recessive null mutation, and provides a new animal model to evaluate GlyR function in vivo. PMID:12954867

  8. 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

  9. Comparison of restriction endonuclease analysis and phenotypic typing methods for differentiation of Yersinia enterocolitica isolates.

    PubMed Central

    Kapperud, G; Nesbakken, T; Aleksic, S; Mollaret, H H

    1990-01-01

    Restriction endonuclease analysis of chromosomal DNA (REAC) was used to study polymorphism in restriction fragment patterns among Yersinia enterocolitica isolates belonging to serogroups O3, O5,27, O8, O9, O13, and O21. Using the enzyme HaeIII and electrophoresis on thin (0.75-mm) vertical 5% polyacrylamide gels, we were able to distinguish at least 22 DNA fragment patterns among the 72 strains examined. The method showed the greatest discriminatory power with regard to serogroup O8, within which as many as 10 different DNA fragment patterns were detected among the 16 strains examined. Compared with O8, serogroups O3 and O9 were relatively homogeneous with regard to REAC patterns. The discriminatory power of the method was compared with H-antigen typing, biotyping, phage typing, antimicrobial susceptibility typing, and restriction enzyme analysis of the virulence plasmid (REAP), by means of Simpson's index of diversity. The results showed that REAC and REAP constitute an effective supplement or alternative to conventional phenotypic methods for tracing epidemiologically related isolates of Y. enterocolitica. Our finding that human and porcine isolates exhibited the same REAC, REAP, and H-antigen patterns provides additional support for the hypothesis that pigs play an important role in the epidemiology of human Y. enterocolitica infection. Images PMID:2199484

  10. 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.

  11. The General Linear Model and Direct Standardization: A Comparison.

    ERIC Educational Resources Information Center

    Little, Roderick J. A.; Pullum, Thomas W.

    1979-01-01

    Two methods of analyzing nonorthogonal (uneven cell sizes) cross-classified data sets are compared. The methods are direct standardization and the general linear model. The authors illustrate when direct standardization may be a desirable method of analysis. (JKS)

  12. 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.

  13. 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

  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. A Comparison of Paradoxical and Nonparadoxical Interpretations and Directives.

    ERIC Educational Resources Information Center

    Feldman, Daniel A.; And Others

    1982-01-01

    Explored the effects of consistent and inconsistent combinations of paradoxical and nonparadoxical interpretations and directives in brief counseling with moderately depressed college students. Paradoxical interpretations were associated with more symptom remission than were nonparadoxical interpretations. The nature of the directives students…

  16. 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…

  17. Defining key features of the broad autism phenotype: a comparison across parents of multiple- and single-incidence autism families.

    PubMed

    Losh, Molly; Childress, Debra; Lam, Kristen; Piven, Joseph

    2008-06-01

    This study examined the frequency of personality, language, and social-behavioral characteristics believed to comprise the broad autism phenotype (BAP), across families differing in genetic liability to autism. We hypothesized that within this unique sample comprised of multiple-incidence autism families (MIAF), single-incidence autism families (SIAF), and control Down syndrome families (DWNS), a graded expression would be observed for the principal characteristics conferring genetic susceptibility to autism, in which such features would express most profoundly among parents from MIAFs, less strongly among SIAFs, and least of all among comparison parents from DWNS families, who should display population base rates. Analyses detected linear expression of traits in line with hypotheses, and further suggested differential intrafamilial expression across family types. In the vast majority of MIAFs both parents displayed BAP characteristics, whereas within SIAFs, it was equally likely that one, both, or neither parent show BAP features. The significance of these findings is discussed in relation to etiologic mechanisms in autism and relevance to molecular genetic studies.

  18. Comparison of cone directionality determined by psychophysical and reflectometric techniques

    PubMed Central

    He, J.C.; Marcos, S; Burns, S.A.

    2010-01-01

    We measured the directionality of the cones using both a psychophysical (Stiles-Crawford I) technique and an optical technique. Both sets of measurements were made in the same subjects using as similar stimuli as possible. Both types of measurements gave similar estimates of the location in the pupil towards which the cones were optimally aligned. However, the two measurements gave very dissimilar estimates of the width of the directional sensitivity. On average optical measurements were half as broad as psychophysical measurements in the fovea, but there were substantial individual differences. At 2 deg retinal eccentricty the difference between techniques was even more marked. PMID:10517020

  19. Correction of the Crb1rd8 Allele and Retinal Phenotype in C57BL/6N Mice Via TALEN-Mediated Homology-Directed Repair

    PubMed Central

    Low, Benjamin E.; Krebs, Mark P.; Joung, J. Keith; Tsai, Shengdar Q.; Nishina, Patsy M.; Wiles, Michael V.

    2014-01-01

    Purpose. We directly corrected the mouse Crb1rd8 gene mutation, which is present in many inbred laboratory strains derived from C57BL/6N and complicates genetic studies of retinal disease in mice. Methods. Fertilized C57BL/6NJ oocytes were coinjected with mRNAs encoding a transcription activator-like effector nuclease (TALEN) targeting the Crb1rd8 allele plus single-stranded oligonucleotides to correct the allele. The oligonucleotides included additional nucleotide changes to distinguish the corrected allele (Crb1em1Mvw) from wild-type Crb1 and to minimize TALEN recutting. Oligonucleotide length, concentration of injected oligonucleotides and TALEN mRNAs were varied to optimize homology-directed repair of the locus. Following microinjection, embryos were carried to term in pseudopregnant females. Correction efficiency was assessed by PCR analysis of the Crb1em1Mvw allele. Phenotypic correction was demonstrated by fundus imaging and optical coherence tomography of live mice, and by confocal fluorescence microscopy of retinal flat mounts. Results. Under optimal conditions, homology-directed repair was observed in 27% (8/30) of live-born animals and showed minimal illegitimate recombination of donor DNA. However, extensive founder mosaicism was evident, emphasizing the need to analyze offspring of founder animals. Unlike C57BL/6NJ mice, which exhibited external limiting membrane fragmentation and regional retinal dysplasia, heterozygous Crb1em1Mvw/Crb1rd8 mice showed a normal retinal phenotype. Conclusions. The C57BL/6NJ-Crb1rd8 mutation and its associated retinal phenotypes were corrected efficiently by TALEN-mediated homology-directed repair. The C57BL/6NJ-Crb1em1Mvw mice generated by this strategy will enhance ocular phenotyping efforts based on the C57BL/6N background, such as those implemented by the International Mouse Phenotyping Consortium (IMPC) project. PMID:24346171

  20. 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.…

  1. 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.

  2. 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…

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

    DOE PAGES

    Del Nobile, Eugenio

    2014-01-01

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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

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

    PubMed

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

    2016-05-01

    The Koolen-de Vries syndrome (KdVS; OMIM #610443), also known as the 17q21.31 microdeletion syndrome, is a clinically heterogeneous disorder characterised by (neonatal) hypotonia, developmental delay, moderate intellectual disability, and characteristic facial dysmorphism. Expressive language development is particularly impaired compared with receptive language or motor skills. Other frequently reported features include social and friendly behaviour, epilepsy, musculoskeletal anomalies, congenital heart defects, urogenital malformations, and ectodermal anomalies. The syndrome is caused by a truncating variant in the KAT8 regulatory NSL complex unit 1 (KANSL1) gene or by a 17q21.31 microdeletion encompassing KANSL1. Herein we describe a novel cohort of 45 individuals with KdVS of whom 33 have a 17q21.31 microdeletion and 12 a single-nucleotide variant (SNV) in KANSL1 (19 males, 26 females; age range 7 months to 50 years). We provide guidance about the potential pitfalls in the laboratory testing and emphasise the challenges of KANSL1 variant calling and DNA copy number analysis in the complex 17q21.31 region. Moreover, we present detailed phenotypic information, including neuropsychological features, that contribute to the broad phenotypic spectrum of the syndrome. Comparison of the phenotype of both the microdeletion and SNV patients does not show differences of clinical importance, stressing that haploinsufficiency of KANSL1 is sufficient to cause the full KdVS phenotype. PMID:26306646

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

    PubMed

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

    2016-05-01

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

  13. A comparison of early floral ontogeny in wild-type and floral homeotic mutant phenotypes of Primula.

    PubMed

    Webster, Margaret A; Gilmartin, Philip A M

    2003-04-01

    Primula flowers are heteromorphic with individual plants producing either pin-form or thrum-form flowers. We have used scanning electron microscopy to observe early development of wild-type flowers of primrose (Primula vulgaris), cowslip (P. veris), and the polyanthus hybrid (P. x tommasinii x P. vulgaris). Floral ontogeny in Primula is different from that observed in the well-studied models Antirrhinum majus and Arabidopsis thaliana and our studies reveal morphological landmark events that define the sequence of early floral development in Primula into specific stages. Pin-form and thrum-form flowers are indistinguishable during early development with differentiation of the two floral morphs occurring beyond the differentiation of floral organs. Early ontogeny of flowers with homeotic mutant phenotypes was also studied to determine the timing of developmental reprogramming in these mutants. Phenotypes studied included Hose in Hose and Jack in the Green that develop petaloid sepals and leafy sepals, respectively, and Jackanapes plants that carry both these dominant mutations. Recessive double and semi- double flowers that produce additional whorls of petals and/or stamens in place of carpels were also studied. We describe a previously undocumented recessive Primula mutant phenotype, sepaloid, that produces sepals in place of petals and stamens, and a new non-homeotic, dominant mutant phenotype Split Perianth, in which sepals and petals fail to fuse to form the typical calyx and corolla structures. The molecular basis of these mutant phenotypes in relation to the ABC model is discussed.

  14. 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.

  15. Comparison of the pseudorandom noise code and pulsed direct-detection lidars for atmospheric probing.

    PubMed

    Machol, J L

    1997-08-20

    The advantages and limitations of using the pseudorandom-noise (PN)-code technique in comparison with pulsed direct detection are discussed. Because the signal-to-noise ratio (SNR) of the PN codes is dependent on the average atmospheric return, strong returns from short ranges and clouds determine the SNR for all ranges. The SNR of a profile obtained by pulsed direct detection exceeds that of the PN-code technique for laser beams with the same average power.

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

    PubMed Central

    Falahat, Saeed; Shojapour, Mana; Sadeghi, Abdorrahim

    2016-01-01

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

  17. 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.

  18. 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...

  19. A Comparison of Three Self-Report Measures of the Broader Autism Phenotype in a Non-Clinical Sample

    ERIC Educational Resources Information Center

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

    2011-01-01

    Three self-report measures of the broader autism phenotype (BAP) were evaluated in terms of their internal consistency, distribution of scores, factor structure, and criterion-related validity in a non-clinical sample. All measures showed a continuous distribution. The SRS-A and BAPQ showed expected sex differences and were superior to the AQ in…

  20. 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;...

  1. 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

  2. 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

  3. Comparison of directional selectivity in identified spiking and nonspiking mechanosensory neurons in the crayfish Orconectes limosus.

    PubMed Central

    Tautz, J; Plummer, M R

    1994-01-01

    We have recorded electrical activity from two identified synaptically coupled mechanosensory interneurons in the abdominal nervous system of the crayfish Orconectes limosus and have studied their responses to constant-velocity water-jet stimuli presented from different directions. The two neurons, the ascending caudal photoreceptor (CPR) and the local directionally selective neuron, responded preferentially to stimuli delivered ipsilaterally to their dendritic input regions. Both neurons featured responses consisting of a phasic excitatory "on" response and a tonic depolarizing plateau. The different response components showed various degrees of directional selectivity: The initial "on" peak of the response was the least sensitive and the plateau was the most sensitive to stimulus direction. The CPR showed a sharp cut-off in responsiveness to contralateral stimuli, whereas the local directionally selective neuron showed a more gradual decrease in its directional responsiveness. This difference is a consequence of the feed-forward lateral inhibition that the local directionally selective neuron exerts on the CPR and of the threshold for initiation of action potentials in the CPR. A comparison of the spiking response of the CPR with its generator potential shows that the number and frequency of action potentials are a more sensitive indicator of directional preference than the generator potential response. The directional characteristic of the CPR is discussed as a filter matched to a specific spatial aspect of biologically relevant water movements. Images PMID:7517037

  4. 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.

  5. 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.

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

    PubMed Central

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

    2015-01-01

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

  7. 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

  8. Genetic and phenotypic comparisons of viral genotypes from two nucleopolyhedroviruses interacting with a common host species, Spodoptera litura (Lepidoptera: Noctuidae).

    PubMed

    Takatsuka, Jun; Okuno, Shohei; Nakai, Madoka; Kunimi, Yasuhisa

    2016-09-01

    Nucleopolyhedroviruses (NPVs) are known to be highly variable, both genetically and phenotypically, at several scales such as different geographic locations or a single host. A previous study using several geographic isolates indicated that two types of NPV, Spodoptera littoralis NPV (SpliNPV) and S. litura NPV (SpltNPV) types, were isolated from the common cutworm, Spodoptera litura (Fabricius), a polyphagous insect that causes serious damage to many forage crops and vegetables. That study also indicated that the SpliNPV type was widely distributed in Japan. Here, we investigated the genotypic and phenotypic variation of cloned NPVs that infect S. litura; such variation is an important resource for biological control agents, and may represent the genetic diversity of an NPV species. Eighteen genotypically distinct NPVs were cloned from four field-collected NPV isolates using an in vivo cloning technique. They were divided into two virus types according to the similarity of banding patterns of DNA fragments generated by restriction endonucleases, and Southern hybridization analysis. Partial polyhedrin gene sequences revealed that the two types corresponded to SpliNPV and SpltNPV. Bioassays seem to suggest that the SpliNPV virus type was, overall, more infectious and killed S. litura larvae faster, but yielded fewer viral occlusion bodies, than the SpltNPV type. These data provide a basis for explaining the distribution pattern of SpliNPV and SpltNPV types in S. litura populations in Japan. PMID:27449677

  9. Comparison of Gene Expression and Genome-Wide DNA Methylation Profiling between Phenotypically Normal Cloned Pigs and Conventionally Bred Controls

    PubMed Central

    Li, Shengting; Li, Jian; Lin, Lin; Nielsen, Anders Lade; Sørensen, Charlotte Brandt; Vajta, Gábor; Wang, Jun; Zhang, Xiuqing; Du, Yutao; Yang, Huanming; Bolund, Lars

    2011-01-01

    Animal breeding via Somatic Cell Nuclear Transfer (SCNT) has enormous potential in agriculture and biomedicine. However, concerns about whether SCNT animals are as healthy or epigenetically normal as conventionally bred ones are raised as the efficiency of cloning by SCNT is much lower than natural breeding or In-vitro fertilization (IVF). Thus, we have conducted a genome-wide gene expression and DNA methylation profiling between phenotypically normal cloned pigs and control pigs in two tissues (muscle and liver), using Affymetrix Porcine expression array as well as modified methylation-specific digital karyotyping (MMSDK) and Solexa sequencing technology. Typical tissue-specific differences with respect to both gene expression and DNA methylation were observed in muscle and liver from cloned as well as control pigs. Gene expression profiles were highly similar between cloned pigs and controls, though a small set of genes showed altered expression. Cloned pigs presented a more different pattern of DNA methylation in unique sequences in both tissues. Especially a small set of genomic sites had different DNA methylation status with a trend towards slightly increased methylation levels in cloned pigs. Molecular network analysis of the genes that contained such differential methylation loci revealed a significant network related to tissue development. In conclusion, our study showed that phenotypically normal cloned pigs were highly similar with normal breeding pigs in their gene expression, but moderate alteration in DNA methylation aspects still exists, especially in certain unique genomic regions. PMID:22022462

  10. Comparison of Phenotypic with Genotypic Procedures for Confirmation of Coagulase-Negative Staphylococcus Catheter-Related Bloodstream Infections

    PubMed Central

    Aldea-Mansilla, Carmen; García de Viedma, Darío; Cercenado, Emilia; Martín-Rabadán, Pablo; Marín, Mercedes; Bouza, Emilio

    2006-01-01

    We sought here to review the present definition of catheter-related bloodstream infections (CR-BSI) due to coagulase-negative staphylococci (CNS) by comparing the routine phenotypic methods with a genotypic procedure that considers different morphotypes. Our phenotypic characterization of CNS isolates included routine identification with biotype and antibiotype. The genotypic diagnosis was based on longer incubation periods with the consideration of all morphotypes and molecular typing by pulsed-field gel electrophoresis techniques. We prospectively selected 61 episodes of suspected CR-BSI by CNS occurring during 1 year, based on the presence of a compatible clinical setting and the isolation of one or more CNS from blood and catheter tip. Of these episodes, 47 (77%) were identified as true episodes of CR-BSI based on the presence of microorganisms of the same genotype in the blood and on the catheter tip. The sensitivity, specificity, positive predictive, negative predictive, accuracy, positive likelihood ratio, and negative likelihood ratio values obtained by different phenotypic microbiological approaches to establish the diagnosis of CR-BSI were as follows: identity at species level (78.7%, 85.7%, 94.9%, 54.5%, 80.3%, 5.51, and 0.25, respectively); identity of species and biotype (59.6%, 92.9%, 96.6%, 40.6%, 67.2%, 8.34, and 0.44, respectively); identity of species and antibiotype (61.7%, 92.9%, 96.7%, 41.9%, 68.8%, 8.64, and 0.41, respectively); and identity of species, biotype, and antibiotype (48.9%, 92.9%, 95.8%, 35.1%, 59%, 6.85, and 0.55, respectively). Our study demonstrates the inaccuracy of the diagnosis of CNS CR-BSI when the current definition based on conventional routine microbiological practice is followed. A new definition of CNS CR-BSI is necessary, at least as an epidemiological and research tool. PMID:17021078

  11. Phenotype variability and early onset ataxia symptoms in spinocerebellar ataxia type 7: comparison and correlation with other spinocerebellar ataxias.

    PubMed

    Albuquerque, Marcus Vinicius Cristino de; Pedroso, José Luiz; Braga Neto, Pedro; Barsottini, Orlando Graziani Povoas

    2015-01-01

    The spinocerebellar ataxias (SCA) are a group of neurodegenerative disorders characterized by heterogeneous clinical presentation. Spinocerebellar ataxia type 7 (SCA7) is caused by an abnormal CAG repeat expansion and includes cerebellar signs associated with visual loss and ophthalmoplegia. Marked anticipation and dynamic mutation is observed in SCA7. Moreover, phenotype variability and very early onset of symptoms may occur. In this article, a large series of Brazilian patients with different SCA subtypes was evaluated, and we compared the age of onset of SCA7 with other SCA. From the 26 patients with SCA7, 4 manifested their symptoms before 10-year-old. Also, occasionally the parents may have the onset of symptoms after their children. In conclusion, our study highlights the genetic anticipation phenomenon that occurs in SCA7 families. Patients with very early onset ataxia in the context of a remarkable family history, must be considered and tested for SCA7.

  12. 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

  13. 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

  14. 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.

  15. 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

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

    PubMed

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

    2014-04-15

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

  17. 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

  18. Comparison of specific IgE antibodies to wheat component allergens in two phenotypes of wheat allergy.

    PubMed

    Nam, Young-Hee; Hwang, Eui-Kyung; Jin, Hyun Jung; Lee, Jeong Min; Shin, Yoo-Seob; Ye, Young-Min; Palacin, Arantxa; Salcedo, Gabriel; Lee, Soo-Young; Park, Hae-Sim

    2013-11-01

    Specific IgE to gliadin was proposed as a marker for wheat dependent exercise induced anaphylaxis, while Tri a 14 was found to induce IgE response in baker's asthma. We evaluated whether these components could be used for discriminating phenotypes of wheat allergy. Twenty-nine patients who were wheat-induced anaphylaxis and/or urticaria (n=21, group I) and baker's asthma (n=8, group II) were enrolled. The prevalence of serum specific IgE to Tri a 14 was higher in group II (25%) than in group I (4.8%), while the serum specific IgE to gliadin was significantly higher in group I (70%) than in group II (12.5%). The cutoff value for predicting the baker's asthma using the ratio of serum specific IgE to Tri a 14 to gliadin was 742.8 optical density×1,000/(kU/L) with high sensitivity and specificity. These findings suggest that Tri a 14/gliadin may be a potential marker for predicting baker's asthma.

  19. 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

  20. A comparison of the phenotypic and genetic stability of recombinant Trichoderma spp. generated by protoplast- and Agrobacterium-mediated transformation.

    PubMed

    Cardoza, Rosa Elena; Vizcaino, Juan Antonio; Hermosa, Maria Rosa; Monte, Enrique; Gutiérrez, Santiago

    2006-08-01

    Four different Trichoderma strains, T. harzianum CECT 2413, T. asperellum T53, T. atroviride T11 and T. longibrachiatum T52, which represent three of the four sections contained in this genus, were transformed by two different techniques: a protocol based on the isolation of protoplasts and a protocol based on Agrobacterium-mediated transformation. Both methods were set up using hygromycin B or phleomycin resistance as the selection markers. Using these techniques, we obtained phenotypically stable transformants of these four different strains. The highest transformation efficiencies were obtained with the T. longibrachiatum T52 strain: 65-70 transformants/microg DNA when transformed with the plasmid pAN7-1 (hygromycin B resistance) and 280 transformants/107 spores when the Agrobacterium-mediated transformation was performed with the plasmid pUR5750 (hygromycin B resistance). Overall, the genetic analysis of the transformants showed that some of the strains integrated and maintained the transforming DNA in their genome throughout the entire transformation and selection process. In other cases, the integrated DNA was lost.

  1. Comparison of phenotype between patients with Prader-Willi syndrome due to deletion 15q and uniparental disomy 15.

    PubMed

    Cassidy, S B; Forsythe, M; Heeger, S; Nicholls, R D; Schork, N; Benn, P; Schwartz, S

    1997-02-11

    Prader-Willi syndrome (PWS) is a complex multiple anomaly syndrome that has been shown to result from deficient expression of paternal chromosome 15(q11-q13). In most cases, it is caused either by deletion of this region in the paternally inherited chromosome 15 or by maternal uniparental disomy (UPD) of chromosome 15. In order to determine whether there are phenotypic differences between patients whose PWS is caused by these two different mechanisms, 54 affected individuals (37 with deletion, 17 with UPD) were personally examined and studied using molecular techniques. The previously recognized increased maternal age in patients with UPD and increased frequency of hypopigmentation in those with deletion were confirmed. Although the frequency and severity of most other manifestations of PWS did not differ significantly between the two groups, those with UPD were less likely to have a "typical" facial appearance. In addition, this group was less likely to show some of the minor manifestations such as skin picking, skill with jigsaw puzzles, and high pain threshold. Females and those with UPD were also older, on average. Possible mechanisms by which these differences could occur and the implications of these differences for diagnosis are described. PMID:9021017

  2. A direct comparison of exoEarth yields for starshades and coronagraphs

    NASA Astrophysics Data System (ADS)

    Stark, Christopher C.; Cady, Eric J.; Clampin, Mark; Domagal-Goldman, Shawn; Lisman, Doug; Mandell, Avi M.; McElwain, Michael W.; Roberge, Aki; Robinson, Tyler D.; Savransky, Dmitry; Shaklan, Stuart B.; Stapelfeldt, Karl R.

    2016-07-01

    The scale and design of a future mission capable of directly imaging extrasolar planets will be influenced by the detectable number (yield) of potentially Earth-like planets. Currently, coronagraphs and starshades are being considered as instruments for such a mission. We will use a novel code to estimate and compare the yields for starshade- and coronagraph-based missions. We will show yield scaling relationships for each instrument and discuss the impact of astrophysical and instrumental noise on yields. Although the absolute yields are dependent on several yet-unknown parameters, we will present several limiting cases allowing us to bound the yield comparison.

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

    PubMed Central

    Meisel, Joseph W.; Gokel, George W.

    2016-01-01

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

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

    PubMed

    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

  5. 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.

  6. Comparison of two direct neutralizing assay formats using recombinant follicle-stimulating hormone as agonist.

    PubMed

    Ryding, J; Hjertberg, E; Rasmussen, B B

    2013-12-31

    Characterizing anti-drug antibodies for neutralizing activity is commonly part of the immunogenicity testing package for most therapeutic proteins. Cell-based neutralization assays can generally be categorized as direct- or indirect assays depending on whether they are associated with therapeutics with agonistic- or antagonistic properties. This paper's aim is a comparison of the two direct neutralization assay formats; the variable- and fixed concentration assay format, using recombinant follicle-stimulating hormone as drug agonist. Essential validation- and performance parameters, such as sample through-put, cut-point, precision, sensitivity and drug tolerance, were compared. The fixed concentration assay format offers superior sample through-put (40 versus 6 samples), precision (coefficient of variation of ≤14% versus 34%) and almost 6 times better sensitivity and is generally recommended as the better option particularly for quasi-quantitative assessments of neutralizing antibodies.

  7. 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.

  8. Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals

    PubMed Central

    Knoll-Gellida, Anja; André, Michèle; Gattegno, Tamar; Forgue, Jean; Admon, Arie; Babin, Patrick J

    2006-01-01

    Background The ability of an oocyte to develop into a viable embryo depends on the accumulation of specific maternal information and molecules, such as RNAs and proteins. A serial analysis of gene expression (SAGE) was carried out in parallel with proteomic analysis on fully-grown ovarian follicles from zebrafish (Danio rerio). The data obtained were compared with ovary/follicle/egg molecular phenotypes of other animals, published or available in public sequence databases. Results Sequencing of 27,486 SAGE tags identified 11,399 different ones, including 3,329 tags with an occurrence superior to one. Fifty-eight genes were expressed at over 0.15% of the total population and represented 17.34% of the mRNA population identified. The three most expressed transcripts were a rhamnose-binding lectin, beta-actin 2, and a transcribed locus similar to the H2B histone family. Comparison with the large-scale expressed sequence tags sequencing approach revealed highly expressed transcripts that were not previously known to be expressed at high levels in fish ovaries, like the short-sized polarized metallothionein 2 transcript. A higher sensitivity for the detection of transcripts with a characterized maternal genetic contribution was also demonstrated compared to large-scale sequencing of cDNA libraries. Ferritin heavy polypeptide 1, heat shock protein 90-beta, lactate dehydrogenase B4, beta-actin isoforms, tubulin beta 2, ATP synthase subunit 9, together with 40 S ribosomal protein S27a, were common highly-expressed transcripts of vertebrate ovary/unfertilized egg. Comparison of transcriptome and proteome data revealed that transcript levels provide little predictive value with respect to the extent of protein abundance. All the proteins identified by proteomic analysis of fully-grown zebrafish follicles had at least one transcript counterpart, with two exceptions: eosinophil chemotactic cytokine and nothepsin. Conclusion This study provides a complete sequence data set of

  9. 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

  10. 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.

  11. 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.

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

    PubMed

    Jou, Jerwen

    2003-01-01

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

  13. 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.

  14. Comparison of Mechanical Properties of Fiber-Reinforced Sand under Triaxial Compression and Direct Shear

    NASA Astrophysics Data System (ADS)

    Noorzad, Reza; Zarinkolaei, Seyed Taher Ghoreyshi

    2015-10-01

    This research investigates the behavior of sand reinforced with polypropylene fiber. To do this, 40 direct shear tests and 40 triaxial tests were performed on the coastal beaches of Babolsar, a city in the North of Iran. The effect of parameters such as fiber content, length of fiber and normal or confining pressure on the behavior of Babolsar sand have been studied. In this study, four various fiber contents (0, 0.25, 0.5 and 1 percent), three different lengths of fiber (6, 12 and 18 mm) and four normal or confining pressures (50, 100, 200 and 400 kPa) have been employed. The test results show that fiber inclusion has a significant effect on the behavior of sand. In both direct shear and triaxial tests, the addition of fibers improved shear strength parameters (C, '), increased peak shear strength and axial strain at failure, and also limited the amount of post-peak reduction in shear resistance. The comparison of the test results revealed that due to better fiber orientation toward the direction of principal tensile strain in triaxial test as compared to direct shear tests, the fiber efficiency and its effect on soil behavior is much more significant in triaxial specimens.

  15. 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

  16. 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

  17. 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.

  18. 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…

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

    PubMed

    Gao, Yu; Kodadek, Thomas

    2015-03-01

    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.

  20. 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.

  1. 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.

  2. Direct comparison of unloading compliance and potential drop techniques in J-integral testing

    SciTech Connect

    McGowan, J.J.; Nanstad, R.K.

    1984-01-01

    Single-specimen J-integral testing is performed commonly with the unloading compliance technique. Use of modern instrumentation techniques and powerful desktop computers have made this technique a standard. However, this testing technique is slow and tedious, with the loading rate fixed at a slow quasi-static rate. For these reasons the dc potential drop technique was investigated for crack length measurement during a J-integral test. For direct comparison, both unloading compliance and potential drop were used simultaneously during a J-integral test. The results showed good agreement between the techniques. However, the potential drop technique showed an offset in crack length due to plastic blunting processes. Taking this offset into account, J/sub Ic/ values calculated by both techniques compared well.

  3. 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.

  4. Comparison of direct simulation Monte Carlo chemistry and vibrational models applied to oxygen shock measurements

    SciTech Connect

    Wysong, Ingrid; Gimelshein, Sergey; Bondar, Yevgeniy; Ivanov, Mikhail

    2014-04-15

    Validation of three direct simulation Monte Carlo chemistry models—total collision energy, Quantum Kinetic, and Kuznetsov state specific (KSS)—is conducted through the comparison of calculated vibrational temperatures of molecular oxygen with measured values inside a normal shock wave. First, the 2D geometry and numerical approach used to simulate the shock experiments is verified. Next, two different vibrational relaxation models are validated by comparison with data for the M = 9.3 case where dissociation is small in the nonequilibrium region of the shock and with newly obtained thermal rates. Finally, the three chemistry model results are compared for M = 9.3 and 13.4 in the region where the vibrational temperature is greatly different from the rotational and translational temperature, and thus nonequilibrium dissociation is important. It is shown that the peak vibrational temperature is very sensitive to the initial nonequilibrium rate of reaction in the chemistry model and that the vibrationally favored KSS model is much closer to the measured peak, but the post-peak behavior indicates that some details of the model still need improvement.

  5. 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.

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

    PubMed

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

    2005-04-01

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

  7. Evaluation of Ica Gene in Comparison with Phenotypic Methods for Detection of Biofilm Production by Coagulase Negative Staphylococci in a Tertiary Care Hospital

    PubMed Central

    Priyan, R.M. Vasantha; Jagatheeswari, P.A.T.; Charles, Jhansi; Dhanalakshmi, V.; Lallitha, S.; Rajendran, T.; Divya, B.

    2015-01-01

    Background Biofilm producing bacteria are responsible for several chronic infections and are difficult to treat as they show much greater resistance to antibiotics. The major virulence factor determining the pathogenicity of CoNS has now well defined and found to be biofilm production. Objective The study was conducted to isolate and characterize Coagulase Negative Staphylococci (CoNS) and their ability to form biofilms was evaluated by phenotypic and genotypic methods. Materials and Methods A total of 96 clinical isolates of CoNS were characterized and subjected to biofilm detection by tissue culture plate method (TCP), tube method (TM), congo red agar method (CRA) and PCR. Results Staphylococcus epidermidis was the most commonly isolated species 76(79.17%). The ica gene was present in 35 (36.45%) of CoNS isolates which were detected as biofilm producers by TCP. Biofilm producing isolates showed higher antibiotic resistance(72.1%). Majority of biofilm producers had strong association with medical device related infections. Conclusion To compare PCR based dectection method for presence of ica genes with TCP, the test share the specific identification rates. The sensitivity and specificity of TCP method in detection of biofilm was high in comparison with TM and CRA. TCP can be recommended as a general screening test for biofilm detection. PMID:26435944

  8. 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

  9. Direct comparison of serotonin effects on siphon versus tail sensory neurons in Aplysia.

    PubMed

    Wright, W G; Kirschman, D

    1995-01-01

    Modulation of the strength of siphon and tail withdrawal reflexes in Aplysia involves, in part, changes in the sensory neurons that initiate these reflexes. Different observations and experiments on modulation in siphon and tail sensory neurons together contribute to the working model of mechanisms of learning and memory in Aplysia, yet no direct comparison of modulation in these two classes of sensory neurons has yet been made. The purpose of the present study was to directly compare modulation between siphon and tail sensory neurons in the same experimental conditions. In particular, we focused on the effects of serotonin on two firing properties of sensory neurons: spike duration and excitability. We applied serotonin (5-HT) onto both siphon and tail sensory neurons under the same conditions and found that both spike duration and excitability were significantly enhanced. This enhancement was statistically indistinguishable between siphon and tail sensory neurons tested simultaneously in the same preparation. Thus, these two different classes of sensory neurons respond to 5-HT in very similar, if not identical, ways. We conclude that if there are differences in 5-HT induced modulation between siphon and tail sensory neurons at the biophysical level, such differences are not strongly manifested at the level of changes in firing properties.

  10. DIRECT COMPARISON BETWEEN MODELING AND EXPERIMENT: AN (ALPHA)-Fe ION IMPLANTATION STUDY

    SciTech Connect

    Marian, J; Wirth, B D; Perlado, J M; Diaz de la Rubia, T; Schaublin, R; Lodi, D; Hernandez, M; de Diego, G; Stoller, R E

    2001-01-25

    Advances in computational capability and modeling techniques, as well as improvements in experimental characterization methods offer the possibility of directly comparing modeling and experiment investigations of irradiation effects in metals. As part of a collaboration among the Instituto de Fusion Nuclear (DENIM), Lawrence Livermore National Laboratory (LLNL) and CIEMAT, single and polycrystalline {alpha}-Fe samples have been irradiated with 150 keV Fe-ions to doses up to several dpa. The irradiated microstructure is to be examined with both transmission electron microscopy (TEM) and positron annihilation spectroscopy (PAS). Concurrently, we have modeled the damage accumulation in Fe under these irradiation conditions using a combination of molecular dynamics (MD) and kinetic Monte Carlo (KMC). We aim to make direct comparison between the simulation results and the experiments by simulating TEM images and estimating positron lifetimes for the predicted microstructures. While the identity of the matrix defect features cannot be determined from TEM observations alone, we propose that both large self-interstitial loops, trapped at impurities within the material, and small, spherical nanovoids form.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. Direct measurement of ozone production rates in Houston in 2009 and comparison with two estimation methods

    NASA Astrophysics Data System (ADS)

    Cazorla, M.; Brune, W. H.; Ren, X.; Lefer, B.

    2012-01-01

    Net ozone production rates, P(O3), were measured directly using the Penn State Measurement of Ozone Production Sensor (MOPS) during the Study of Houston Atmospheric Radical Precursors (SHARP, 2009). Measured P(O3) peaked in the late morning, with values between 15 ppbv h-1 and 100 ppbv h-1, although values of 40-80 ppbv h-1 were typical for higher ozone days. These measurements were compared against ozone production rates calculated using measurements of hydroperoxyl (HO2), hydroxyl (OH), and nitric oxide (NO) radicals, called "calculated P(O3)". The same comparison was done using modeled radicals obtained from a box model with the RACM2 mechanism, called "modeled P(O3)". Measured and calculated P(O3) had similar peak values but the calculated P(O3) tended to peak earlier in the morning when NO values were higher. Measured and modeled P(O3) had a similar dependence on NO, but the modeled P(O3) was only half the measured P(O3). The modeled P(O3) is less than the calculated P(O3) because the modeled HO2 is less than the measured HO2. While statistical analyses are not conclusive regarding the comparison between MOPS measurements and the two estimation methods, the calculated P(O3) with measured HO2 produces peak values similar to the measured P(O3) when ozone is high. Although the MOPS is new and more testing is required to verify its observations, the measurements in the SHARP field campaign show the potential of this new technique for contributing to the understanding of ozone-producing chemistry and to the monitoring of ozone's response to future air quality regulatory actions.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Direct measurement of ozone production rates in Houston in 2009 and comparison with two estimation methods

    NASA Astrophysics Data System (ADS)

    Cazorla, M.; Brune, W. H.; Ren, X.; Lefer, B.

    2011-10-01

    Ozone production rates, P(O3), were measured directly using the Penn State Measurement of Ozone Production Sensor (MOPS) during the Study of Houston Atmospheric Radical Precursors (SHARP 2009). Measured P(O3) peaked in the late morning, with values between 15 ppbv h-1 and 100 ppbv h-1, although values of 40-80 ppbv h-1 were typical for higher ozone days. These measurements were compared against ozone production rates calculated using measurements of hydroperoxyl (HO2), hydroxyl (OH), and nitric oxide (NO) radicals, called "calculated P(O3)". The same comparison was done using modeled radicals obtained from a box model with the RACM2 mechanism, called "modeled P(O3)". Measured and calculated P(O3) had similar peak values but the calculated P(O3) tended to peak earlier in the morning when NO values were higher. Measured and modeled P(O3) had a similar dependence on NO, but the modeled P(O3) was only half the measured P(O3). This difference indicates possible missing radical sources in the box model with the RACM2 mechanism and thus has implications for the ability of air quality models to accurately predict ozone production rates.

  2. 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

  3. 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.

  4. Laser-induced stimulated Raman scattering in the forward direction of a droplet: comparison of Mie theory with geometrical optics.

    PubMed

    Srivastava, V; Jarzembski, M A

    1991-02-01

    Comparison of Mie theory calculations of the internal electromagnetic source function for a 120-microm-diameter water droplet with geometrical optics suggests that the field enhancement located at the critical ring region encircling the axis in the forward direction of the droplet can support stimulated Raman scattering as found experimentally.

  5. 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…

  6. 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

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

    NASA Astrophysics Data System (ADS)

    Duchon, Claude E.; Wilk, Gregory E.

    1994-02-01

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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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…

  14. 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

  15. 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

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

    PubMed Central

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

    2013-01-01

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

  17. 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...

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

    ERIC Educational Resources Information Center

    Sahakyan, Lili; Foster, Nathaniel L.

    2009-01-01

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

  19. 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.

  20. 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...

  1. [Comparison of cost-effectiveness between Urimem and direct freezing for urinary protein preservation].

    PubMed

    Wang, Mingming; Liu, Xuejiao; Jia, Lulu; Sun, Ying; Gao, Youhe; Li, Mingxi

    2014-07-01

    To compare two enrichment and preservation methods of urinary proteins, stored in polyvinylidene difluoride (PVDF) membrane (Urimem) or direct freezing, we examined the differences between the two methods in time, space, costs of supplies and electricity, degree of protein degradation and convenience of the sample handling. The urimem method is superior in the storage space, the cost of electricity and the clinical convenience compared to the direct freezing method. However, the direct freezing method is superior in the time and the cost of supplies to the urimem method. The enrichment and preservation of urinary proteins using urimem have more cost-effective benefits compared to those of the direct freezing method.

  2. Characterization of transgenic mice--a comparison of protocols for welfare evaluation and phenotype characterization of mice with a suggestion on a future certificate of instruction.

    PubMed

    Jegstrup, I; Thon, R; Hansen, A K; Hoitinga, M Ritskes

    2003-01-01

    A thorough welfare evaluation performed as part of a general phenotype characterization for both transgenic and traditional mouse strains could not only contribute to the improvement of the welfare of laboratory animals, but could also be of benefit to scientists, laboratory veterinarians and the inspecting authorities. A literature review has been performed to identify and critically evaluate already existing protocols for phenotype and welfare characterization. There are several relevant schemes available, among others the SHIRPA method, the modified score sheet of Morton and Griffiths, the FRIMORFO phenotype characterization scheme and the behavioural phenotype schemes as described by Crawley. These protocols have been evaluated according to four goals: Their ability (1) to reveal any special needs or problems with a transgenic strain, (2) to cover the informational needs of the purchaser/user of the strain, (3) to refine the welfare of the transgenic animal model by identifying relevant humane endpoints, (4) to prevent the duplication of animal models that have already been developed. The protocols described are useful for characterizing the phenotype and judging welfare disturbances, however the total amount of information and the degree of detail varies considerably from one scheme to another. We present a proposal regarding the practical application of the various schemes that will secure proper treatment and the identification of humane endpoints. It is advocated that with every purchase of a particular strain, an instruction document should accompany the strain. This document needs to give detailed descriptions of the typical characteristics of the strain, as well as necessary actions concerning relevant treatment and humane endpoints. At the moment no such documents are required. The introduction of these types of documents will contribute to improvements in animal welfare as well as experimental results in laboratory animal experimentation.

  3. Performance of commonly used genotypic assays and comparison with phenotypic assays of HIV-1 coreceptor tropism in acutely HIV-1-infected patients

    PubMed Central

    Ceresola, Elisa Rita; Nozza, Silvia; Sampaolo, Michela; Pignataro, Angela Rosa; Saita, Diego; Ferrarese, Roberto; Ripa, Marco; Deng, Wenjie; Mullins, James I.; Boeri, Enzo; Tambussi, Giuseppe; Toniolo, Antonio; Lazzarin, Adriano; Clementi, Massimo; Canducci, Filippo

    2015-01-01

    Objectives Although founder viruses in primary HIV-1 infections (PHIs) typically use the CCR5 coreceptor (R5-tropic), 3%–19% of subjects also harbour CXCR4-using viruses (X4-tropic), making tropism determination before CCR5 antagonist usage mandatory. Genotypic methods can be used to accurately determine HIV-1 tropism in chronically infected patients. Methods We compared the results of genotypic methods [geno2pheno, PSSMx4r5 including a novel nucleotide-input version (ntPSSM) and distant segments (ds)Kernel] to predict coreceptor usage in a cohort of 67 PHIs. Specimens with discrepant results were phenotypically tested after cloning the V3 gene region into proviral backbones. Recombinant viruses were used to infect U87 indicator cell lines bearing CD4 and either CCR5 or CXCR4. Results Geno2pheno10%, PSSMx4r5 and (ds)Kernel gave identical predictions in 85% of cases. Geno2pheno10% predicted the presence of CXCR4 viruses in 18% of patients. Two patients were predicted to carry X4-tropic viruses by all algorithms and X4-tropic viruses were detected in at least one of the recombinant AD8 or NL4-3 backbone-based assays. Ten samples resulted in discordant predictions with at least one algorithm. Full concordance between tropism prediction by using population sequencing and phenotypic assays was observed only with ntPSSM. Geno2pheno prediction and the phenotypic assay gave the same results in a minority of ‘discordant’ patients. Conclusions Compared with both PSSMx4r5 versions, (ds)Kernel and our phenotypic assay, geno2pheno10% overestimated the frequency of X4-tropic viruses (18% versus 3%). ntPSSM was able to detect one additional X4 virus compared with (ds)Kernel that was confirmed with the phenotypic assay. PMID:25608585

  4. Comparison of Self-Directed Learning Readiness of Fire Executives to the Norm and Public Managers.

    ERIC Educational Resources Information Center

    Clark, Burton A.

    A study was conducted to compare the self-directed learning readiness of National Fire Academy (NFA) fire executive development students to the theoretical norm and to other public managers. Procedures included testing 30 NFA fire executive development students with the Self-Directed Learning Readiness Scale (SDLRS). The distribution of fire…

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

    ERIC Educational Resources Information Center

    Oh, Hyeonjoo; Moses, Tim

    2012-01-01

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

  6. 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.

  7. 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.

  8. Comparison between direct microscopy and flow cytometry for rRNA-based quantification of Candidatus Accumulibacter phosphatis in activated sludge.

    PubMed

    Perez-Feito, Rafael; Peccia, Jordan; Noguera, Daniel R

    2006-02-01

    A comparison of the quantification of a specific microbial group in activated sludge by fluorescent in-situ hybridization, coupled with either direct microscopic counting or flow cytometry, was performed using an enhanced-biological-phosphorus-removal, sequencing-batch reactor. The population dynamics of Candidatus Accumulibacter phosphatis (Cand. A. phosphatis) was evaluated during two separate runs of the reactor. With the operational conditions used, Cand. A. phosphatis was enriched until a failure in the pH controller eliminated its ecological advantage. As a result, the comparison of quantification techniques included Cand. A. phosphatis concentrations as low as 11% and as high as 96% of the total cells in the samples. The analysis demonstrated that, regardless of the particular limitations of each technique, both provided similar results when the activated-sludge flocs were easily dispersed. However, when the activated-sludge samples contained flocs that were difficult to disperse, flow cytometry failed to provide quantitative results. PMID:16566525

  9. Comparison of vector velocity imaging using directional beamforming and transverse oscillation for a convex array transducer

    NASA Astrophysics Data System (ADS)

    Jensen, Jørgen Arendt

    2014-03-01

    Vector velocity imaging can reveal both the magnitude and direction of the blood velocity. Several techniques have been suggested for estimating the velocity, and this paper compares the performance for directional beam-forming and transverse oscillation (TO) vector flow imaging (VFI). Data have been acquired using the SARUS experimental ultrasound scanner connected to a BK 8820e (BK Medical, Herlev, Denmark) convex array probe with 192 active elements. A duplex sequence with 129 B-mode emissions interleaved with 129 flow emissions has been made. The flow was generated in a recirculating flow rig with a stationary, laminar flow, and the volume flow was measured by a MAG 3000 (Danfos, Sønderbog, Denmark) magnetic flow meter for reference. Data were beamformed with an optimized transverse oscillation scheme for the TO VFI, and standard fourth-order estimators were employed for the velocity estimation. Directional RF lines were beamformed along the flow direction and cross-correlation employed to estimate the velocity magnitude. The velocities were determined for beam-to-flow angles of 60, 75 and 90 degrees. Using 32 emissions the standard deviation relative to the peak velocity for TO estimation was 7.0% at a beam-to-flow angle of 75° . This was 3.8% for directional beamforming and at 60° it was 2.2%. The general improvement, however, comes at an increase by a factor of roughly 11 in the number of calculations for the directional beamformation compared to the TO method.

  10. Macrophage activation and human immunodeficiency virus infection: HIV replication directs macrophages towards a pro-inflammatory phenotype while previous activation modulates macrophage susceptibility to infection and viral production.

    PubMed

    Porcheray, Fabrice; Samah, Boubekeur; Léone, Cathie; Dereuddre-Bosquet, Nathalie; Gras, Gabriel

    2006-05-25

    Macrophages are pivotal for the regulation of immune and inflammatory responses, but whether their role in HIV infection is protective or deleterious remains unclear. In this study, we investigated the effect of pro- and anti-inflammatory stimuli on macrophage sensitivity to two different aspects of HIV infection: their susceptibility to infection stricto sensu, which we measured by endpoint titration method, and their ability to support virus spread, which we measured by using an RT activity assay in infection kinetics. We show a partially protective role for pro-inflammatory agents as well as for IL-4. We also illustrate that various different stimuli display differential effects on macrophage susceptibility to HIV and on virus replication that occurs thereafter. On the other hand, HIV replication strongly repressed CD206 and CD163 expression, thus clearly orientating macrophages towards a pro-inflammatory phenotype, but independently of TNF. Taken together, our results emphasize that HIV infection of macrophages sets up inflammation at the cell level but through unexpected mechanisms. This may limit target susceptibility and participate in virus clearance but may also result in tissue damage.

  11. 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.

  12. 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

  13. Precision direct photon spectra at high energy and comparison to the 8 TeV ATLAS data

    NASA Astrophysics Data System (ADS)

    Schwartz, Matthew D.

    2016-09-01

    The direct photon spectrum is computed to the highest currently available precision and compared to ATLAS data from 8 TeV collisions at the LHC. The prediction includes threshold resummation at next-to-next-to-next-to-leading logarithmic order through the program PeTeR, matched to next-to-leading fixed order with fragmentation effects using JetPhox and includes the resummation of leading-logarithmic electroweak Sudakov effects. Remarkably, improved agreement with data can be seen when each component of the calculation is added successively. This comparison demonstrates the importance of both threshold logs and electroweak Sudakov effects. Numerical values for the predictions are included.

  14. Comparison of indirect and direct quantification of glycidol fatty acid ester in edible oils.

    PubMed

    Shimizu, Masao; Kudo, Naoto; Shiro, Hiroki; Yasunaga, Koichi; Masukawa, Yoshinori; Katsuragi, Yoshihisa; Yasumasu, Takeshi

    2010-01-01

    Two different methods for determining the levels of glycidol fatty acid esters (GEs) in edible oil-the German official indirect method and the direct LC-MS method-are compared. In some cases, the indirect method showed lower GE levels than the direct method. This was investigated using model studies, which revealed two possible causative factors during the acid treatment of the indirect method: (1) incomplete elimination of GE in oil that was high in GEs initially and (2) generation of GEs and/or its relevant compounds in oil that was rich in partial acylglycerol. Both these factors contributed to the subsequent underestimation of GE levels. The above technical limitations of the indirect method found in the present study has led to the inference that the direct method can more precisely determine the GE levels for a wider range of fats and oil products than the indirect method.

  15. A Comparison of SIR-B Directional Ocean Wave Spectra with Aircraft Scanning Radar Spectra.

    PubMed

    Beal, R C; Monaldo, F M; Tilley, D G; Irvine, D E; Walsh, E J; Jackson, F C; Hancock, D W; Hines, D E; Swift, R N; Gonzalez, F L; Lyzenga, D R; Zambresky, L F

    1986-06-20

    Directional ocean wave spectra derived from Shuttle Imaging Radar-B (SIR-B) L-band imagery collected off the coast of southern Chile on 11 and 12 October 1984 were compared with independent spectral estimates from two airborne scanning radars. In sea states with significant wave heights ranging from 3 to 5 meters, the SIR-B-derived spectra at 18 degrees and 25 degrees off nadir yielded reasonable estimates of wavelengths, directions, and spectral shapes for all wave systems encountered, including a purely azimuth-traveling system. A SIR-B image intensity variance spectrum containing predominantly range-traveling waves closely resembles an independent aircraft estimate of the slope variance spectrum. The prediction of a U.S. Navy global spectral ocean wave model on 11 October 1984 exhibited no significant bias in dominant wave number but contained a directional bias of about 30 degrees espect to the mean of the aircraft and spacecraft estimates.

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  20. 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.

  1. 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.

  2. 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

  3. 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…

  4. 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...

  5. 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…

  6. 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.

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

    PubMed

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

    1998-01-01

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

  8. 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…

  9. 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…

  10. 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…

  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. Comparison of muscle fiber directions between different levator ani muscle subdivisions: in vivo MRI measurements in women

    PubMed Central

    Kim, Jinyong; Miller, Janis M.; Ashton-Miller, James A.; DeLancey, John O. L.

    2014-01-01

    Introduction and hypothesis This study describes a technique to quantify muscle fascicle directions in the levator ani (LA) and tests the null hypothesis that the in vivo fascicle directions for each LA subdivision subtend the same parasagittal angle relative to a horizontal reference axis. Methods Visible muscle fascicle direction in the each of the three LA muscle subdivisions, the pubovisceral (PVM; synonymous with pubococcygeal), puborectal (PRM), and iliococcygeal (ICM) muscles, as well as the external anal sphincter (EAS), were measured on 3-T sagittal MRI images in a convenience sample of 14 healthy women in whom muscle fascicles were visible. Mean ± standard deviation (SD) angle values relative to the horizontal were calculated for each muscle subdivision. Repeated measures ANOVA and post-hoc paired t tests were used to compare muscle groups. Results Pubovisceral muscle fiber inclination was 41±8.0°, PRM was −19±10.1°, ICM was 33±8.8°, and EAS was −43±6.4°. These fascicle directions were statistically different (p<0.001). Pairwise comparisons among levator subdivisions showed angle differences of 60° between PVM and PRM, and 52° between ICM and PRM. An 84° difference existed between PVM and EAS. The smallest angle difference between levator divisions was between PVM and ICM 8°. The difference between PRM and EAS was 24°. All pairwise comparisons were significant (p<0.001). Conclusions The null hypothesis that muscle fascicle inclinations are similar in the three subdivisions of the levator ani and the external anal sphincter was rejected. The largest difference in levator subdivision inclination, 60°, was found between the PVM and PRM. PMID:24832855

  13. Phenotypic and genetic characterization of Lactococcus garvieae isolated in Spain from lactococcosis outbreaks and comparison with isolates of other countries and sources.

    PubMed

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

    2000-10-01

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

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

    PubMed

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

    2015-01-01

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

  15. Direct site-specific glycoform identification and quantitative comparison of glycoprotein therapeutics: imiglucerase and velaglucerase alfa.

    PubMed

    Ye, Hongping; Hill, John; Gucinski, Ashley C; Boyne, Michael T; Buhse, Lucinda F

    2015-03-01

    Gaucher disease, the most common lysosomal metabolic disorder, can be treated with enzyme replacement therapy (ERT). Recombinant human glucocerebrosidase imiglucerase (Cerezyme(®)), produced in Chinese hamster ovary cells, has been used for ERT of Gaucher disease for 20 years. Another recombinant glucocerebrosidase velaglucerase alfa (VPRIV), expressed in a human fibroblast cell line, was approved by the US Food and Drug Administration in 2010. The amino acid sequence difference at residue 495 of these two products is well documented. The overall N-linked qualitative glycan composition of these two products has also been reported previously. Herein, employing our recently developed approach utilizing isobaric tandem mass tag (TMT) labeling and an LTQ Orbitrap XL electron transfer dissociation (ETD) hybrid mass spectrometer, the site-specific glycoforms of these products were identified with ETD and collision-induced dissociation (CID) spectra. The quantitative comparison of site-specific glycans was achieved utilizing higher-energy collisional dissociation (HCD) spectra with a NanoMate used as both a fraction collector and a sample introduction device. From the trypsin-digested mixture of these two products, over 90 glycopeptides were identified by accurate mass matching. In addition to those previously reported, additional glycopeptides were detected with moderate abundance. The relative amount of each glycoform at a specific glycosylation site was determined based on reporter signal intensities of the TMT labeling reagents. This is the first report of site-specific simultaneous qualitative and quantitative comparison of glycoforms for Cerezyme(®) and VPRIV. The results demonstrate that this method could be utilized for biosimilarity determination and counterfeit identification of glycoproteins. PMID:25501675

  16. 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.

  17. 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

  18. 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

  19. Community Reinforcement and Family Training: a pilot comparison of group and self-directed delivery.

    PubMed

    Manuel, Jennifer K; Austin, Julia L; Miller, William R; McCrady, Barbara S; Tonigan, J Scott; Meyers, Robert J; Smith, Jane Ellen; Bogenschutz, Michael P

    2012-07-01

    In a randomized clinical pilot study, 40 concerned significant others (CSOs) of treatment-refusing alcohol- and drug-using individuals were randomized to either Community Reinforcement and Family Training (CRAFT) conducted in a group format (Group CRAFT) or a Self-Directed CRAFT condition. Although results indicated no significant between-group difference in engaging treatment-refusing substance-using individuals (referred to as identified patients or IPs) into treatment, the engagement rate in Group CRAFT was similar to rates previously reported with individual CRAFT. For the intent-to-treat analysis, 60% of Group CRAFT CSOs engaged their loved one into treatment, as compared with 40% in Self-Directed CRAFT. Of CSOs in the Group condition who received at least one session of group therapy, 71% engaged their IP into treatment. CSOs in both conditions reported improvements in family cohesion and conflict at the 3- and 6-month follow-up, replicating prior CRAFT findings.

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

    PubMed

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

    2015-03-01

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

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

    PubMed

    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 (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.

  2. Evolution of indirect reciprocity in groups of various sizes and comparison with direct reciprocity.

    PubMed

    Suzuki, Shinsuke; Akiyama, Eizo

    2007-04-01

    Recently many studies have investigated the evolution of indirect reciprocity through which cooperative action is returned by a third individual, e.g. individual A helped B and then receives help from C. Most studies on indirect reciprocity have presumed that only two individuals take part in a single interaction (group), e.g. A helps B and C helps A. In this paper, we investigate the evolution of indirect reciprocity when more than two individuals take part in a single group, and compare the result with direct reciprocity through which cooperative action is directly returned by the recipient. Our analyses show the following. In the population with discriminating cooperators and unconditional defectors, whether implementation error is included or not, (i) both strategies are evolutionarily stable and the evolution of indirect reciprocity becomes more difficult as group size increases, and (ii) the condition for the evolution of indirect reciprocity under standing reputation criterion where the third individuals distinguish between justified and unjustified defections is more relaxed than that under image scoring reputation criterion in which the third individuals do not distinguish with. Furthermore, in the population that also includes unconditional cooperators, (iii) in the presence of errors in implementation, the discriminating strategy is evolutionarily stable not only under standing but also under image scoring if group size is larger than two. Finally, (iv) in the absence of errors in implementation, the condition for the evolution of direct reciprocity is equivalent to that for the evolution of indirect reciprocity under standing, and, in the presence of errors, the condition for the evolution of direct reciprocity is very close to that for the evolution of indirect reciprocity under image scoring.

  3. RNase protection assays and RNA gel blots: a direct comparison of sensitivity.

    PubMed

    Higgs, D C; Colbert, J T

    1992-01-01

    RNase protection assays are commonly thought to be a more sensitive means of detecting and quantitating specific mRNAs than are RNA gel blots (Northern blots). We have directly compared the sensitivity of these two approaches by assaying for known amounts of in vitro synthesized beta-glucuronidase mRNA. With the probes and protocols employed here, the ability to detect a specific mRNA was similar whether RNase protection or RNA gel blot analyses were performed.

  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. Direct health care costs of treating seasonal affective disorder: a comparison of light therapy and fluoxetine.

    PubMed

    Cheung, Amy; Dewa, Carolyn; Michalak, Erin E; Browne, Gina; Levitt, Anthony; Levitan, Robert D; Enns, Murray W; Morehouse, Rachel L; Lam, Raymond W

    2012-01-01

    Objective. To compare the direct mental health care costs between individuals with Seasonal Affective Disorder randomized to either fluoxetine or light therapy. Methods. Data from the CANSAD study was used. CANSAD was an 8-week multicentre double-blind study that randomized participants to receive either light therapy plus placebo capsules or placebo light therapy plus fluoxetine. Participants were aged 18-65 who met criteria for major depressive episodes with a seasonal (winter) pattern. Mental health care service use was collected for each subject for 4 weeks prior to the start of treatment and for 4 weeks prior to the end of treatment. All direct mental health care services costs were analysed, including inpatient and outpatient services, investigations, and medications. Results. The difference in mental health costs was significantly higher after treatment for the light therapy group compared to the medication group-a difference of $111.25 (z = -3.77, P = 0.000). However, when the amortized cost of the light box was taken into the account, the groups were switched with the fluoxetine group incurring greater direct care costs-a difference of $75.41 (z = -2.635, P = 0.008). Conclusion. The results suggest that individuals treated with medication had significantly less mental health care cost after-treatment compared to those treated with light therapy.

  7. A direct multi-volume rendering method aiming at comparisons of 3-D images and models.

    PubMed

    Jacq, J J; Roux, C J

    1997-03-01

    We present a new method for direct volume rendering of multiple three-dimensional (3-D) functions using a density emitter model. This work aims at obtaining visual assessment of the results of a 3-D image registration algorithm which operates on anisotropic and non segmented medical data. We first discuss the fundamentals associated with direct, simultaneous rendering of such datasets. Then, we recall the fuzzy classification and fuzzy surface rendering theory within the density emitter model terminology, and propose an extension of standard direct volume rendering that can handle the rendering of two or more 3-D functions; this consists of the definition of merging rules that are applied on emitter clouds. The included rendering applications are related on one hand, to volume-to-volume registration, and on the other hand, to surface-to-volume registration: the first case is concerned with global elastic registration of CT data, and the second one presents fitting of an implicit surface over a CT data subset. In these two medical imaging application cases, our rendering scheme offers a comprehensive appreciation of the relative position of structural information.

  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. Comparison of the Bruker MALDI-TOF mass spectrometry system and conventional phenotypic methods for identification of Gram-positive rods.

    PubMed

    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.

  11. 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

  12. 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

  13. 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

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

    PubMed

    Tüzemen, Nazmiye Ulkü; Doğan, Nihal

    2014-01-01

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

  15. 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

  16. 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

  17. 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.

  18. 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.

  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. 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

  1. Comparison of blind intubation through supraglottic devices and direct laryngoscopy by novices: a simulation manikin study

    PubMed Central

    Kim, Young Yong; Kang, Gu Hyun; Kim, Won Hee; Choi, Hyun Young; Jang, Yong Soo; Lee, Young Jae; Kim, Jae Guk; Kim, Hyeongtae; Kim, Gyoung Yong

    2016-01-01

    Objective This study aimed to compare intubation performance between blind intubation through supraglottic airway devices and direct laryngoscopy by novices under manikin simulation. We hypothesized that the intubation time by novices using supraglottic airway devices was superior to that with the Macintosh laryngoscope (MCL). Methods A prospective, randomized crossover study was conducted with 95 participants, to evaluate i-gel, air-Q, LMA Fastrach, and MCL devices. Primary outcomes were the intubation time and the success rate for intubation. Results The i-gel showed the shortest insertion and tube passing time among the four devices; the i-gel and air-Q also showed the shortest total intubation time (all P<0.0083; i-gel vs. air-Q, P=0.03). The i-gel and MCL showed the highest cumulative success rate (all P<0.0083; i-gel vs. MCL, P=0.12). Conclusion Blind intubation through the i-gel showed almost equal intubation performance compared to direct laryngoscopy. PMID:27752621

  2. Comparison of nine methods of indicating the direction to objects: data from blind adults.

    PubMed

    Haber, L; Haber, R N; Penningroth, S; Novak, K; Radgowski, H

    1993-01-01

    Nine methods of indicating the direction to object locations were tested on twenty blind adult subjects. The task was to indicate the location of active auditory targets distributed in a semicircle with a 1.7 m radius around the subject. Target location, practice, and feedback were systematically varied for each method. The greatest accuracy and lowest variability were found for pointing methods that used body parts (directing the nose at the target, facing it with the chest, and pointing with the index finger) and extensions of body parts (pointing with a hand-held cane or with a short stick). Two less accurate methods involved rotating a dial. The least accurate methods involved drawing and a verbal description in terms of clockface labels. Method interacted significantly with target location, and with individual differences. In general, the body-part and extension method were affected less than other methods by target location and individual differences. The findings suggest that a pointing response that uses body part or an extension of a body part is the best choice for experimental or diagnostic measurement of object location by blind subjects. Differences between the results of this study of blind subjects and auditory localization accuracy in sighted subjects are discussed, and the implications for spatial processing in the blind are considered.

  3. 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

  4. An acoustic comparison of two women's infant- and adult-directed speech

    NASA Astrophysics Data System (ADS)

    Andruski, Jean; Katz-Gershon, Shiri

    2003-04-01

    In addition to having prosodic characteristics that are attractive to infant listeners, infant-directed (ID) speech shares certain characteristics of adult-directed (AD) clear speech, such as increased acoustic distance between vowels, that might be expected to make ID speech easier for adults to perceive in noise than AD conversational speech. However, perceptual tests of two women's ID productions by Andruski and Bessega [J. Acoust. Soc. Am. 112, 2355] showed that is not always the case. In a word identification task that compared ID speech with AD clear and conversational speech, one speaker's ID productions were less well-identified than AD clear speech, but better identified than AD conversational speech. For the second woman, ID speech was the least accurately identified of the three speech registers. For both speakers, hard words (infrequent words with many lexical neighbors) were also at an increased disadvantage relative to easy words (frequent words with few lexical neighbors) in speech registers that were less accurately perceived. This study will compare several acoustic properties of these women's productions, including pitch and formant-frequency characteristics. Results of the acoustic analyses will be examined with the original perceptual results to suggest reasons for differences in listener's accuracy in identifying these two women's ID speech in noise.

  5. 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.

  6. A direct comparison of short-term audiomotor and visuomotor memory.

    PubMed

    Ward, Amanda M; Loucks, Torrey M; Ofori, Edward; Sosnoff, Jacob J

    2014-04-01

    Audiomotor and visuomotor short-term memory are required for an important variety of skilled movements but have not been compared in a direct manner previously. Audiomotor memory capacity might be greater to accommodate auditory goals that are less directly related to movement outcome than for visually guided tasks. Subjects produced continuous isometric force with the right index finger under auditory and visual feedback. During the first 10 s of each trial, subjects received continuous auditory or visual feedback. For the following 15 s, feedback was removed but the force had to be maintained accurately. An internal effort condition was included to test memory capacity in the same manner but without external feedback. Similar decay times of ~5-6 s were found for vision and audition but the decay time for internal effort was ~4 s. External feedback thus provides an advantage in maintaining a force level after feedback removal, but may not exclude some contribution from a sense of effort. Short-term memory capacity appears longer than certain previous reports but there may not be strong distinctions in capacity across different sensory modalities, at least for isometric force.

  7. 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

  8. 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

  9. A direct comparison of non-destructive techniques for determining bridging stress distributions

    NASA Astrophysics Data System (ADS)

    Greene, R. B.; Gallops, S.; Fünfschilling, S.; Fett, T.; Hoffmann, M. J.; Ager, J. W.; Kruzic, J. J.

    2012-08-01

    Crack bridging is an important source of crack propagation resistance in many materials and the bridging stress distribution as a function of crack opening displacement is widely believed to represent a true material property uninfluenced by sample geometry, loading conditions, and other extrinsic factors. Accordingly, accurate measurement of the bridging stress distribution is needed and many non-destructive methods have been developed. However, there are many challenges to accurately determining bridging stresses. A comparison of bridging stresses measured using R-curve, crack opening displacement (COD), and spectroscopy methods has been made using two bridging ceramics, Y2O3 and MgO doped Si3N4 and 99.5% pure Al2O3. The COD method is surface sensitive and gives a lower peak bridging stress compared to the R-curve technique which samples through the entire material thickness. This is attributed to a more compliant near surface bridging zone. Conversely, when R-curves rise steeply over the first few micrometers of growth from a notch, an effect of negative T-stress is expected to raise the R-curve determined peak bridging stress. Spectroscopy methods were only found to yield reliable bridging stress results if a reasonable through thickness volume of material is sampled. It was found that 2.5% of the specimen thickness achieved using fluorescence spectroscopy appears adequate for Al2O3 while 0.1-0.2% of the sample thickness achieved using Raman spectroscopy for Si3N4 appears inadequate. Overall, it is concluded that in the absence of T-stresses a bridging distribution can be determined that is a true material property. Also, a new method is proposed for determining the bridging stresses of fatigue cracks from (1) the bridging stress distribution for monotonically loaded cracks and (2) experimental fatigue data.

  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. 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.

  13. 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.

  14. Marital assortment and phenotypic convergence: longitudinal evidence.

    PubMed

    Caspi, A; Herbener, E S

    1993-01-01

    This study provides a direct test of whether the observed similarity of spouses is due to initial assortment rather than to convergence of phenotypes. With data from three well-known longitudinal studies, phenotypic convergence is examined using both variable- and person-centered analyses. The longitudinal evidence does not support the hypothesis that couples increasingly resemble each other with time. Spouse correlations most likely reflect initial assortment at marriage and not the convergence of phenotypes.

  15. 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.

  16. 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

  17. 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

  18. Mimicking the Nanostructure of Bone: Comparison of Polymeric Process-Directing Agents

    PubMed Central

    Thula, Taili T.; Svedlund, Felicia; Rodriguez, Douglas E.; Podschun, Jacob; Pendi, Laura; Gower, Laurie B.

    2012-01-01

    The nanostructure of bone has been replicated using a polymer-induced liquid-precursor (PILP) mineralization process. This polymer-mediated crystallization process yields intrafibrillar mineralization of collagen with uniaxially-oriented hydroxyapatite crystals. The process-directing agent, an anionic polymer which we propose mimics the acidic non-collagenous proteins associated with bone formation, sequesters calcium and phosphate ions to form amorphous precursor droplets that can infiltrate the interstices of collagen fibrils. In search of a polymeric agent that produces the highest mineral content in the shortest time, we have studied the influence of various acidic polymers on the in vitro mineralization of collagen scaffolds via the PILP process. Among the polymers investigated were poly-L aspartic acid (PASP), poly-L-glutamic acid (PGLU), polyvinylphosphonic acid (PVPA), and polyacrylic acid (PAA). Our data indicate that PASP and the combination of PGLU/PASP formed stable mineralization solutions, and yielded nano-structured composites with the highest mineral content. Such studies contribute to our goal of preparing biomimetic bone graft substitutes with composition and structure that mimic bone. PMID:22328971

  19. Mimicking the Nanostructure of Bone: Comparison of Polymeric Process-Directing Agents.

    PubMed

    Thula, Taili T; Svedlund, Felicia; Rodriguez, Douglas E; Podschun, Jacob; Pendi, Laura; Gower, Laurie B

    2011-01-01

    The nanostructure of bone has been replicated using a polymer-induced liquid-precursor (PILP) mineralization process. This polymer-mediated crystallization process yields intrafibrillar mineralization of collagen with uniaxially-oriented hydroxyapatite crystals. The process-directing agent, an anionic polymer which we propose mimics the acidic non-collagenous proteins associated with bone formation, sequesters calcium and phosphate ions to form amorphous precursor droplets that can infiltrate the interstices of collagen fibrils. In search of a polymeric agent that produces the highest mineral content in the shortest time, we have studied the influence of various acidic polymers on the in vitro mineralization of collagen scaffolds via the PILP process. Among the polymers investigated were poly-L aspartic acid (PASP), poly-L-glutamic acid (PGLU), polyvinylphosphonic acid (PVPA), and polyacrylic acid (PAA). Our data indicate that PASP and the combination of PGLU/PASP formed stable mineralization solutions, and yielded nano-structured composites with the highest mineral content. Such studies contribute to our goal of preparing biomimetic bone graft substitutes with composition and structure that mimic bone.

  20. GPS scintillation effects associated with polar cap patches and substorm auroral activity: direct comparison

    NASA Astrophysics Data System (ADS)

    Jin, Yaqi; Moen, Jøran I.; Miloch, Wojciech J.

    2014-08-01

    We directly compare the relative GPS scintillation levels associated with regions of enhanced plasma irregularities called auroral arcs, polar cap patches, and auroral blobs that frequently occur in the polar ionosphere. On January 13, 2013 from Ny-Ålesund, several polar cap patches were observed to exit the polar cap into the auroral oval, and were then termed auroral blobs. This gave us an unprecedented opportunity to compare the relative scintillation levels associated with these three phenomena. The blobs were associated with the strongest phase scintillation (σϕ), followed by patches and arcs, with σϕ up to 0.6, 0.5, and 0.1 rad, respectively. Our observations indicate that most patches in the nightside polar cap have produced significant scintillations, but not all of them. Since the blobs are formed after patches merged into auroral regions, in space weather predictions of GPS scintillations, it will be important to enable predictions of patches exiting the polar cap.

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

    PubMed

    Murakami, Taro; Hashiya, Kazuhide

    2014-01-01

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

  2. 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.

  3. 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.

  4. 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.

  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. Sea level variation as an indicator of Florida current volume transport: comparisons with direct measurements.

    PubMed

    Maul, G A; Chew, F; Bushnell, M; Mayer, D A

    1985-01-18

    Sea level measurements from tide gauges at Miami, Florida, and Cat Cay, Bahamas, and bottom pressure measurements from a water depth of 50 meters off Jupiter, Florida, and a water depth of 10 meters off Memory Rock, Bahamas, were correlated with 81 concurrent direct volume transport observations in the Straits of Florida. Daily-averaged sea level from either gauge on the Bahamian side of the Straits was poorly correlated with transport. Bottom pressure off Jupiter had a linear coefficient of determination ofr(2) = 0.93, and Miami sea level, when adjusted for weather effects, had r(2) = 0.74; the standard errors of estimating transports were +/- 1.2 x 10(6) and +/- 1.9 x 10(6) cubic meters per second, respectively. A linear multivariate regression, which combined bottom pressure, weather, and the submarine cable observations between Jupiter and the Bahamas, had r(2) = 0.94 with a standard error of estimating transport of +/- 1.1 x 10(6) cubic meters per second. These results suggest that a combination of easily obtained observations is sufficient to adequatelv monitor the daily volume transport fluctuations of the Florida Current. PMID:17742102

  7. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    PubMed

    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.

  8. 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

  9. Comparison of Direct Anterior and Lateral Approaches in Total Hip Arthroplasty

    PubMed Central

    Yue, Chen; Kang, Pengde; Pei, Fuxing

    2015-01-01

    Abstract The direct anterior approach (DAA) to total hip arthroplasty has been promoted as a minimally invasive alternative to the lateral approach, which we sought to verify by systematically reviewing and meta-analyzing the literature comparing clinical, radiographic, and surgical outcomes. Two reviewers independently searched PubMed, OVID, and Web of Science databases for randomized controlled trials (RCTs) and cohort studies comparing the DAA and lateral approach for total hip arthroplasty. Quality of RCTs was assessed using the Jadad scoring system, quality of cohort studies, using the Minors system. Data were extracted and meta-analyzed or qualitatively synthesized for primary outcomes (function, complications, and hospitalization time) and several secondary outcomes. Data were extracted from 12 trials involving 4901 arthroplasty procedures. Meta-analysis showed that DAA was associated with significantly shorter hospitalization than the lateral approach, as well as greater functional rehabilitation and lower perceived pain during the early postoperative period. On the other hand, DAA was associated with longer surgery time. The 2 approaches were associated with similar rates of perioperative surgical complications and transfusions, as well as similar radiographic analysis results. Although DAA may provide shorter hospitalization and faster recovery during the early postoperative period, the available evidence is still insufficient to conclude whether the DAA or lateral approach is superior for total hip arthroplasty. More high-quality studies and subsequent meta-analyses are needed. PMID:26683920

  10. 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

  11. 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.

  12. 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.

  13. Comparison of immunohistochemistry, electron microscopy, and direct fluorescent antibody test for the detection of bovine coronavirus.

    PubMed

    Dar, A M; Kapil, S; Goyal, S M

    1998-04-01

    Bovine coronavirus (BCV) is 1 of the major causes of calf diarrhea and has also been implicated in respiratory infections of young calves and winter dysentery of adult cattle. Currently, transmission electron microscopy (TEM), direct fluorescent antibody (DFA), and enzyme-linked immunosorbent assay (ELISA) techniques are considered standard methods for the diagnosis of BCV infection. However, these techniques are not useful if fresh tissues and intestinal contents are not available for examination. The detection of viral antigens in formalin-fixed, paraffin-embedded tissues using immunohistochemistry (IHC) is a suitable alternative. In the present study, 166 tissue specimens were tested by IHC for the presence of BCV. These tissues were from animals whose feces were positive for rotavirus and/or coronavirus by TEM. Some of these samples were also tested by DFA. Thus, TEM, DFA, and IHC were compared for the detection of BCV. There was 56% agreement among the 3 methods (overall kappa = 0.368). When IHC was compared with TEM, 78% agreement was observed (kappa = 0.475). Similarly, IHC and DFA had 64% agreement (kappa = 0.277). These kappa values indicate a moderate degree of agreement between IHC and TEM; agreement between IHC and DFA was fair. The results of this study indicate that IHC may be a suitable adjunct for the detection of BCV because of its simplicity, ease of use, and relatively close correlation with TEM results. PMID:9576342

  14. 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.

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

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

  18. 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

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

    PubMed

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

    2004-11-01

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

  20. 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

  1. Phenotypic Characterization of Chicken Thymic Stromal Elements

    PubMed Central

    Wilson, Trevor J.; Bean, Andrew G.; Ward, Harry A.; Gershwin, M. Eric

    1992-01-01

    Phenotypic profiles of the thymic stromal components provide an excellent approach to elucidating the nature of the microenvironment of this organ. To address this issue in chickens, we have produced an extensive panel of 18 mAb to the thymic stroma. These mAb have been extensively characterized with respect to their phenotypic specificities and reveal that the stromal cells are equally as complex as the T cells whose maturation they direct. They further demonstrate that, in comparison to the mammalian thymus, there is a remarkable degree of conservation in thymic architecture between phylogenetically diverse species. Eleven mAb reacted with thymic epithelial cells: MUI-73 was panepithelium, MUI-54 stained all cortical and medullary epithelium but only a minority of the subcapsule, MUI-52 was specific for isolated stellate cortical epithelial cells, MUI-62, -69, and -71 were specific for the medulla (including Hassall’s corpusclelike structures), MUI-51, -53, -70, and -75 reacted only with the type-I epithelium, or discrete regions therein, lining the subcapsular and perivascular regions and MUI-58 demonstrated the antigenic similarity between the subcapsule and the medulla. Seven other mAb identified distinct isolated stromal cells throughout the cortex and medulla. Large thymocyte-rich regions, which often spanned from the outer cortex to medulla, lacked epithelial cells. These mAb should prove invaluable for determining the functional significance of thymic stromal-cell subsets to thymopoiesis. PMID:1387829

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

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

    PubMed

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

    2009-03-01

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

  8. 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

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

    SciTech Connect

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

    1994-09-01

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

  10. 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

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

    DOE PAGES

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

  12. 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

  13. 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

  14. 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

  15. Autonomic Evaluation of Patients With Gastroparesis and Neurostimulation: Comparisons of Direct/Systemic and Indirect/Cardiac Measures

    PubMed Central

    Stocker, Abigail; Abell, Thomas L.; Rashed, Hani; Kedar, Archana; Boatright, Ben; Chen, Jiande

    2016-01-01

    Background Disorders of nausea, vomiting, abdominal pain, and related problems often are manifestations of gastrointestinal, neuromuscular, and/or autonomic dysfunction. Many of these patients respond to neurostimulation, either gastric electrical stimulation or electroacupuncture. Both of these therapeutic techniques appear to influence the autonomic nervous system which can be evaluated directly by traditional testing and indirectly by heart rate variability. Methods We studied patients undergoing gastric neuromodulation by both systemic autonomic testing (39 patients, six males and 33 females, mean age 38 years) and systemic autonomic testing and heart rate variability (35 patients, seven males and 28 females, mean age 37 years) testing before and after gastric neuromodulation. We also performed a pilot study using both systemic autonomic testing and heart rate variability in a small number of patients (five patients, all females, mean age 48.6 years) with diabetic gastroparesis at baseline to compare the two techniques at baseline. Systemic autonomic testing and heart rate variability were performed with standardized techniques and gastric electrical stimulation was performed as previously described with electrodes implanted serosally in the myenteric plexus. Results Both systemic autonomic testing and heart rate variability measures were often abnormal at baseline and showed changes after gastric neuromodulation therapy in two groups of symptomatic patients. Pilot data on a small group of similar patients with systemic automatic nervous measures and heart rate variability showed good concordance between the two techniques. Conclusions Both traditional direct autonomic measures and indirect measures such as heart rate variability were evaluated, including a pilot study of both methods in the same patient group. Both appear to be useful in evaluation of patients at baseline and after stimulation therapies; however, a future full head-to-head comparison is

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  17. 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.

  18. 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.

  19. 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.

  20. Component processes in contour integration: a direct comparison between snakes and ladders in a detection and a shape discrimination task.

    PubMed

    Vancleef, Kathleen; Wagemans, Johan

    2013-11-01

    In contour integration, a relevant question is whether snakes and ladders are processed similarly. Higher presentation time thresholds for ladders in detection tasks indicate this is not the case. However, in a detection task only processing differences at the level of element linking and possibly contour localization might be picked up, while differences at the shape encoding level cannot be noticed. In this study, we make a direct comparison of detection and shape discrimination tasks to investigate if processing differences in the visual system between snakes and ladders are limited to contour detection or extend to higher level contour processing, like shape encoding. Stimuli consisted of elements that were oriented collinearly (snakes) or orthogonally (ladders) to the contour path and were surrounded by randomly oriented background elements. In two tasks, six experienced subjects either detected the contour when presented with a contour and a completely random stimulus or performed a shape discrimination task when presented with two contours with different curvature. Presentation time was varied in 9 steps between 8 and 492 ms. By applying a generalized linear mixed model we found that differences in snake and ladder processing are not limited to a detection stage but are also apparent at a shape encoding stage.

  1. 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.

  2. Direct simulation of electron transfer using ring polymer molecular dynamics: comparison with semiclassical instanton theory and exact quantum methods.

    PubMed

    Menzeleev, Artur R; Ananth, Nandini; Miller, Thomas F

    2011-08-21

    The use of ring polymer molecular dynamics (RPMD) for the direct simulation of electron transfer (ET) reaction dynamics is analyzed in the context of Marcus theory, semiclassical instanton theory, and exact quantum dynamics approaches. For both fully atomistic and system-bath representations of condensed-phase ET, we demonstrate that RPMD accurately predicts both ET reaction rates and mechanisms throughout the normal and activationless regimes of the thermodynamic driving force. Analysis of the ensemble of reactive RPMD trajectories reveals the solvent reorganization mechanism for ET that is anticipated in the Marcus rate theory, and the accuracy of the RPMD rate calculation is understood in terms of its exact description of statistical fluctuations and its formal connection to semiclassical instanton theory for deep-tunneling processes. In the inverted regime of the thermodynamic driving force, neither RPMD nor a related formulation of semiclassical instanton theory capture the characteristic turnover in the reaction rate; comparison with exact quantum dynamics simulations reveals that these methods provide inadequate quantization of the real-time electronic-state dynamics in the inverted regime.

  3. Effects of social comparison direction, threat, and self-esteem on affect, self-evaluation, and expected success.

    PubMed

    Aspinwall, L G; Taylor, S E

    1993-05-01

    Two studies explored the conditions under which social comparisons are used to manage negative affect and naturalistic threats. Study 1 examined induced mood and dispositional self-esteem as determinants of affective responses to upward and downward comparisons. Consistent with a mood repair prediction, only low-self-esteem Ss in whom a negative mood had been induced reported improved mood after exposure to downward comparison information. Study 2 examined the impact of naturalistic threats on responses to comparison information. Relative to a no-comparison baseline, low-self-esteem Ss who had experienced a recent academic setback reported more favorable self-evaluations and greater expectations of future success in college after exposure to downward comparison information. These results remained significant after controlling statistically for general distress. Implications for downward comparison theory are discussed.

  4. 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

  5. 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.

  6. 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…

  7. 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

  8. Unguided clinical and actuarial assessment of re-offending risk: a direct comparison with sex offenders in Denmark.

    PubMed

    Bengtson, Susanne; Långström, Niklas

    2007-06-01

    Meta-analyses suggest that actuarial risk assessments outperform unguided clinical judgment for prediction of recidivism in criminal offenders. However, there is a lack of direct comparisons of the predictive accuracy of clinical judgment and actuarial risk scales for sexual offenders. We followed up 121 male sex offenders (> or =18 years) subjected to pre-trial forensic psychiatric assessment in Denmark in 1978-1992 (mean post-detainment time = 16.4 years) to compare the predictive validity of unstructured clinical judgment of recidivism risk with that of the well-established Static-99 (Hanson and Thornton, Law and Human Behavior 24:119-136, 2000) and an extension of the Static-99, the Static-2002 (Hanson and Thornton, Notes on the development of Static-2002 (Rep. No. 2003-01), Public Safety and Emergency Preparedness Canada, Ottawa, Canada, 2003). The predictive accuracy of unguided judgment did not exceed chance for any sexual, severe sexual or any violent (sexual or non-sexual) reconviction (AUCs of the ROC curve = 0.52, 95%CI = 0.41-0.63; 0.50, 95%CI = 0.34-0.67; and 0.57, 95%CI = 0.40-0.73, respectively). In contrast, all three outcomes were predicted significantly better than chance by the Static-99 (AUC = 0.62, 95%CI = 0.52-0.72; 0.72, 95%CI = 0.59-0.84; and 0.71, 95%CI = 0.56-0.86) and the Static-2002 (AUC = 0.67, 95%CI = 0.57-0.77; 0.69, 95%CI = 0.56-0.83; and 0.70, 95%CI = 0.55-0.86). Static-99 outperformed clinical judgment for sexual recidivision (chi(2) = 5.11, df = 1, p < .05). The Static-2002 was significantly more accurate for the prediction of any sexual recidivism as compared to unguided clinical judgment but its advantage fell just short of statistical significance for severe sexual recidivism (chi(2) = 3.56, df = 1, p = 0.06). When tested for recidivism within 2 years, none of the three prediction methods yielded results significantly better than chance for any outcome. This direct trial of the unguided clinical method argues against its

  9. 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.

  10. [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.

  11. A direct comparison of the sensitivity of CT and MR cardiac perfusion using a myocardial perfusion phantom

    PubMed Central

    Otton, James; Morton, Geraint; Schuster, Andreas; Bigalke, Boris; Marano, Riccardo; Olivotti, Luca; Nagel, Eike; Chiribiri, Amedeo

    2013-01-01

    Background Direct comparison of CT and magnetic resonance (MR) perfusion techniques has been limited and in vivo assessment is affected by physiological variability, timing of image acquisition, and parameter selection. Objective We precisely compared high-resolution k-t SENSE MR cardiac perfusion at 3 T with single-phase CT perfusion (CTP) under identical imaging conditions. Methods We used a customized MR imaging and CT compatible dynamic myocardial perfusion phantom to represent the human circulation. CT perfusion studies were performed with a Philips iCT (256 slice) CT, with isotropic resolution of 0.6 mm3. MR perfusion was performed with k-t SENSE acceleration at 3 T and spatial resolution of 1.2 × 1.2 × 10 mm. The image contrast between normal and underperfused myocardial compartments was quantified at various perfusion and photon energy settings. Noise estimates were based on published clinical data. Results Contrast by CTP highly depends on photon energy and also timing of imaging within the myocardial perfusion upslope. For an identical myocardial perfusion deficit, the native image contrast-to-noise ratio (CNR) generated by CT and MR are similar. If slice averaging is used, the CNR of a perfusion deficit is expected to be greater for CTP than MR perfusion (MRP). Perfect timing during single time point CTP imaging is difficult to achieve, and CNR by CT decreases by 24%–31% two seconds from the optimal imaging time point. Although single-phase CT perfusion offers higher spatial resolution, MRP allows multiple time point sampling and quantitative analysis. Conclusion The ability of CTP and current optimal MRP techniques to detect simulated myocardial perfusion deficits is similar. PMID:23622506

  12. [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

  13. Phenotypic models of T cell activation.

    PubMed

    Lever, Melissa; Maini, Philip K; van der Merwe, P Anton; Dushek, Omer

    2014-09-01

    T cell activation is a crucial checkpoint in adaptive immunity, and this activation depends on the binding parameters that govern the interactions between T cell receptors (TCRs) and peptide-MHC complexes (pMHC complexes). Despite extensive experimental studies, the relationship between the TCR-pMHC binding parameters and T cell activation remains controversial. To make sense of conflicting experimental data, a variety of verbal and mathematical models have been proposed. However, it is currently unclear which model or models are consistent or inconsistent with experimental data. A key problem is that a direct comparison between the models has not been carried out, in part because they have been formulated in different frameworks. For this Analysis article, we reformulated published models of T cell activation into phenotypic models, which allowed us to directly compare them. We find that a kinetic proofreading model that is modified to include limited signalling is consistent with the majority of published data. This model makes the intriguing prediction that the stimulation hierarchy of two different pMHC complexes (or two different TCRs that are specific for the same pMHC complex) may reverse at different pMHC concentrations.

  14. [Intermediate phenotype of schizophrenia].

    PubMed

    Hashimoto, Ryota

    2013-04-01

    Genes are major contributors to schizophrenia. The intermediate phenotype concept represents a strategy for identifying risk genes for schizophrenia and for characterizing the neural systems affected by risk gene variants to elucidate quantitative, mechanistic aspects of brain function implicated in schizophrenia. Intermediate phenotypes are defined by being heritable, being able to measure quantitatively; being related to the disorder and its symptoms in the general population; being stable over time; showing increased expression in unaffected relatives of probands; and cosegregation with the disorder in families. Intermediate phenotypes in schizophrenia are neurocognition, neuroimaging, neurophysiology, etc. In this review, we present concept, recent work, and future perspective of intermediate phenotype.

  15. Phenotype definition in epilepsy.

    PubMed

    Winawer, Melodie R

    2006-05-01

    Phenotype definition consists of the use of epidemiologic, biological, molecular, or computational methods to systematically select features of a disorder that might result from distinct genetic influences. By carefully defining the target phenotype, or dividing the sample by phenotypic characteristics, we can hope to narrow the range of genes that influence risk for the trait in the study population, thereby increasing the likelihood of finding them. In this article, fundamental issues that arise in phenotyping in epilepsy and other disorders are reviewed, and factors complicating genotype-phenotype correlation are discussed. Methods of data collection, analysis, and interpretation are addressed, focusing on epidemiologic studies. With this foundation in place, the epilepsy subtypes and clinical features that appear to have a genetic basis are described, and the epidemiologic studies that have provided evidence for the heritability of these phenotypic characteristics, supporting their use in future genetic investigations, are reviewed. Finally, several molecular approaches to phenotype definition are discussed, in which the molecular defect, rather than the clinical phenotype, is used as a starting point.

  16. 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

  17. SUPPLEMENTARY COMPARISON: Bilateral direct comparison of Josephson array voltage standards of the PTB (Germany) and PEL (Croatia): Draft B report for EUROMET.EM-S28

    NASA Astrophysics Data System (ADS)

    Behr, Ralf; Ilić, Damir; Šala, Alan

    2008-01-01

    A comparison of the 10 V Josephson array voltage standard of the Physikalisch-Technische Bundesanstalt (PTB), Germany, was made with that of the Primarni Elektromagnetski Laboratorij (PEL), Croatia, in April 2007. The results are in very good agreement and the measured overall relative combined standard uncertainty is better than 1 part in 1010. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by EURAMET, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  18. 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.

  19. Phenytoin free fraction determination: comparison of an improved direct serum injection high-performance liquid chromatographic method to ultrafiltration coupled with fluorescence polarization immunoassay.

    PubMed

    Gurley, B J; Marx, M; Olsen, K

    1995-08-18

    Recent developments in restricted-access media (RAM) liquid chromatography make the simultaneous determination of total and free phenytoin concentrations possible by direct injection of drug-containing serum samples. A comparison of phenytoin free fraction determination by ultrafiltration coupled with fluorescence polarization immunoassay (TDX) to an improved direct injection RAM-HPLC method is presented. Our improved method differs from those previously reported with regard to column type, mobile-phase composition, and column temperature. Replicate samples analyzed by each method yielded similar values for serum phenytoin free fraction. PMID:8548029

  20. Equal sensitivity of the new generation QuantiFERON-TB Gold plus in direct comparison with the previous test version QuantiFERON-TB Gold IT.

    PubMed

    Hoffmann, H; Avsar, K; Göres, R; Mavi, S-C; Hofmann-Thiel, S

    2016-08-01

    QuantiFERON-TB Gold IT analyses interferon-γ release from CD4(+) T cells after stimulation with specific tuberculosis (TB) antigens. Its sensitivity is approximately 80% for active TB. A new test generation (QFTGplus) also analyses the response of CD8(+) T cells. We investigated both test generations in a direct head-to-head comparison in a German pulmonary hospital. Sensitivity rates for active TB were identical, no matter whether diagnosis was bacteriologically confirmed or not.

  1. 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.

  2. Wind directions predicted from global circulation models and wind directions determined from eolian sandstones of the western United States-A comparison

    USGS Publications Warehouse

    Parrish, Judith T.; Peterson, F.

    1988-01-01

    Wind directions for Middle Pennsylvanian through Jurassic time are predicted from global circulation models for the western United States. These predictions are compared with paleowind directions interpreted from eolian sandstones of Middle Pennsylvanian through Jurassic age. Predicted regional wind directions correspond with at least three-quarters of the paleowind data from the sandstones; the rest of the data may indicate problems with correlation, local effects of paleogeography on winds, and lack of resolution of the circulation models. The data and predictions suggest the following paleoclimatic developments through the time interval studied: predominance of winter subtropical high-pressure circulation in the Late Pennsylvanian; predominance of summer subtropical high-pressure circulation in the Permian; predominance of summer monsoonal circulation in the Triassic and earliest Jurassic; and, during the remainder of the Jurassic, influence of both summer subtropical and summer monsoonal circulation, with the boundary between the two systems over the western United States. This sequence of climatic changes is largely owing to paleogeographic changes, which influenced the buildup and breakdown of the monsoonal circulation, and possibly owing partly to a decrease in the global temperature gradient, which might have lessened the influence of the subtropical high-pressure circulation. The atypical humidity of Triassic time probably resulted from the monsoonal circulation created by the geography of Pangaea. This circulation is predicted to have been at a maximum in the Triassic and was likely to have been powerful enough to draw moisture along the equator from the ocean to the west. ?? 1988.

  3. The overshoot and phenotypic equilibrium in characterizing cancer dynamics of reversible phenotypic plasticity.

    PubMed

    Chen, Xiufang; Wang, Yue; Feng, Tianquan; Yi, Ming; Zhang, Xingan; Zhou, Da

    2016-02-01

    The paradigm of phenotypic plasticity indicates reversible relations of different cancer cell phenotypes, which extends the cellular hierarchy proposed by the classical cancer stem cell (CSC) theory. Since it is still questionable if the phenotypic plasticity is a crucial improvement to the hierarchical model or just a minor extension to it, it is worthwhile to explore the dynamic behavior characterizing the reversible phenotypic plasticity. In this study we compare the hierarchical model and the reversible model in predicting the cell-state dynamics observed in biological experiments. Our results show that the hierarchical model shows significant disadvantages over the reversible model in describing both long-term stability (phenotypic equilibrium) and short-term transient dynamics (overshoot) in cancer cell populations. In a very specific case in which the total growth of population due to each cell type is identical, the hierarchical model predicts neither phenotypic equilibrium nor overshoot, whereas the reversible model succeeds in predicting both of them. Even though the performance of the hierarchical model can be improved by relaxing the specific assumption, its prediction to the phenotypic equilibrium strongly depends on a precondition that may be unrealistic in biological experiments. Moreover, it still does not show as rich dynamics as the reversible model in capturing the overshoots of both CSCs and non-CSCs. By comparison, it is more likely for the reversible model to correctly predict the stability of the phenotypic mixture and various types of overshoot behavior.

  4. The Drosophila phenotype ontology

    PubMed Central

    2013-01-01

    Background Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to group annotations in biologically meaningful ways. Accurate manual annotation requires clear textual definitions for terms. Accurate grouping and fruitful programatic usage require high-quality formal definitions that can be used to automate classification. The Drosophila phenotype ontology (DPO) has been used to annotate over 159,000 phenotypes in FlyBase to date, but until recently lacked textual or formal definitions. Results We have composed textual definitions for all DPO terms and formal definitions for 77% of them. Formal definitions reference terms from a range of widely-used ontologies including the Phenotype and Trait Ontology (PATO), the Gene Ontology (GO) and the Cell Ontology (CL). We also describe a generally applicable system, devised for the DPO, for recording and reasoning about the timing of death in populations. As a result of the new formalisations, 85% of classifications in the DPO are now inferred rather than asserted, with much of this classification leveraging the structure of the GO. This work has significantly improved the accuracy and completeness of classification and made further development of the DPO more sustainable. Conclusions The DPO provides a set of well-defined terms for annotating Drosophila phenotypes and for grouping and querying the resulting annotation sets in biologically meaningful ways. Such queries have already resulted in successful function predictions from phenotype annotation. Moreover, such formalisations make extended queries possible, including cross-species queries via the external ontologies used in formal definitions. The DPO is openly available under an open source license in both OBO and OWL formats. There is good potential for it to be used more broadly by the Drosophila

  5. Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms.

    PubMed

    Rokyta, Darin R; Margres, Mark J; Calvin, Kate

    2015-09-09

    Protein expression is a major link in the genotype-phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms.

  6. 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

  7. 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.

  8. A new method to infer causal phenotype networks using QTL and phenotypic information.

    PubMed

    Wang, Huange; van Eeuwijk, Fred A

    2014-01-01

    In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs) to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO) algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG) algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request. PMID:25144184

  9. The integrated phenotype.

    PubMed

    Murren, Courtney J

    2012-07-01

    Proper functioning of complex phenotypes requires that multiple traits work together. Examination of relationships among traits within and between complex characters and how they interact to function as a whole organism is critical to advancing our understanding of evolutionary developmental plasticity. Phenotypic integration refers to the relationships among multiple characters of a complex phenotype, and their relationships with other functional units (modules) in an organism. In this review, I summarize a brief history of the concept of phenotypic integration in plant and animal biology. Following an introduction of concepts, including modularity, I use an empirical case-study approach to highlight recent advance in clarifying the developmental and genomic basis of integration. I end by highlighting some novel approaches to genomic and epigenetic perturbations that offer promise in further addressing the role of phenotypic integration in evolutionary diversification. In the age of the phenotype, studies that examine the genomic and developmental changes in relationships of traits across environments will shape the next chapter in our quest for understanding the evolution of complex characters.

  10. Direct comparison between X-ray nanotomography and scanning electron microscopy for the microstructure characterization of a solid oxide fuel cell anode

    SciTech Connect

    Quey, R.; Suhonen, H.; Laurencin, J.; Cloetens, P.; Bleuet, P.

    2013-04-15

    X-ray computed nanotomography (nano-CT) and scanning electron microscopy (SEM) have been applied to characterize the microstructure of a Solid Oxide Fuel Cell (SOFC) anode. A direct comparison between the results of both methods is conducted on the same region of the microstructure to assess the spatial resolution of the nano-CT microstructure, SEM being taken as a reference. A registration procedure is proposed to find out the position of the SEM image within the nano-CT volume. It involves a second SEM observation, which is taken along an orthogonal direction and gives an estimate reference SEM image position, which is then refined by an automated optimization procedure. This enables an unbiased comparison between the cell porosity morphologies provided by both methods. In the present experiment, nano-CT is shown to underestimate the number of pores smaller than 1 μm and overestimate the size of the pores larger than 1.5 μm. - Highlights: ► X-ray computed nanotomography (nano-CT) and SEM are used to characterize an SOFC anode. ► A methodology is proposed to compare the nano-CT and SEM data on the same region. ► The spatial resolution of the nano-CT data is assessed from that comparison.

  11. A comparison of response spectrum and direct integration analysis methods as applied to a nuclear component support structure. Revision 1

    SciTech Connect

    Bryan, B.J.; Flanders, H.E. Jr.

    1992-12-31

    Seismic qualification of Class I nuclear components is accomplished using a variety of analytical methods. This paper compares the results of time history dynamic analyses of a heat exchanger support structure using response spectrum and time history direct integration analysis methods. Dynamic analysis is performed on the detailed component models using the two methods. A nonlinear elastic model is used for both the response spectrum and direct integration methods. A nonlinear model which includes friction and nonlinear springs, is analyzed using time history input by direct integration. The loads from the three cases are compared.

  12. Precueing time but not direction of postural perturbation induces early muscular activation: comparison between young and elderly individuals.

    PubMed

    Silva, Marina Brito; Coelho, Daniel Boari; de Lima-Pardini, Andrea Cristina; Martinelli, Alessandra Rezende; Baptista, Thais da Silva; Ramos, Renato Teodoro; Teixeira, Luis Augusto

    2015-02-19

    In this study, we evaluated the effect of precueing characteristics of an impending perturbation to upright stance on reactive responses of distal leg muscles. Young and older individuals were compared in a task of recovering stable upright stance following rotation of the supporting platform to induce anterior or posterior body sway. Directions of the supporting platform rotation were randomized across trials. Immediately before postural perturbation participants were cued about direction and/or time of platform rotation, or performed the task under directional and temporal uncertainty of the impending perturbation. Results showed that precueing time of perturbation led to earlier muscular activation onset, while precueing perturbation direction did not modulate either latency or magnitude of muscular activation. Those effects were similar between age groups. Our findings suggest that awareness of the perturbation time favored shorter response latencies in both the young and older individuals.

  13. Intensity-modulated radiation therapy using static ports of tomotherapy (TomoDirect): comparison with the TomoHelical mode

    PubMed Central

    2013-01-01

    Purpose With the new mode of Tomotherapy, irradiation can be delivered using static ports of the TomoDirect mode. The purpose of this study was to evaluate the characteristics of TomoDirect plans compared to conventional TomoHelical plans. Methods TomoDirect and TomoHelical plans were compared in 46 patients with a prostate, thoracic wall or lung tumor. The mean target dose was used as the prescription dose. The minimum coverage dose of 95% of the target (D95%), conformity index (CI), uniformity index (UI), dose distribution in organs at risk and treatment time were evaluated. For TomoDirect, 2 to 5 static ports were used depending on the tumor location. Results For the prostate target volume, TomoDirect plans could not reduce the rectal dose and required a longer treatment time than TomoHelical. For the thoracic wall target volume, the V5Gy of the lung or liver was lower in TomoDirect than in TomoHelical (p = 0.02). For the lung target volume, TomoDirect yielded higher CI (p = 0.009) but smaller V5Gy of the lung (p = 0.005) than TomoHelical. Treatment time did not differ significantly between the thoracic wall and lung plans. Conclusion Prostate cancers should be treated with the TomoHelical mode. Considering the risk of low-dose radiation to the lung, the TomoDirect mode could be an option for thoracic wall and lung tumors. PMID:23517931

  14. 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

  15. Direct Comparison of the Performance of a Bio-inspired Synthetic Nickel Catalyst and a [NiFe]-Hydrogenase, Both Covalently Attached to Electrodes

    SciTech Connect

    Rodriguez-Macia, Patricia; Dutta, Arnab; Lubitz, Wolfgang; Shaw, Wendy J.; Rudiger, Olaf

    2015-10-12

    The active site of hydrogenases has been a source of inspiration for the development of molecular catalysts. However, direct comparisons between molecular catalysts and enzymes have not been possible because different techniques are used to evaluate both types of catalysts, minimizing our ability to determine how far we’ve come in mimicking the impressive enzymatic performance. Here we directly compare the catalytic properties of the [Ni(PCy2NGly2)2]2+ complex with the [NiFe]-hydrogenase from Desulfobivrio vulgaris Miyazaki F (DvMF) immobilized to a functionalized electrode under identical conditions. At pH=7, the enzyme has higher performance in both activity and overpotential, and is more stable, while at low pH, the molecular catalyst outperforms the enzyme in all respects. The Ni complex also has increased tolerance to CO. This is the first direct comparison of enzymes and molecular complexes, enabling a unique understanding of the benefits and detriments of both systems, and advancing our understanding of the utilization of these bioinspired complexes in fuel cells. AD and WJS acknowledge the Office of Science Early Career Research Program through the US Department of Energy (US DOE), Office of Science, Office of Basic Energy Sciences (BES), and Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the US DOE.

  16. AIMAR survey on COPD phenotypes

    PubMed Central

    2014-01-01

    Background COPD is characterized by considerable diversity in terms of clinical signs and symptoms, physiopathological mechanisms, response to treatment and disease progression. For this reason, the identification of different patient subgroups (or possible phenotypes) is important both for prognosis and for therapeutic objectives. Based on the foregoing, AIMAR has decided to conduct a survey on the perception of the prevalence of the different clinical COPD phenotypes/subtypes in the clinical practice of physicians who treat patients with chronic obstructive pulmonary disease, and on their therapeutic objectives. Methods The survey consisted of 19 multiple-choice questions, compiled through a form published online. All the data and answers entered into the system were checked for consistency and completeness directly online at the time they were entered, and each respondent could only complete the questionnaire once. Results The survey took place from May through October 2012. A total of 1,434 questionnaires (60% of the sample approached) were eligible for analysis, broken down as follows: 537 pulmonologists, 666 general practitioners (GPs), 72 internal medicine specialists, 36 allergists, 30 geriatricians, 93 other specialists. The results show that a significant proportion of GPs (33%) identified more than 50 patients in their practices with a diagnosis of COPD. Although most patients are or have been in treatment with a long-acting bronchodilator, the most common reasons for seeing a GP or a specialist were exacerbations and worsening of the symptoms, suggesting the importance of an appropriate background therapy in order to reduce the risk of disease instability. The frequent exacerbator phenotype was the most commonly found phenotype in clinical practice (by 75% of specialists and 66% of GPs); patients with a prevalent phenotype of chronic bronchitis were reported more often by GPs, while specialists reported a higher number of patients with a prevalent

  17. 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.

  18. Comparison of IPDA lidar receiver sensitivity for coherent detection and for direct detection using sine-wave and pulsed modulation.

    PubMed

    Sun, Xiaoli; Abshire, James B

    2012-09-10

    We use theoretical models to compare the receiver signal to noise ratio (SNR) vs. average rate of detected signal photons for an integrated path differential absorption (IPDA) lidar using coherent detection with continuous wave (CW) lasers and direct detection with sine-wave and pulse modulations. The results show the coherent IPDA lidar has high receiver gain and narrow bandwidth to overcome the effects of detector circuit noise and background light, but the actual receiver performance can be limited by the coherent mixing efficiency, speckle and other factors. For direct detection, using sine-wave modulation allows the use of a low peak power laser transmitter and synchronous detection. The pulse modulation technique requires higher laser peak powers but is more efficient than sine-wave modulation in terms of average detected signal photon rate required to achieve a given receiver SNR. We also conducted experiments for the direct detection cases and the results agreed well with theory.

  19. 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

  20. 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

  1. Comparison of the physical optics code with the GOIE method and the direct solution of Maxwell equations obtained by FDTD

    NASA Astrophysics Data System (ADS)

    Konoshonkin, Alexander V.; Kustova, Natalia V.; Borovoi, Anatoli G.; Ishimoto, Hiroshi; Masuda, Kazuhiko; Okamoto, Hajime

    2015-11-01

    A comparison of the physical optics code and GOIE method to solve the problem of light scattering by hexagonal ice crystals has been presented. It was found that in the case of diffraction on a hole in the perpendicular screen, both methods give the same diffraction scattering cross section for the diffraction angles up to 60 degrees. The polarization elements of the Mueller matrix in this case differ significantly even for the angles of 15-30 degrees. It is also shown that in the case of diffraction on the tilted screen, the difference between these methods may be significant. The comparison of the results with the exact solution obtained by FDTD has confirmed that the difference between these methods is not significant for the case of diffraction on the perpendicular screen, but it is slightly preferable to use the GOIE for the calculations. The good agreement with the exact solution confirms the possibility of using the method of physical optics to solve the problem of light scattering by particles with characteristic size greater than 10 microns.

  2. 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…

  3. Interactions of Tollmien-Schlichting waves and Dean vortices. Comparison of direct numerical simulation and a weakly nonlinear theory

    NASA Technical Reports Server (NTRS)

    Singer, Bart A.; Zang, Thomas A.

    1989-01-01

    Direct numerical simulation is used to evaluate a weakly nonlinear theory describing the interaction of Tollmien-Schlichting waves with Dean vortices in curved channel flow. The theory and the simulation agree for certain combinations of parameters, but the two approaches give conflicting results for other combinations. Some possibilities for these discrepancies are discussed.

  4. Skill Instruction in Outdoor Leadership: A Comparison of a Direct Instruction Model and a Discovery-Learning Model

    ERIC Educational Resources Information Center

    Thomas, Glyn

    2007-01-01

    In this paper I discuss some of the strengths and weaknesses of two different approaches to teaching motor skills to students in outdoor education and outdoor recreation settings. Using acronyms to describe their stages: DEDICT is a six step, direct instructional model that some outdoor leaders may already be familiar with; and FERAL is my…

  5. 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...

  6. 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...

  7. Direct measurement of single and multiple passband intelligibilities: Comparison with estimates based upon the Speech Intelligibility Index

    NASA Astrophysics Data System (ADS)

    Warren, Richard M.; Bashford, James A.; Lenz, Peter W.

    2001-05-01

    The intelligibility of individual bands spanning the speech spectrum is of interest for theoretical and practical reasons, and has been the subject of considerable experimental investigation. Direct measurement of passband intelligibility can be confounded with contributions from filter slopes, but by employing sufficiently high orders of FIR filtering, the present study has removed all slope contributions and measured directly intelligibilities of 1-octave and 1/3-octave passbands. Stimuli employed were based upon the same commercial recording of monosyllabic words and the same frequency bands used for the Speech Intelligibility Index (SII) [American National Standards Institute, S3.5, 1997]. SII employs an indirect procedure for estimating intelligibility: lists of band ``importance'' values are derived from intelligibility scores for high-pass and low-pass speech having incrementally varied cutoff frequencies. These importance values are correlated with intelligibility, and were transformed into intelligibility estimates using the published transfer function. Directly measured intelligibilities differ for some, but not all, SII-based intelligibility estimates for bands heard singly and in combination. Direct determination of intelligibilities of individual and multiple passbands is suggested as a simple and accurate alternative to the methods based upon SII and other indirect procedures for estimating the intelligibility of frequency-limited speech. [Work supported by NIH.

  8. NCHEMS Costing and Data Management System and the Purdue University Cost Study: A Comparison of Narrowly Defined Direct Costs.

    ERIC Educational Resources Information Center

    Eikenberry, F. L.; Gleason, W. M.

    One critical aspect of costing system methodologies is examined: the effects of average costing by course level on program unit cost. The direct costing methodologies used in two costing systems are compared. One is the internally developed Purdue University Cost Study; the other, the NCHEMS Costing and Data Management System. The comparison…

  9. Using Direct Behavior Rating (DBR) to Screen for School Social Risk: A Preliminary Comparison of Methods in a Kindergarten Sample

    ERIC Educational Resources Information Center

    Chafouleas, Sandra M.; Kilgus, Stephen P.; Hernandez, Paul

    2009-01-01

    In this study, preliminary evidence of the potential for Direct Behavior Rating (DBR) in screening assessment of school social behavior is provided through evaluation of the concurrent validity of DBR with a commonly used criterion measure. The teacher-completed form of the "Social Skills Rating System" (SSRS) was selected as the criterion measure…

  10. 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…

  11. Estimation of Bi induced changes in the direct E0 band gap of III-V-Bi alloys and comparison with experimental data

    NASA Astrophysics Data System (ADS)

    Samajdar, D. P.; Dhar, S.

    2016-03-01

    Quantum dielectric Theory (QDT) is used to explain the band gap bowing effect observed in III-V-Bismides such as InSb1-xBix, InAs1-xBix, InP1-xBix, GaSb1-xBix, GaAs1-xBix and GaP1-xBix. The dependence of the direct E0 band gap for these alloys on Bi mole fraction is calculated using QDT which requires the evaluation of the bowing parameter c. The bowing parameter gives the deviation of the direct E0 band gap from the linear relationship of E0 with Bi mole fraction. The band gap reduction values obtained using QDT are compared with those calculated using Virtual Crystal approximation (VCA) and Valence Band Anticrossing (VBAC) model as well as with the reported experimental data and the results of the comparison shows excellent agreement.

  12. 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

  13. 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

  14. 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.

  15. 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, Virginia 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

  16. 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

  17. 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…

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

    DOE PAGES

    Kolbus, Lindsay M.; Payzant, E. Andrew; Cornwell, Paris A.; 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

  19. Comparison of Analytical Methods: Direct Emission versus First-Derivative Fluorometric Methods for Quinine Determination in Tonic Waters

    NASA Astrophysics Data System (ADS)

    Pandey, Siddharth; Borders, Tammie L.; Hernández, Carmen E.; Roy, Lindsay E.; Reddy, Gaddum D.; Martinez, Geo L.; Jackson, Autumn; Brown, Guenevere; Acree, William E., Jr.

    1999-01-01

    An undergraduate laboratory experiment is designed for the quantitative determination of quinine in tonic water samples. It is based upon direct fluorescence emission and first-derivative spectroscopic methods. Unlike other published laboratory experiments, our method exposes students to the general method of derivative spectroscopy, an important, often-used analytical technique for eliminating sample matrix and background absorbance effects and for treating overlapped spectral bands. The statistical treatment allows students to compare concentrations directly calculated from the measured fluorescence emission intensity with values obtained from the first-derivative emission spectra, to ascertain whether there is a difference between the two analytical methods. Method selection and validation are important items routinely encountered by practicing analytical chemists.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. Influence of apoE content on receptor binding of large, bouyant LDL in subjects with different LDL subclass phenotypes.

    PubMed

    Barbagallo, C M; Levine, G A; Blanche, P J; Ishida, B Y; Krauss, R M

    1998-03-01

    We investigated the influence of apolipoprotein (apo) E-containing particles on LDL receptor binding of large, buoyant LDL subfractions (LDL I) from subjects with predominantly large (phenotype A) and small (phenotype B) LDL particles. Direct binding by human fibroblast LDL receptors was tested at 4 degrees C before and after removal of apoE-containing particles by immunoaffinity chromatography. The binding affinity of total LDL I in phenotype B was greater than that in phenotype A (Kd of 1.83+/-0.3 and 3.43+/-0.9 nmol/L, respectively, P<.05). LDL I from phenotype B subjects had a higher apoE to apoB molar ratio than did that from phenotype A (0.16+/-0.04 versus 0.06+/-0.02, P<.05). Nondenaturing gradient gel electrophoresis of apoE-containing LDL I isolated by immunoaffinity chromatography revealed a substantially larger peak particle diameter than in apoE-free LDL I, and comparison of LDL I composition before and after immunoaffinity chromatography suggested an increase in triglyceride content of apoE-containing particles. After removal of these particles, there was a greater than twofold reduction in LDL receptor affinity of phenotype B LDL (Kd of 1.83+/-0.3 to 3.76+/-0.6, P<.01), whereas in phenotype A no change was observed (Kd of 3.43+/-0.9 to 3.57+/-0.4, respectively). The receptor affinity of apoE-free LDL I from phenotype A and B subjects did not differ. These findings confirm that large, buoyant LDL particles from phenotype B subjects have a higher LDL receptor affinity than does LDL I from phenotype A subjects and suggest that this difference is due to an increased content of large, triglyceride-enriched, apoE-containing lipoproteins. It is possible that the accumulation of these particles reflects abnormalities in the metabolism of remnant lipoproteins that contribute to atherosclerosis risk in phenotype B subjects.

  5. 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.

  6. 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

  7. Implementing directives that involve prepositions with children with autism: a comparison of spoken cues with two types of augmented input.

    PubMed

    Schlosser, Ralf W; Laubscher, Emily; Sorce, James; Koul, Rajinder; Flynn, Suzanne; Hotz, Lindsy; Abramson, Jennifer; Fadie, Holly; Shane, Howard

    2013-06-01

    Some children with autism face considerable challenges with comprehension, including difficulties following spoken directives involving prepositional relations. The use of augmented input through visual modalities might be an effective means for supplementing spoken language. The purpose of this preliminary study was to compare spoken input with two augmented input modalities (i.e., speech + visual cues) in terms of children's ability to follow directives involving prepositions. The augmented input modalities consisted of static scene cues (i.e., photographic or pictorial visual scenes that portray relevant concepts and their relationships) and dynamic scene cues (i.e., full-motion video clips that depict the actions underlying relevant concepts and their relationships). A within-subjects design involving nine children with autism or pervasive developmental disorders-not otherwise specified was used to examine the effectiveness of the three input conditions. Results indicated that both static scene cues and dynamic scene cues were more effective than spoken cues, but there were no differences between static scene cues and dynamic scene cues. Results are discussed in terms of appropriate instructional inputs for children with autism. Limitations are noted and directions for future research are posited.

  8. Comparison of gold nanoparticle mediated photoporation: vapor nanobubbles outperform direct heating for delivering macromolecules in live cells.

    PubMed

    Xiong, Ranhua; Raemdonck, Koen; Peynshaert, Karen; Lentacker, Ine; De Cock, Ine; Demeester, Jo; De Smedt, Stefaan C; Skirtach, Andre G; Braeckmans, Kevin

    2014-06-24

    There is a great interest in delivering macromolecular agents into living cells for therapeutic purposes, such as siRNA for gene silencing. Although substantial effort has gone into designing nonviral nanocarriers for delivering macromolecules into cells, translocation of the therapeutic molecules from the endosomes after endocytosis into the cytoplasm remains a major bottleneck. Laser-induced photoporation, especially in combination with gold nanoparticles, is an alternative physical method that is receiving increasing attention for delivering macromolecules in cells. By allowing gold nanoparticles to bind to the cell membrane, nanosized membrane pores can be created upon pulsed laser illumination. Depending on the laser energy, pores are created through either direct heating of the AuNPs or by vapor nanobubbles (VNBs) that can emerge around the AuNPs. Macromolecules in the surrounding cell medium can then diffuse through the pores directly into the cytoplasm. Here we present a systematic evaluation of both photoporation mechanisms in terms of cytotoxicity, cell loading, and siRNA transfection efficiency. We find that the delivery of macromolecules under conditions of VNBs is much more efficient than direct photothermal disturbance of the plasma membrane without any noticeable cytotoxic effect. Interestingly, by tuning the laser energy, the pore size could be changed, allowing control of the amount and size of molecules that are delivered in the cytoplasm. As only a single nanosecond laser pulse is required, we conclude that VNBs are an interesting photoporation mechanism that may prove very useful for efficient high-throughput macromolecular delivery in live cells.

  9. Comparison of the cytotoxicity of high-level disinfectants by the MTT assay and direct contact assay.

    PubMed

    Ryu, Mizuyuki; Matsumura, Reiko; Quan, Glenlelyn; Furuta, Taro

    2013-01-01

    Most critical instruments are not designed for heat sterilization and autoclaving. These items are usually treated with chemical agents such as peracetic acid(PAA), glutaraldehyde (GA) and ortho-phthalaldehyde (OPA). MTT assay is often used to evaluate the in vitro cytotoxicity of these chemical agents. In this study, disinfectants were allowed to come in direct contact with cells. Their cytotoxicity was evaluated based on cell viability and adhesive properties. The results obtained from the direct contact method were compared with those obtained from the conventional MTT assay wherein the disinfectants were added into a nutrient medium. It was found that the two methods yielded very different results, especially when aldehyde- and halogen-containing disinfectants were tested, and that toxicity may be underestimated in the MTT assay. Hence, it can be assumed that the direct contact assay is more accurate when evaluating the cytotoxicity of residual chemicals. It was also observed that the cytotoxicity of PAA was lower than that of GA and OPA. PMID:24366629

  10. Survival benefit and additional value of preoperative chemoradiotherapy in resectable gastric and gastro-oesophageal junction cancer: a direct and adjusted indirect comparison meta-analysis.

    PubMed

    Kumagai, K; Rouvelas, I; Tsai, J A; Mariosa, D; Lind, P A; Lindblad, M; Ye, W; Lundell, L; Schuhmacher, C; Mauer, M; Burmeister, B H; Thomas, J M; Stahl, M; Nilsson, M

    2015-03-01

    Several phase I/II studies of chemoradiotherapy for gastric cancer have reported promising results, but the significance of preoperative radiotherapy in addition to chemotherapy has not been proven. In this study, a systematic literature search was performed to capture survival and postoperative morbidity and mortality data in randomised clinical studies comparing preoperative (chemo)radiotherapy or chemotherapy versus surgery alone, or preoperative chemoradiotherapy versus chemotherapy for gastric and/or gastro-oesophageal junction (GOJ) cancer. Hazard ratios (HRs) for overall mortality were extracted from the original studies, individual patient data provided from the principal investigators of eligible studies or the earlier published meta-analysis. The incidences of postoperative morbidities and mortalities were also analysed. In total 18 studies were eligible and data were available from 14 of these. The meta-analysis on overall survival yielded HRs of 0.75 (95% CI 0.65-0.86, P < 0.001) for preoperative (chemo)radiotherapy and 0.83 (95% CI 0.67-1.01, P = 0.065) for preoperative chemotherapy when compared to surgery alone. Direct comparison between preoperative chemoradiotherapy and chemotherapy resulted in an HR of 0.71 (95% CI 0.45-1.12, P = 0.146). Combination of direct and adjusted indirect comparisons yielded an HR of 0.86 (95% CI 0.69-1.07, P = 0.171). No statistically significant differences were seen in the risk for postoperative morbidity or mortality between preoperative treatments and surgery alone, or preoperative (chemo)radiotherapy and chemotherapy. Preoperative (chemo)radiotherapy for gastric and GOJ cancer showed significant survival benefit over surgery alone. In comparisons between preoperative chemotherapy and (chemo)radiotherapy, there is a trend towards improved survival when adding radiotherapy, without increased postoperative morbidity or mortality.

  11. 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

  12. Phenotypic plasticity of native vs. invasive purple loosestrife: a two-state multivariate approach.

    PubMed

    Chun, Young Jin; Collyer, Michael L; Moloney, Kirk A; Nason, John D

    2007-06-01

    The differences in phenotypic plasticity between invasive (North American) and native (German) provenances of the invasive plant Lythrum salicaria (purple loosestrife) were examined using a multivariate reaction norm approach testing two important attributes of reaction norms described by multivariate vectors of phenotypic change: the magnitude and direction of mean trait differences between environments. Data were collected for six life history traits from native and invasive plants using a split-plot design with experimentally manipulated water and nutrient levels. We found significant differences between native and invasive plants in multivariate phenotypic plasticity for comparisons between low and high water treatments within low nutrient levels, between low and high nutrient levels within high water treatments, and for comparisons that included both a water and nutrient level change. The significant genotype x environment (G x E) effects support the argument that invasiveness of purple loosestrife is closely associated with the interaction of high levels of soil nutrient and flooding water regime. Our results indicate that native and invasive plants take different strategies for growth and reproduction; native plants flowered earlier and allocated more to flower production, while invasive plants exhibited an extended period of vegetative growth before flowering to increase height and allocation to clonal reproduction, which may contribute to increased fitness and invasiveness in subsequent years.

  13. 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.

  14. Direct Determination of Trace Antimony in Natural Waters by Photochemical Vapor Generation ICPMS: Method Optimization and Comparison of Quantitation Strategies.

    PubMed

    Gao, Ying; Sturgeon, Ralph E; Mester, Zoltán; Hou, Xiandeng; Zheng, Chengbin; Yang, Lu

    2015-08-01

    A novel and sensitive approach for the accurate determination of antimony (Sb) in natural waters is described using photochemical vapor generation (PVG) coupled with inductively coupled plasma mass spectrometry (ICPMS) for detection. Utilizing a unique flow-through photochemical reactor capable of subjecting the samples to deep-UV (185 nm) radiation, generation efficiency was found to be independent of whether Sb(III), Sb(V), or organometallic species [trimethyltantimony(V)dibromine, TMSb(V)] were present, eliminating the shortcoming of Sb species depended sensitivity encountered during direct solution nebulization by ICPMS. Furthermore, the potentially severe matrix effect from seawater was efficiently eliminated by using a mixture of 5% (v/v) formic and 15% acetic acids (v/v) as the photochemical reductant, making direct determination of Sb in seawater feasible. The proposed method provides a 15-fold improvement in sensitivity over direct solution nebulization. A method detection limit of 0.0006 ng g(-1) based on external calibration was obtained (0.0002 ng g(-1) for isotope dilution), yielding a 15-fold improvement over that for direct solution nebulization. Accuracy is demonstrated by analysis of two water certified reference materials (CRMs, e.g., SLRS-6 and NIST 1640a) with satisfying results. In addition, spike recoveries of 100.6 ± 5.5% and 100.8 ± 3.8% (standard deviation, n = 3) were obtained for NASS-6 and CASS-5 seawater CRMs, respectively, since no certified values for Sb has been established for these materials. The performance of several calibration strategies, including double isotope dilution (ID), multiple and single-point gravimetric standard additions with internal standardization, as well as multiple and single-point gravimetric standard additions alone was examined. High precision of determination of Sb in four natural water samples (0.51-1.4%) was realized based on ID calibration, whereas one-point gravimetric standard addition calibration

  15. GTP-binding peptide of beta-tubulin. Localization by direct photoaffinity labeling and comparison with nucleotide-binding proteins

    SciTech Connect

    Linse, K.; Mandelkow, E.M.

    1988-10-15

    The binding site of the guanine moiety of GTP on beta-tubulin was located within the peptide consisting of residues 63-77, AILVDLEPGTMDSVR. The result was obtained using direct photoaffinity labeling, peptide sequencing, and limited proteolysis. Peptides were identified by end-labeling with a monoclonal antibody against beta-tubulin whose epitope was located between 3 and 4 kDa from the C terminus. The sequence of the GTP-binding site is consistent with predictions from other GTP-binding proteins such as elongation factor Tu or ras p21.

  16. 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.

  17. 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.

  18. Comparison of remote video and diver's direct observations to quantify reef fishes feeding on benthos in coral and rocky reefs.

    PubMed

    Longo, G O; Floeter, S R

    2012-10-01

    This study compared remote underwater video and traditional direct diver observations to assess reef fish feeding impact on benthos across multiple functional groups within different trophic categories (e.g. herbivores, zoobenthivores and omnivores) and in two distinct reef systems: a subtropical rocky reef and a tropical coral reef. The two techniques were roughly equivalent, both detecting the species with higher feeding impact and recording similar bite rates, suggesting that reef fish feeding behaviour at the study areas are not strongly affected by the diver's presence. PMID:23020575

  19. Comparison of remote video and diver's direct observations to quantify reef fishes feeding on benthos in coral and rocky reefs.

    PubMed

    Longo, G O; Floeter, S R

    2012-10-01

    This study compared remote underwater video and traditional direct diver observations to assess reef fish feeding impact on benthos across multiple functional groups within different trophic categories (e.g. herbivores, zoobenthivores and omnivores) and in two distinct reef systems: a subtropical rocky reef and a tropical coral reef. The two techniques were roughly equivalent, both detecting the species with higher feeding impact and recording similar bite rates, suggesting that reef fish feeding behaviour at the study areas are not strongly affected by the diver's presence.

  20. 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

  1. 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.

  2. Direct measurement of stellar neutron capture rates of 14C and comparison with the Coulomb breakup method

    NASA Astrophysics Data System (ADS)

    Reifarth, Rene; Heil, M.; Plag, R.; Besserer, U.; Couture, A.; Dababneh, S.; Dörr, L.; Forssén, C.; Görres, J.; Haight, R. C.; Mengoni, A.; O'Brien, S.; Patronis, N.; Rundberg, R. S.; Uberseder, E.; Wiescher, M.; Wilhelmy, J. B.

    The neutron capture cross section of 14 C has been shown to be important for several neutron driven nucleosynthesis scenarios. Due to the high neutron abundance it is expected that the 14 C(n,γ) reaction competes strongly with other neutron-induced reactions on 14 C. The 14 C(n,γ) reaction is also important to validate (n,γ) cross sections obtained via the inverse reaction by the Coulomb breakup method. In principle, 14 C belongs to the few cases where this correspondence can be validated in a convincingly clean way. So far, the example of 14 C is obscured, however, by discrepancies between several experiments and theory. In this contribution we report on a re- analysis of the direct measurements of the 14 C(n,γ) reaction presented on the last NIC conference (Vancouver, 2004). The neutron energies used during the experiment ranged from 30 to 800 keV. The earlier presented disagreement between the direct measurements and the Coulomb breakup method has been resolved.

  3. Studying Extreme Ultraviolet Wave Transients with a Digital Laboratory: Direct Comparison of Extreme Ultraviolet Wave Observations to Global Magnetohydrodynamic Simulations

    NASA Astrophysics Data System (ADS)

    Downs, Cooper; Roussev, Ilia I.; van der Holst, Bart; Lugaz, Noé; Sokolov, Igor V.; Gombosi, Tamas I.

    2011-02-01

    In this work, we describe our effort to explore the signatures of large-scale extreme ultraviolet (EUV) transients in the solar corona (EUV waves) using a three-dimensional thermodynamic magnetohydrodynamic model. We conduct multiple simulations of the 2008 March 25 EUV wave (~18:40 UT), observed both on and off of the solar disk by the STEREO-A and B spacecraft. By independently varying fundamental parameters thought to govern the physical mechanisms behind EUV waves in each model, such as the ambient magneto-sonic speed, eruption free energy, and eruption handedness, we are able to assess their respective contributions to the transient signature. A key feature of this work is the ability to synthesize the multi-filter response of the STEREO Extreme UltraViolet Imagers directly from model data, which gives a means for direct interpretation of EUV observations with full knowledge of the three-dimensional magnetic and thermodynamic structures in the simulations. We discuss the implications of our results with respect to some commonly held interpretations of EUV waves (e.g., fast-mode magnetosonic wave, plasma compression, reconnection front, etc.) and present a unified scenario which includes both a wave-like component moving at the fast magnetosonic speed and a coherent driven compression front related to the eruptive event itself.

  4. 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.

  5. 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

  6. Comparison of Direct Plating Media for the Isolation and Enumeration of Enterococci in Certain Frozen Foods1

    PubMed Central

    Burkwall, Mary K.; Hartman, Paul A.

    1964-01-01

    A total of 15 agar media were examined for their yield, selectivity, readability, and simplicity of preparation and use. A thallium medium of Barnes was selected as the better of the high yield-fair selectivity type of medium and an azide-citrate medium of Reinbold appeared to be the better of the low yield-high selectivity type of medium. Sodium carbonate (optimal concentration, 0.20%) was found to increase recovery substantially when added to certain media, especially in the presence of 0.05% Tween 80. When these two ingredients were incorporated into a medium modified after Slanetz and Bartley, the resultant medium was superior to other media for the isolation and enumeration of enterococci in certain frozen foods, such as peas and hamburger, by the direct plating method. PMID:14106933

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. Unsteady heat transfer and direct comparison to steady-state measurements in a rotor-wake experiment

    NASA Technical Reports Server (NTRS)

    Obrien, J. E.; Simoneau, R. J.; Morehouse, K. A.; Lagraff, J. E.

    1986-01-01

    Circumferentially local and time-resolved heat transfer measurements were obtained for a circular cylinder in crossflow located downstream of a rotating spoked wheel wake generator in a steady flow tunnel. The unsteady heat transfer effects were obtained by developing an extension of a thin film gauge technique employed to date exclusively in short-duration facilities. The time-average thin film results and conventional steady-state heat transfer measurements were compared. Time-averaged wake-induced stagnation heat transfer enhancement levels above the nowake case were about 10 percent for the four cylinder Reynolds numbers. This enhancement level was nearly independent of bar passing frequency and was related directly to the time integral of the heat transfer spikes observed at the bar passing frequency. It is observed that the wake-induced heat transfer spikes have peak magnitudes averaging 30 to 40 percent above the interwake heat transfer level.

  12. Unsteady heat transfer and direct comparison to steady-state measurements in a rotor-wake experiment

    NASA Technical Reports Server (NTRS)

    Obrien, J. E.; Simoneau, R. J.; Lagraff, J. E.; Morehouse, K. A.

    1986-01-01

    Circumferentially local and time-resolved heat transfer measurements were obtained for a circular cylinder in crossflow located downstream of a rotating spoked wheel wake generator in a steady flow tunnel. The unsteady heat transfer effects were obtained by developing an extension of a thin film gauge technique employed to date exclusively in short-duration facilities. The time-average thin film results and conventional steady-state heat transfer measurements were compared. Time-averaged wake-induced stagnation heat transfer enhancement levels above the nowake case were about 10% for the four cylinder Reynolds numbers. This enhancement level was nearly independent of bar passing frequency and was related directly to the time integral of the heat transfer spikes observed at the bar passing frequency. It is observed that the wake-induced heat transfer spikes have peak magnitudes averaging 30 to 40% above the interwake heat transfer level.

  13. 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

  14. 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

  15. Single cell dynamic phenotyping

    PubMed Central

    Patsch, Katherin; Chiu, Chi-Li; Engeln, Mark; Agus, David B.; Mallick, Parag; Mumenthaler, Shannon M.; Ruderman, Daniel

    2016-01-01

    Live cell imaging has improved our ability to measure phenotypic heterogeneity. However, bottlenecks in imaging and image processing often make it difficult to differentiate interesting biological behavior from technical artifact. Thus there is a need for new methods that improve data quality without sacrificing throughput. Here we present a 3-step workflow to improve dynamic phenotype measurements of heterogeneous cell populations. We provide guidelines for image acquisition, phenotype tracking, and data filtering to remove erroneous cell tracks using the novel Tracking Aberration Measure (TrAM). Our workflow is broadly applicable across imaging platforms and analysis software. By applying this workflow to cancer cell assays, we reduced aberrant cell track prevalence from 17% to 2%. The cost of this improvement was removing 15% of the well-tracked cells. This enabled detection of significant motility differences between cell lines. Similarly, we avoided detecting a false change in translocation kinetics by eliminating the true cause: varied proportions of unresponsive cells. Finally, by systematically seeking heterogeneous behaviors, we detected subpopulations that otherwise could have been missed, including early apoptotic events and pre-mitotic cells. We provide optimized protocols for specific applications and step-by-step guidelines for adapting them to a variety of biological systems. PMID:27708391

  16. Comparison between direct-sequence and multicarrier spread-spectrum acoustic communications in time-varying channels.

    PubMed

    van Walree, P A

    2010-12-01

    Underwater communication experiments have been conducted in the Norwegian Oslofjord. Two modulation schemes are compared in a 7-kHz frequency band on a 14-kHz center frequency. The first scheme is direct-sequence spread spectrum (DSSS), using a 7-chip spreading code to achieve a raw data rate of 1000 bps on a single carrier. The second scheme is multicarrier spread spectrum (MCSS) and accomplishes spreading by using seven subbands. The DSSS receiver equalizes on the chips prior to explicit symbol despreading, whereas MCSS features joint multiband equalization and despreading. Four channels are examined, from nearly static to overspread. In slowly varying channels, MCSS offers the best performance. DSSS has the best tracking potential for rapidly varying channels, where the challenge is to obtain reliable chip decisions before symbol despreading. The tracking potential can be realized to some extent by hypothesis-feedback equalization. It is further shown that adaptive equalizers are capable of code conversion, i.e., the DSSS receiver can demodulate the MCSS waveform, and vice versa. Neither receiver requires knowledge of the spreading code in order to despread the data.

  17. 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

  18. 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.

  19. Direct Comparison of (19)F qNMR and (1)H qNMR by Characterizing Atorvastatin Calcium Content.

    PubMed

    Liu, Yang; Liu, Zhaoxia; Yang, Huaxin; He, Lan

    2016-01-01

    Quantitative nuclear magnetic resonance (qNMR) is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR ((1)H qNMR) and only a few fluorine qNMR ((19)F qNMR) were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both (19)F and (1)H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that (19)F qNMR has similar precision and sensitivity to (1)H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from (19)F qNMR is that the analyte signal is with less or no interference from impurities. (19)F qNMR is an excellent approach to quantify fluorine-containing analytes. PMID:27688925

  20. Comparison of GlideScope Videolaryngoscopy to Direct Laryngoscopy for Intubation of a Pediatric Simulator by Novice Physicians.

    PubMed

    Rabiner, Joni E; Auerbach, Marc; Avner, Jeffrey R; Daswani, Dina; Khine, Hnin

    2013-01-01

    Objective. To compare novice clinicians' performance using GlideScope videolaryngoscopy (GVL) to direct laryngoscopy (DL). Methods. This was a prospective, randomized crossover study. Incoming pediatric interns intubated pediatric simulators in four normal and difficult airway scenarios with GVL and DL. Primary outcomes included time to intubation and rate of successful intubation. Interns rated their satisfaction of the devices and chose the preferred device. Results. Twenty-five interns were included. In the normal airway scenario, there were no differences in mean time for intubation with GVL or DL (61.4 versus 67.4 seconds, P = NS) or number of successful intubations (19 versus 18, P = NS). In the difficult airway scenario, interns took longer to intubate with GVL than DL (87.7 versus 61.3 seconds, P = 0.018), but there were no differences in successful intubations (14 versus 15, P = NS). There was a trend towards higher satisfaction for GVL than DL (7.3 versus 6.4, P = NS), and GVL was chosen as the preferred device by a majority of interns (17/25, 68%). Conclusions. For novice clinicians, GVL does not improve time to intubation or intubation success rates in a pediatric simulator model of normal and difficult airway scenarios. Still, these novice clinicians overall preferred GVL.

  1. 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

  2. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    PubMed Central

    Liu, Yang; Liu, Zhaoxia; Yang, Huaxin

    2016-01-01

    Quantitative nuclear magnetic resonance (qNMR) is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR) and only a few fluorine qNMR (19F qNMR) were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that 19F qNMR has similar precision and sensitivity to 1H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from 19F qNMR is that the analyte signal is with less or no interference from impurities. 19F qNMR is an excellent approach to quantify fluorine-containing analytes. PMID:27688925

  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. Direct multi-scale coupling of a transport code to gyrokinetic turbulence codes, with comparisons to tokamak experiments

    NASA Astrophysics Data System (ADS)

    Barnes, Michael

    2009-11-01

    To faithfully simulate ITER and other modern fusion devices, one must resolve electron and ion fluctuation scales in a five-dimensional phase space and time. Simultaneously, one must account for the interaction of this turbulence with the slow evolution of the large-scale plasma profiles. Because of the enormous range of scales involved and the high dimensionality of the problem, resolved first-principles simulations of the full core volume over the confinement time are very challenging using conventional (brute force) techniques. In order to address this problem, we have developed a new approach in which turbulence calculations from multiple gyrokinetic flux tube simulations are coupled together using gyrokinetic transport equations to obtain self-consistent equilibrium profiles and corresponding turbulent fluxes. This multi-scale approach is embodied in a new code, Trinity, which is capable of evolving equilibrium profiles for multiple species, including electromagnetic effects and realistic magnetic geometry, at a fraction of the cost of conventional direct numerical simulations. Key components in the cost reduction are the extreme parallelism enabled by the use of coupled flux tubes and the use of a nonlinear implicit algorithm to take large time steps when evolving the equilibrium. In this talk, we describe the multi-scale model employed in Trinity and present simulation results using nonlinear fluxes calculated with the gyrokinetic turbulence codes GS2 and GENE. We compare the numerical predictions from Trinity simulations with experimental results from a number of fusion devices, including JET and MAST.

  5. The dimensional nature of externalizing behaviors in adolescence: evidence from a direct comparison of categorical, dimensional, and hybrid models.

    PubMed

    Walton, Kate E; Ormel, Johan; Krueger, Robert F

    2011-05-01

    Researchers have recognized the importance of developing an accurate classification system for externalizing disorders, though much of this work has been framed by a priori preferences for categorical vs. dimensional constructs. Newer statistical technologies now allow categorical and dimensional models of psychopathology to be compared empirically. In this study, we directly compared the fit of categorical and dimensional models of externalizing behaviors in a large and representative community sample of adolescents at two time points separated by nearly 2.5 years (N = 2027; mean age at Time 1 = 11.09 years; 50.8% female). Delinquent and aggressive behaviors were assessed with child and parent Child Behavior Checklist reports. Latent trait, latent class, and factor mixture models were fit to the data, and at both time points, the latent trait model provided the best fit to the data. The item parameters were inspected and interpreted, and it was determined that the items were differentially sensitive across all regions of the dimension. We conclude that classification models can be based on empirical evidence rather than a priori preferences, and while current classification systems conceptualize externalizing problems in terms of discrete groups, they can be better conceptualized as dimensions.

  6. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    PubMed Central

    Liu, Yang; Liu, Zhaoxia; Yang, Huaxin

    2016-01-01

    Quantitative nuclear magnetic resonance (qNMR) is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR) and only a few fluorine qNMR (19F qNMR) were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that 19F qNMR has similar precision and sensitivity to 1H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from 19F qNMR is that the analyte signal is with less or no interference from impurities. 19F qNMR is an excellent approach to quantify fluorine-containing analytes.

  7. 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

  8. 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.

  9. 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

  10. Comparison between human awake, meditation and drowsiness EEG activities based on directed transfer function and MVDR coherence methods.

    PubMed

    Dissanayaka, Chamila; Ben-Simon, Eti; Gruberger, Michal; Maron-Katz, Adi; Sharon, Haggai; Hendler, Talma; Cvetkovic, Dean

    2015-07-01

    This study examined the electroencephalogram functional connectivity (coherence) and effective connectivity (flow of information) of selected brain regions during three different attentive states: awake, meditation and drowsiness. For the estimation of functional connectivity (coherence), Welch and minimum variance distortionless response (MVDR) methods were compared. The MVDR coherence was found to be more suitable since it is both data and frequency dependent and enables higher spectral resolution, while Welch's periodogram-based approach is both data and frequency independent. The directed transfer function (DTF) method was applied in order to estimate the effective connectivity or brain's flow of information between different regions during each state. DTF enables to identify the main brain areas that initiate EEG activity and the spatial distribution of these activities with time. Analysis was conducted using the EEG data of 30 subjects (ten awake, ten drowsy and ten meditating) focusing on six main electrodes (F3, F4, C3, C4, P3, P4, O1 and O2). For each subject, EEG data were recorded during 5-min baseline and 15 min of a specific condition (awake, meditation or drowsiness). Statistical analysis included the Kruskal-Wallis (KW) nonparametric analysis of variance followed by post hoc tests with Bonferroni alpha correction. The results reveal that both states of drowsiness and meditation states lead to a marked difference in the brain's flow of information (effective connectivity) as shown by DTF analyses. In specific, a significant increase in the flow of information in the delta frequency band was found only in the meditation condition and was further found to originate from frontal (F3, F4), parietal (P3, P4) and occipital (O1, O2) regions. Altogether, these results suggest that a change in attentiveness leads to significant changes in the spectral profile of the brain's information flow as well as in its functional connectivity and that these changes can

  11. A comparison of ethanol and butanol as oxygenates using a direct-injection, spark-ignition (DISI) engine.

    SciTech Connect

    Wallner, T.; Miers, S. A.; McConnell, S.

    2009-05-01

    This study was designed to evaluate a 'what if' scenario in terms of using butanol as an oxygenate in place of ethanol in an engine calibrated for gasoline operation. No changes to the stock engine calibration were performed for this study. Combustion analysis, efficiency, and emissions of pure gasoline, 10% ethanol, and 10% butanol blends in a modern direct-injection four-cylinder spark-ignition engine were analyzed. Data were taken at engine speeds of 1000 rpm up to 4000 rpm with load varying from 0 N m (idle) to 150 N m. Relatively minor differences existed between the three fuels for the combustion characteristics such as heat release rate, 50% mass fraction burned, and coefficient of variation in indicated mean effective pressure at low and medium engine loads. However at high engine loads the reduced knock resistance of the butanol blend forced the engine control unit to retard the ignition timing substantially, compared with the gasoline baseline and, even more pronounced, compared with the ethanol blend. Brake specific volumetric fuel consumption, which represented a normalized volumetric fuel flow rate, was lowest for the gasoline baseline fuel due to the higher energy density. The 10% butanol blend had a lower volumetric fuel consumption compared with the ethanol blend, as expected, based on energy density differences. The results showed little difference in regulated emissions between 10% ethanol and 10% butanol. The ethanol blend produced the highest peak specific NO{sub x} due to the high octane rating of ethanol and effective antiknock characteristics. Overall, the ability of butanol to perform equally as well as ethanol from an emissions and combustion standpoint, with a decrease in fuel consumption, initially appears promising. Further experiments are planned to explore the full operating range of the engine and the potential benefits of higher blend ratios of butanol.

  12. A comparison of different transarterial embolization techniques for direct carotid cavernous fistulas: a single center experience in 32 patients

    PubMed Central

    Lu, Xiaojian; Hussain, Mohammed; Ni, Lanchun; Huang, Qinfeng; Zhou, Fei; Gu, Zhikai; Chen, Jian; Ding, Yuchuan; Xu, Feng

    2014-01-01

    Objective Transarterial treatment of direct carotid cavernous fistulas (DCCF) via embolic materials has been well documented. This study reports, validates, and compares with existing literature our experience treating DCCFs via endovascular approaches by using detachable balloons, coils, and covered stents. Methods Between June 2006 to October 2011, 32 patients (21 male, 11 female) with 32 DCCFs (30 traumatic, 2 spontaneous cavernous ICA aneurysms) were embolized endovascularly. Followup was performed for at least 6 months. Results Among the 32 DCCFs, 21 (65.6%) were embolized using detachable balloons, eight (25.0%) with coils, one (3.1%) with balloons and coils, and two (6.3%) with covered stents. Complete DCCF obliteration was achieved in 31 (96.9%) cases. One fistula failed to respond due to premature balloon detachment. Intracranial bruit in 31 (100%) chemosis and exophthalmos in 28 (100%) cases resolved after embolization. Visual acuity and oculomotor palsy improved in 18 (90%) and 18 (69.2%) cases, respectively. There was no evidence of DCCF recurrence. Thirteen DCCFs were followed up by MRI and five by DSA. In these cases, four (4/13, 30.8%) balloon-embolized DCCFs showed pseudoaneurysms. Three patients were asymptomatic; one had minor left oculomotor palsy. Conclusions Our results correlate and reinforce literature regarding endovascular treatment of DCCFs. Application of Transarterial embolization with detachable balloons, despite extensive use has been decreasing. Coil embolization is an effective and safe alternative for treatment, especially when balloon embolization fails. Covered stent placement may be used as another alternative for selected cases. PMID:25566340

  13. 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

  14. 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

  15. Direct comparison of the hygroscopic properties of ammonium sulfate and sodium chloride aerosol at relative humidities approaching saturation.

    PubMed

    Walker, Jim S; Wills, Jon B; Reid, Jonathan P; Wang, Liangyu; Topping, David O; Butler, Jason R; Zhang, Yun-Hong

    2010-12-01

    Holographic optical tweezers are used to make comparative measurements of the hygroscopic properties of single component aqueous aerosol containing sodium chloride and ammonium sulfate over a range of relative humidity from 84% to 96%. The change in RH over the course of the experiment is monitored precisely using a sodium chloride probe droplet with accuracy better than ±0.09%. The measurements are used to assess the accuracy of thermodynamic treatments of the relationship between water activity and solute mass fraction with particular attention focused on the dilute solute limit approaching saturation vapor pressure. The consistency of the frequently used Clegg-Brimblecombe-Wexler (CBW) treatment for predicting the hygroscopic properties of sodium chloride and ammonium sulfate aerosol is confirmed. Measurements of the equilibrium size of ammonium sulfate aerosol are found to agree with predictions to within an uncertainty of ±0.2%. Given the accuracy of treating equilibrium composition, the inconsistencies highlighted in recent calibration measurements of critical supersaturations of sodium chloride and ammonium sulfate aerosol cannot be attributed to uncertainties associated with the thermodynamic predictions and must have an alternative origin. It is concluded that the CBW treatment can allow the critical supersaturation to be estimated for sodium chloride and ammonium sulfate aerosol with an accuracy of better than ±0.002% in RH. This corresponds to an uncertainty of ≤1% in the critical supersaturation for typical supersaturations of 0.2% and above. This supports the view that these systems can be used to accurately calibrate instruments that measure cloud condensation nuclei concentrations at selected supersaturations. These measurements represent the first study in which the equilibrium properties of two particles of chemically distinct composition have been compared simultaneously and directly alongside each other in the same environment.

  16. 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

  17. Carbon Nanotube Emissions from Arc Discharge Production: Classification of Particle Types with Electron Microscopy and Comparison with Direct Reading Techniques

    PubMed Central

    Ludvigsson, Linus; Isaxon, Christina; Nilsson, Patrik T.; Tinnerberg, Hakan; Messing, Maria E.; Rissler, Jenny; Skaug, Vidar; Gudmundsson, Anders; Bohgard, Mats; Hedmer, Maria; Pagels, Joakim

    2016-01-01

    Introduction: An increased production and use of carbon nanotubes (CNTs) is occurring worldwide. In parallel, a growing concern is emerging on the adverse effects the unintentional inhalation of CNTs can have on humans. There is currently a debate regarding which exposure metrics and measurement strategies are the most relevant to investigate workplace exposures to CNTs. This study investigated workplace CNT emissions using a combination of time-integrated filter sampling for scanning electron microscopy (SEM) and direct reading aerosol instruments (DRIs). Material and Methods: Field measurements were performed during small-scale manufacturing of multiwalled carbon nanotubes using the arc discharge technique. Measurements with highly time- and size-resolved DRI techniques were carried out both in the emission and background (far-field) zones. Novel classifications and counting criteria were set up for the SEM method. Three classes of CNT-containing particles were defined: type 1: particles with aspect ratio length:width >3:1 (fibrous particles); type 2: particles without fibre characteristics but with high CNT content; and type 3: particles with visible embedded CNTs. Results: Offline sampling using SEM showed emissions of CNT-containing particles in 5 out of 11 work tasks. The particles were classified into the three classes, of which type 1, fibrous CNT particles contributed 37%. The concentration of all CNT-containing particles and the occurrence of the particle classes varied strongly between work tasks. Based on the emission measurements, it was assessed that more than 85% of the exposure originated from open handling of CNT powder during the Sieving, mechanical work-up, and packaging work task. The DRI measurements provided complementary information, which combined with SEM provided information on: (i) the background adjusted emission concentration from each work task in different particle size ranges, (ii) identification of the key procedures in each work

  18. 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

  19. `Weak A' phenotypes

    PubMed Central

    Cartron, J. P.; Gerbal, A.; Hughes-Jones, N. C.; Salmon, C.

    1974-01-01

    Thirty-five weak A samples including fourteen A3, eight Ax, seven Aend, three Am and three Ae1 were studied in order to determine their A antigen site density, using an IgG anti-A labelled with 125I. The values obtained ranged between 30,000 A antigen sites for A3 individuals, and 700 sites for the Ae1 red cells. The hierarchy of values observed made it possible to establish a quantitative relationship between the red cell agglutinability of these phenotypes measured under standard conditions, and their antigen site density. PMID:4435836

  20. 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

  1. 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

  2. Direct analysis of environmental and biological samples for total mercury with comparison of sequential atomic absorption and fluorescence measurements from a single combustion event

    NASA Astrophysics Data System (ADS)

    Cizdziel, James V.; Tolbert, Candice; Brown, Garry

    2010-02-01

    A Direct Mercury Analyzer (DMA) based on sample combustion, concentration of mercury by amalgamation with gold, and cold vapor atomic absorption spectrometry (CVAAS) was coupled to a mercury-specific cold vapor atomic fluorescence spectrometer (CVAFS). The purpose was to evaluate combustion-AFS, a technique which is not commercially available, for low-level analysis of mercury in environmental and biological samples. The experimental setup allowed for comparison of dual measurements of mercury (AAS followed by AFS) for a single combustion event. The AFS instrument control program was modified to properly time capture of mercury from the DMA, avoiding deleterious combustion products from reaching its gold traps. Calibration was carried out using both aqueous solutions and solid reference materials. The absolute detection limits for mercury were 0.002 ng for AFS and 0.016 ng for AAS. Recoveries for reference materials ranged from 89% to 111%, and the precision was generally found to be <10% relative standard deviation (RSD). The two methods produced similar results for samples of hair, finger nails, coal, soil, leaves and food stuffs. However, for samples with mercury near the AAS detection limit (e.g., filter paper spotted with whole blood and segments of tree rings) the signal was still quantifiable with AFS, demonstrating the lower detection limit and greater sensitivity of AFS. This study shows that combustion-AFS is feasible for the direct analysis of low levels of mercury in solid samples that would otherwise require time-consuming and contamination-prone digestion.

  3. Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes

    PubMed Central

    Scharfe, Curt; Lu, Henry Horng-Shing; Neuenburg, Jutta K.; Allen, Edward A.; Li, Guan-Cheng; Klopstock, Thomas; Cowan, Tina M.; Enns, Gregory M.; Davis, Ronald W.

    2009-01-01

    Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the

  4. The Phenotype of Loneliness

    PubMed Central

    Cacioppo, John T.; Cacioppo, Stephanie

    2012-01-01

    Goossens’ (in press) review nicely maps the progression of scientific research from its early focus on loneliness as a dysphoric state that results from the discrepancy between a person's ideal and actual social relationships to its current emphasis on the centrality of loneliness to our very nature as a social species, and he argues that developmental science throughout Europe has a great deal to contribute to our understanding of this construct. He concludes that psychologists should care about research on loneliness for five reasons: (i) it is a well-defined phenotype, (ii) it shows both high stability and individual differences in rates of change across years, (iii) it has adaptive value and evolutionary significance, (iv) it has a genetic substrate that is moderated by social environments, and (v) it has self-maintaining features that can lead to adverse mental health outcomes. Goossen's (2012) review is rife with information and ideas. We focus here on two additional important reasons and on the phenotype of loneliness. PMID:23024688

  5. [Predisposition - obesity phenotype].

    PubMed

    Blüher, M

    2014-05-01

    Obesity belongs to the five most important health burdens in modern societies and reaches with ~20 % prevalence in Germany epidemic proportions. Obesity significantly increases the risk of developing metabolic (e. g. type 2 diabetes), cardiovascular, orthopaedic, psychologic and other disorders. Despite the well established epidemiologic relationship between obesity and these co-morbidities, there is a subgroup of metabolically healthy obese patients, which seems to be protected against metabolic and cardiovascular obesity related disorders. Compared to metabolically unhealthy or high risk obese patients, metabolically healthy obese individuals are characterized by preserved insulin sensitivity, lower liver fat content, lower visceral fat mass, as well as normal adipose tissue function. Noteworthy, metabolically healthy obese individuals do not significantly improve their obesity-associated risk for the development of type 2 diabetes and vascular diseases. Therefore, distinction between metabolically healthy from high-risk obese phenotypes will facilitate the identification of the obese person who will benefit the most from early lifestyle, pharmacological or bariatric surgery interventions. A stratified treatment approach considering these different obesity phenotypes should be introduced into clinical management of obese patients.

  6. Murine fertilized ovum, blastomere and morula cells lacking SP phenotype.

    PubMed

    Xu, YiXin; He, ZhiYing; Zhu, HaiYing; Chen, XueSong; Li, JianXiu; Zhang, HongXia; Pan, XingHua; Hu, YiPing

    2007-12-01

    In the field of stem cell research, SP (side population) phenotype is used to define the property that cells maintain a high efflux capability for some fluorescent dye, such as Hoechst 33342. Recently, many researches proposed that SP phenotype is a phenotype shared by some stem cells and some progenitor cells, and that SP phenotype is regarded as a candidate purification marker for stem cells. In this research, murine fertilized ova (including conjugate and single nucleus fertilized ova), 2-cell stage and 8-cell stage blastomeres, morulas and blastocysts were isolated and directly stained by Hoechst 33342 dye. The results show that fertilized ovum, blastomere and morula cells do not demonstrate any ability to efflux the dye. However, the inner cell mass (ICM) cells of blastocyst exhibit SP phenotype, which is consistent with the result of embryonic stem cells (ESCs) in vitro. These results indicate that the SP phenotype of ICM-derived ESCs is an intrinsic property and independent of the culture condition in vitro, and that SP phenotype is one of the characteristics of at least some pluripotent stem cells, but is not shared by totipotent stem cells. In addition, the result that the SP phenotype of ICM cells disappeared when the inhibitor verapamil was added into medium implies that the SP phenotype is directly associated with ABCG2. These results suggest that not all the stem cells demonstrate SP phenotype, and that SP phenotype might act as a purification marker for partial stem cells such as some pluripotent embryonic stem cells and multipotent adult stem cells, but not for all stem cells exampled by the totipotent stem cells in the very early stage of mouse embryos.

  7. 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.

  8. 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

  9. 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.

  10. A single amino acid mutation alters the capsid protein electrophoretic double-band phenotype of the Plum pox virus strain PPV-Rec.

    PubMed

    Subr, Z W; Kamencayová, M; Nováková, S; Nagyová, A; Nosek, J; Glasa, M

    2010-07-01

    Plum pox virus (PPV) isolates differ by their capsid protein (CP) mobility in SDS-PAGE. These electrophoretic phenotypes are likely to result from post-translational modifications of the CP. We demonstrated that the CP mobility was solely determined by the CP N-terminal region. Sequence comparison pinpointed a possible role of mutations at position 66 in determining the CP phenotype of PPV-Rec isolates. Site-directed mutagenesis of a chimeric clone demonstrated that Gly(66) in the CP resulted in the double-band phenotype, while Arg(66) led to a single-band CP pattern, possibly by preventing the phosphorylation of a nearby Ser residue by steric hindrance.

  11. Salt controls endothelial and vascular phenotype.

    PubMed

    Kusche-Vihrog, Kristina; Schmitz, Boris; Brand, Eva

    2015-03-01

    High salt (NaCl) intake promotes the development of vascular diseases independent of a rise in blood pressure, whereas reduction of salt consumption has beneficial effects for the arterial system. This article summarizes our current understanding of the molecular mechanisms of high salt-induced alterations of the endothelial phenotype, the impact of the individual endothelial genotype, and the overall vascular phenotype. We focus on the endothelial Na(+) channel (EnNaC)-controlled nanomechanical properties of the endothelium, since high Na(+) leads to an EnNaC-induced Na(+)-influx and subsequent stiffening of endothelial cells. The mechanical stiffness of the endothelial cell (i.e., the endothelial phenotype) plays a crucial role as it controls the production of the endothelium-derived vasodilator nitric oxide (NO) which directly affects the tone of the vascular smooth muscle cells. In contrast to soft endothelial cells, stiff endothelial cells release reduced amounts of NO, the hallmark of endothelial dysfunction. This endothelium-born process is followed by the development of arterial stiffness (i.e., the vascular phenotype), predicting the development of vascular end-organ damage such as myocardial infarction, stroke, and renal impairment. In this context, we outline the potential clinical implication of direct (amiloride) and indirect (spironolactone) EnNaC inhibition on vascular function. However, interindividual differences exist in the response to high salt intake which involves different endothelial genotypes. Thus, selected genes and genetic variants contributing to the development of salt-induced endothelial dysfunction and hypertension are discussed. In this review, we focus on the role of salt in endothelial and vascular (dys)function and the link between salt-induced changes of the endothelial and vascular phenotype and its clinical implications.

  12. Comparison of phenotypic methods and matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for the identification of aero-tolerant Actinomyces spp. isolated from soft-tissue infections.

    PubMed

    Ng, L S Y; Sim, J H C; Eng, L C; Menon, S; Tan, T Y

    2012-08-01

    Aero-tolerant Actinomyces spp. are an under-recognised cause of cutaneous infections, in part because identification using conventional phenotypic methods is difficult and may be inaccurate. Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is a promising new technique for bacterial identification, but with limited data on the identification of aero-tolerant Actinomyces spp. This study evaluated the accuracy of a phenotypic biochemical kit, MALDI-TOF MS and genotypic identification methods for the identification of this problematic group of organisms. Thirty aero-tolerant Actinomyces spp. were isolated from soft-tissue infections over a 2-year period. Species identification was performed by 16 s rRNA sequencing and genotypic results were compared with results obtained by API Coryne and MALDI-TOF MS. There was poor agreement between API Coryne and genotypic identification, with only 33% of isolates correctly identified to the species level. MALDI-TOF MS correctly identified 97% of isolates to the species level, with 33% of identifications achieved with high confidence scores. MALDI-TOF MS is a promising new tool for the identification of aero-tolerant Actinomyces spp., but improvement of the database is required in order to increase the confidence level of identification.

  13. 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.

  14. 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.

  15. Phenotypic analyses of Agrobacterium.

    PubMed

    Morton, Elise R; Fuqua, Clay

    2012-05-01

    Agrobacterium species are plant-associated relatives of the rhizobia. Several species cause plant diseases such as crown gall and hairy root, although there are also avirulent species. A. tumefaciens is the most intensively studied species and causes crown gall, a neoplastic disease that occurs on a variety of plants. Virulence is specified by large plasmids, and in the case of A. tumefaciens this is called the Ti (tumor-inducing) plasmid. During pathogenesis virulent agrobacteria copy a segment of the Ti plasmid and transfer it to the plant, where it subsequently integrates into the plant genome, and expresses genes that result in the disease symptoms. A. tumefaciens has been used extensively as a plant genetic engineering tool and is also a model microorganism that has been well studied for host-microbe associations, horizontal gene transfer, cell-cell communication, and biofilm formation. This unit describes standard protocols for simple phenotypic characterizations of A. tumefaciens. PMID:22549164

  16. 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

  17. 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

  18. 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

  19. Direct Comparison of Bibliometric Models.

    ERIC Educational Resources Information Center

    Kinnucan, Mark T.; Wolfram, Dietmar

    1990-01-01

    Describes a technique for statistically comparing bibliometric models and illustrates its use with two examples using Lotka's hypothesis of author productivity and one example using library circulation frequencies. Topics discussed include nested statistical models, analysis of variance, regression, log-linear models, and the likelihood ratio…

  20. 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

  1. Phenotype as Agent for Epigenetic Inheritance

    PubMed Central

    Torday, John S.; Miller, William B.

    2016-01-01

    The conventional understanding of phenotype is as a derivative of descent with modification through Darwinian random mutation and natural selection. Recent research has revealed Lamarckian inheritance as a major transgenerational mechanism for environmental action on genomes whose extent is determined, in significant part, by germ line cells during meiosis and subsequent stages of embryological development. In consequence, the role of phenotype can productively be reconsidered. The possibility that phenotype is directed towards the effective acquisition of epigenetic marks in consistent reciprocation with the environment during the life cycle of an organism is explored. It is proposed that phenotype is an active agent in niche construction for the active acquisition of epigenetic marks as a dominant evolutionary mechanism rather than a consequence of Darwinian selection towards reproductive success. The reproductive phase of the life cycle can then be appraised as a robust framework in which epigenetic inheritance is entrained to affect growth and development in continued reciprocal responsiveness to environmental stresses. Furthermore, as first principles of physiology determine the limits of epigenetic inheritance, a coherent justification can thereby be provided for the obligate return of all multicellular eukaryotes to the unicellular state. PMID:27399791

  2. 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.

  3. Phenotype as Agent for Epigenetic Inheritance.

    PubMed

    Torday, John S; Miller, William B

    2016-07-08

    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.

  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. 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

  6. 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

  7. Phenotype and Function of CD209+ Bovine Blood Dendritic Cells, Monocyte-Derived-Dendritic Cells and Monocyte-Derived Macrophages

    PubMed Central

    Bannantine, John P.; Mack, Victoria; Fry, Lindsay M.; Davis, William C.

    2016-01-01

    Phylogenic comparisons of the mononuclear phagocyte system (MPS) of humans and mice demonstrate phenotypic divergence of dendritic cell (DC) subsets that play similar roles in innate and adaptive immunity. Although differing in phenotype, DC can be classified into four groups according to ontogeny and function: conventional DC (cDC1 and cDC2), plasmacytoid DC (pDC), and monocyte derived DC (MoDC). DC of Artiodactyla (pigs and ruminants) can also be sub-classified using this system, allowing direct functional and phenotypic comparison of MoDC and other DC subsets trafficking in blood (bDC). Because of the high volume of blood collections required to study DC, cattle offer the best opportunity to further our understanding of bDC and MoDC function in an outbred large animal species. As reported here, phenotyping DC using a monoclonal antibody (mAb) to CD209 revealed CD209 is expressed on the major myeloid population of DC present in blood and MoDC, providing a phenotypic link between these two subsets. Additionally, the present study demonstrates that CD209 is also expressed on monocyte derived macrophages (MoΦ). Functional analysis revealed each of these populations can take up and process antigens (Ags), present them to CD4 and CD8 T cells, and elicit a T-cell recall response. Thus, bDC, MoDC, and MoΦ pulsed with pathogens or candidate vaccine antigens can be used to study factors that modulate DC-driven T-cell priming and differentiation ex vivo. PMID:27764236

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

    PubMed Central

    Arbogast, Thomas; Ouagazzal, Abdel-Mouttalib; Chevalier, Claire; Kopanitsa, Maksym; Afinowi, Nurudeen; Migliavacca, Eugenia; Cowling, Belinda S.; Birling, Marie-Christine; Champy, Marie-France; Reymond, Alexandre; Herault, Yann

    2016-01-01

    The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+) or a duplication (Dup/+) of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice. PMID:26872257

  9. Consultation and illness behaviour in response to symptoms: a comparison of models from different disciplinary frameworks and suggestions for future research directions.

    PubMed

    Wyke, Sally; Adamson, Joy; Dixon, Diane; Hunt, Kate

    2013-06-01

    We all get ill and social scientific interest in how we respond - the study of illness behaviour - continues unabated. Existing models are useful, but have been developed and applied within disciplinary silos, resulting in wasted intellectual and empirical effort and an absence of accumulation of knowledge across disciplines. We present a critical review and detailed comparison of three process models of response to symptoms: the Illness Action Model, the Common Sense Model of the Self-Regulation of Health and Illness and the Network Episode Model. We suggest an integrated framework in which symptoms, responses and actions are simultaneously interpreted and evaluated in the light of accumulated knowledge and through interactions. Evaluation may be subconscious and is influenced by the extent to which the symptoms impose themselves, expectations of outcomes, the resources available and understanding of symptoms' salience and possible outcomes. Actions taken are part of a process of problem solving through which both individuals and their immediate social network seek to (re)achieve 'normality'. Response is also influenced by social structure (directly and indirectly), cultural expectations of health, the meaning of symptoms, and access to and understandings of the legitimate use of services. Changes in knowledge, in embodied state and in emotions can all be directly influential at any point. We do not underestimate the difficulty of operationalising an integrated framework at different levels of analysis. Attempts to do so will require us to move easily between disciplinary understandings to conduct prospective, longitudinal, research that uses novel methodologies to investigate response to symptoms in the context of affective as well as cognitive responses and interactions within social networks. While challenging such an approach would facilitate accumulation of knowledge across disciplines and enable movement beyond description to change in individual and

  10. 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.

  11. A comparison of 67Cu- and 131I-labelled forms of monoclonal antibodies SEN7 and SWA20 directed against small-cell lung cancer.

    PubMed

    Smith, A; Zangemeister-Wittke, U; Waibel, R; Schenker, T; Schubiger, P A; Stahel, R A

    1994-01-01

    The intact anti-SCLC monoclonal antibody (MAb) SEN7 and its F(ab')2 were labelled with the beta-emitting isotope 67Cu. Both materials retained their biological activity in vitro as determined by the Lindmo assay. In a direct comparison of in vivo distribution in a xenograph model, 131I- and 67Cu-labelled intact SEN7 showed similar absolute tumour accumulation. Blood levels were markedly lower in the case of the 67Cu-labelled antibody, resulting in improved tumour:blood ratios which reached a maximum of 13:1 compared with only 4.5:1 for 131I-SEN7. In the case of the 67Cu-labelled F(ab')2, very high accumulation of the nuclide was observed in the kidney. Levels of radio copper in liver and spleen were also found to be significantly raised when compared with radio iodine. SWA20, a MAb which had previously failed to show any selective in vivo accumulation in tumour xenografts when labelled with radio iodine showed higher and more stable tumour accumulation when labelled with 67Cu.

  12. 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

  13. 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

  14. Assessing the effects of cognitive experiments on the welfare of captive chimpanzees (Pan troglodytes) by direct comparison of activity budget between wild and captive chimpanzees.

    PubMed

    Yamanashi, Yumi; Hayashi, Misato

    2011-12-01

    We investigated the effects of cognitive experiments by direct comparison of activity budgets between wild and captive chimpanzees. One goal of captive management is to ensure that the activity budgets of captive animals are as similar as possible to those of their wild counterparts. However, such similarity has rarely been achieved. We compared the activity budget among three groups of chimpanzees: wild chimpanzees in Bossou (Guinea, n = 10), and captive chimpanzees who participated in cognitive experiments (experimental chimpanzees, n = 6) or did not participate in the experiments (nonexperimental chimpanzees, n = 6) at the Primate Research Institute (Japan). The experimental chimpanzees voluntarily participated in computer-controlled cognitive tasks and small pieces of fruits were provided as rewards. The data from captivity were obtained on the experimental days (weekdays) and nonexperimental days (weekends). In both study sites, we followed each chimpanzee from about 7 a.m. until the time when chimpanzees started to rest in the evening. The behaviors were recorded every 1 min. The results showed that on weekdays, feeding time and resting time of the experimental chimpanzees were almost the same as those of wild chimpanzees. However, for the nonexperimental chimpanzees, feeding time was significantly shorter and resting time was longer than those of the wild chimpanzees. In contrast, no difference was found in feeding time or resting time of the two groups of captive chimpanzees on weekends. The results suggested that the cognitive experiments worked as an efficient method for food-based enrichment.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. MPHASYS: a mouse phenotype analysis system

    PubMed Central

    Calder, R Brent; Beems, Rudolf B; van Steeg, Harry; Mian, I Saira; Lohman, Paul HM; Vijg, Jan

    2007-01-01

    Background Systematic, high-throughput studies of mouse phenotypes have been hampered by the inability to analyze individual animal data from a multitude of sources in an integrated manner. Studies generally make comparisons at the level of genotype or treatment thereby excluding associations that may be subtle or involve compound phenotypes. Additionally, the lack of integrated, standardized ontologies and methodologies for data exchange has inhibited scientific collaboration and discovery. Results Here we introduce a Mouse Phenotype Analysis System (MPHASYS), a platform for integrating data generated by studies of mouse models of human biology and disease such as aging and cancer. This computational platform is designed to provide a standardized methodology for working with animal data; a framework for data entry, analysis and sharing; and ontologies and methodologies for ensuring accurate data capture. We describe the tools that currently comprise MPHASYS, primarily ones related to mouse pathology, and outline its use in a study of individual animal-specific patterns of multiple pathology in mice harboring a specific germline mutation in the DNA repair and transcription-specific gene Xpd. Conclusion MPHASYS is a system for analyzing multiple data types from individual animals. It provides a framework for developing data analysis applications, and tools for collecting and distributing high-quality data. The software is platform independent and freely available under an open-source license [1]. PMID:17553167

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

    PubMed

    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

    2015-08-01

    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.

  2. 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

  3. The evolutionary consequences of ecological interactions mediated through phenotypic plasticity.

    PubMed

    Fordyce, James A

    2006-06-01

    Phenotypic plasticity describes the capacity of a genotype to exhibit a range of phenotypes in response to variation in the environment. Environmental variation encompasses both abiotic and biotic components of the environment, including interactions among organisms. The strength and outcome of many ecological interactions, ranging from antagonism to mutualism, are mediated through the phenotypically plastic responses of one or more players in the interaction. Herein, three broadly defined, non-mutually exclusive, evolutionary consequences of ecological interactions mediated through phenotypic plasticity are discussed. (1) The predictable plastic response of one partner can favor behaviors, physiological responses, and life history traits of an interacting partner that manipulate, circumvent, or ameliorate the response of that partner. (2) Phenotypic plasticity can generate substantial spatial and temporal variation within and among populations. Such phenotypic variation can depend on the density and identity of interacting players in an ecological community, and can ultimately affect the evolutionary outcome of ecological interactions. (3) Phenotypic plasticity affects the strength and direction of natural selection. Ecological interactions mediated through phenotypic plasticity are ubiquitous in nature, and the potential evolutionary consequences of these interactions illustrate the complexity inherent in understanding evolution in a community context.

  4. A direct comparison of a depth-dependent Radiation stress formulation and a Vortex force formulation within a three-dimensional coastal ocean model

    NASA Astrophysics Data System (ADS)

    Moghimi, Saeed; Klingbeil, Knut; Gräwe, Ulf; Burchard, Hans

    2013-10-01

    In this study a model system consisting of the three-dimensional General Estuarine Transport Model (GETM) and the third generation wind wave model SWAN was developed. Both models were coupled in two-way mode. The effects of waves were included into the ocean model by implementing the depth-dependent Radiation stress formulation (RS) of Mellor (2011a) and the Vortex force formulation (VF) presented by Bennis et al. (2011). Thus, the developed model system offers a direct comparison of these two formulations. The enhancement of the vertical eddy viscosity due to the energy transfer by white capping and breaking waves was taken into account by means of injecting turbulent kinetic energy at the surface. Wave-current interaction inside the bottom boundary layer was considered as well. The implementation of both wave-averaged formulations was validated against three flume experiments. One of these experiments with long period surface waves (swell), had not been evaluated before. The validation showed the capability of the model system to reproduce the three-dimensional interaction of waves and currents. For the flume test cases the wave-induced water level changes (wave set-up and set-down) and the corresponding depth-integrated wave-averaged velocities were similar for RS and VF. Both formulations produced comparable velocity profiles for short period waves. However, for large period waves, VF overestimated the wave set-down near the main breaking points and RS showed artificial offshore-directed transport at the surface where wave shoaling was taking place. Finally the validated model system was applied to a realistic barred beach scenario. For RS and VF the resulting velocity profiles were similar after being significantly improved by a roller evolution method. Both wave-averaged formulations generally provided similar results, but some shortcomings were revealed. Although VF partly showed significant deviations from the measurements, its results were still physically

  5. 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.

  6. 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

  7. The Broad Autism Phenotype Questionnaire

    ERIC Educational Resources Information Center

    Hurley, Robert S. E.; Losh, Molly; Parlier, Morgan; Reznick, J. Steven; Piven, Joseph

    2007-01-01

    The broad autism phenotype (BAP) is a set of personality and language characteristics that reflect the phenotypic expression of the genetic liability to autism, in non-autistic relatives of autistic individuals. These characteristics are milder but qualitatively similar to the defining features of autism. A new instrument designed to measure the…

  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. A direct morphometric comparison of five labeling protocols for multi-atlas driven automatic segmentation of the hippocampus in Alzheimer's disease.

    PubMed

    Nestor, Sean M; Gibson, Erin; Gao, Fu-Qiang; Kiss, Alex; Black, Sandra E

    2013-02-01

    Hippocampal volumetry derived from structural MRI is increasingly used to delineate regions of interest for functional measurements, assess efficacy in therapeutic trials of Alzheimer's disease (AD) and has been endorsed by the new AD diagnostic guidelines as a radiological marker of disease progression. Unfortunately, morphological heterogeneity in AD can prevent accurate demarcation of the hippocampus. Recent developments in automated volumetry commonly use multi-template fusion driven by expert manual labels, enabling highly accurate and reproducible segmentation in disease and healthy subjects. However, there are several protocols to define the hippocampus anatomically in vivo, and the method used to generate atlases may impact automatic accuracy and sensitivity - particularly in pathologically heterogeneous samples. Here we report a fully automated segmentation technique that provides a robust platform to directly evaluate both technical and biomarker performance in AD among anatomically unique labeling protocols. For the first time we test head-to-head the performance of five common hippocampal labeling protocols for multi-atlas based segmentation, using both the Sunnybrook Longitudinal Dementia Study and the entire Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) baseline and 24-month dataset. We based these atlas libraries on the protocols of (Haller et al., 1997; Killiany et al., 1993; Malykhin et al., 2007; Pantel et al., 2000; Pruessner et al., 2000), and a single operator performed all manual tracings to generate de facto "ground truth" labels. All methods distinguished between normal elders, mild cognitive impairment (MCI), and AD in the expected directions, and showed comparable correlations with measures of episodic memory performance. Only more inclusive protocols distinguished between stable MCI and MCI-to-AD converters, and had slightly better associations with episodic memory. Moreover, we demonstrate that protocols including more posterior

  10. Quantification of the Relative Biological Effectiveness for Ion Beam Radiotherapy: Direct Experimental Comparison of Proton and Carbon Ion Beams and a Novel Approach for Treatment Planning

    SciTech Connect

    Elsaesser, Thilo; Weyrather, Wilma K.; Friedrich, Thomas; Durante, Marco; Iancu, Gheorghe; Kraemer, Michael; Kragl, Gabriele; Brons, Stephan; Winter, Marcus; Weber, Klaus-Josef; Scholz, Michael

    2010-11-15

    Purpose: To present the first direct experimental in vitro comparison of the biological effectiveness of range-equivalent protons and carbon ion beams for Chinese hamster ovary cells exposed in a three-dimensional phantom using a pencil beam scanning technique and to compare the experimental data with a novel biophysical model. Methods and Materials: Cell survival was measured in the phantom after irradiation with two opposing fields, thus mimicking the typical patient treatment scenario. The novel biophysical model represents a substantial extension of the local effect model, previously used for treatment planning in carbon ion therapy for more than 400 patients, and potentially can be used to predict effectiveness of all ion species relevant for radiotherapy. A key feature of the new approach is the more sophisticated consideration of spatially correlated damage induced by ion irradiation. Results: The experimental data obtained for Chinese hamster ovary cells clearly demonstrate that higher cell killing is achieved in the target region with carbon ions as compared with protons when the effects in the entrance channel are comparable. The model predictions demonstrate agreement with these experimental data and with data obtained with helium ions under similar conditions. Good agreement is also achieved with relative biological effectiveness values reported in the literature for other cell lines for monoenergetic proton, helium, and carbon ions. Conclusion: Both the experimental data and the new modeling approach are supportive of the advantages of carbon ions as compared with protons for treatment-like field configurations. Because the model predicts the effectiveness for several ion species with similar accuracy, it represents a powerful tool for further optimization and utilization of the potential of ion beams in tumor therapy.

  11. Comparison of a direct-reading device to gravimetric methods for evaluating organic dust aerosols in an enclosed swine production environment.

    PubMed

    Taylor, C D; Reynolds, S J

    2001-01-01

    The production of livestock in enclosed facilities has become an accepted practice, driven by the need for increased efficiency. Exposure to organic dusts, containing various bioactive components, has been identified an important risk factor for the high rate of lung disease found among workers in these environments. Assessment of organic dust exposure requires technical skills and instrumentation not readily available to most agricultural enterprises. Development of a simple, cost-effective method for measuring organic dust levels would be useful in evaluating and controlling exposures in these environments. The objective of this study was to evaluate the usefulness of the direct reading MIE PDM-3 Miniram for estimating organic dust concentrations in enclosed swine production facilities. Responses from the MIE PDM-3 Miniram were compared to gravimetric methods for total and inhalable dust. Total dust determinations were conducted in accordance with the National Institute for Occupational Safety and Health (NIOSH) method 0500. Inhalable particulate mass (IPM) sampling was conducted using SKC brand IOM (Institute of Occupational Medicine) sampling cassettes, which meet the American Conference of Governmental Industrial Hygienists ACGIH criteria for inhalable dust sampling. This study design also allowed for the comparison of traditional total dust method to the IPM method, in collecting organic dusts in an agricultural setting. Fifteen sets of side-by-side samples (Miniram, total dust, and IPM) were collected over a period of six months in a swine confinement building. There were statistically significant differences in the results provided by the three sampling methods. Measurements for inhalable dust exceeded those for total dust in eleven of fifteen samples. The Miniram time-weighted average (TWA) response to the organic dust was always the lower of the three methods. A high degree of correlation was found among all three methods. The Miniram performed well under

  12. Molecular Anchors for Self-Assembled Monolayers on ZnO: A Direct Comparison of the Thiol and Phosphic Acid Moieties

    SciTech Connect

    Perkins, C. L.

    2009-01-01

    Two of the most promising schemes for attaching organic molecules to metal oxides are based on the chemistry of the thiol and phosphonic acid moieties. We have made a direct comparison of the efficacy of these two molecular anchors on zinc oxide by comparing the chemical and physical properties of n-hexane derivatives of both. The surface properties of polycrystalline ZnO thin films and ZnO(000)-O crystals modified with 1-hexanethiol and 1-hexanephosphonic acid were examined with a novel quartz crystal microbalance (QCM)-based flow cell reactor, angle-resolved and temperature-dependent photoelectron spectroscopy, and contact angle measurements. A means of using ammonium chloride as a probe of molecule-ZnO interactions is introduced and used to ascertain the relative quality of self-assembled monolayers (SAMs) based on thiols and phosphonic acids. QCM data shows that a phosphonic acid-anchored alkyl chain only six carbons long can provide significant corrosion protection for ZnO against Bronsted acids, reducing the etch rate relative to the bare ZnO surface by a factor of more than nine. In contrast, we find that monolayers from the analogous molecule hexanethiol are more defective as revealed by their higher ionic permeability and lower hydrophobicity. Substrate attenuation X-ray photoelectron spectroscopy (XPS) experiments were used to determine the thickness of SAMs formed by the two hexane derivatives and it was found that SAMs from phosphonic acids were approximately twice as thick as those formed by hexanethiol. The thermal stability of the two linking groups was also explored and we find that previous claims of highly stable alkanethiolate monolayers on ZnO are suspect. Taken as a whole, our results indicate that the phosphonic acid moiety is preferred over thiols for the attachment of short alkyl groups to ZnO.

  13. Comparison of alteration of cell surface carbohydrates of the chinchilla tubotympanum and colonial opacity phenotype of Streptococcus pneumoniae during experimental pneumococcal otitis media with or without an antecedent influenza A virus infection.

    PubMed

    Tong, H H; Grants, I; Liu, X; DeMaria, T F

    2002-08-01

    Experimental and clinical studies suggest that influenza A virus promotes Streptococcus pneumoniae-induced otitis media; however, the mechanism underlying this synergistic interaction has not been completely defined. In this study, glycoconjugate expression patterns were evaluated on the cell surface in the chinchilla eustachian tube (ET) lumen of a cohort challenged intranasally (i.n.) with S. pneumoniae type 6A, which is predominantly transparent and a cohort with an antecedent influenza A virus infection, followed by i.n. inoculation with S. pneumoniae. The labeling patterns obtained with six lectin probes revealed that the binding of Bandeiraea simplicifolia lectin II, succinylated wheat germ agglutinin, and peanut agglutinin were significantly increased in the lumenal surface of the ET in the cohort infected with both pathogens compared to the cohort inoculated with only S. pneumoniae, which indicated that N-acetylglucosamine (GlcNAc) and D-galactose residues were exposed. A significant decreased labeling with Sambucus nigra agglutinin in the combined influenza A virus and pneumococcus infection cohort suggested that there were few sialic acid residues remaining in the ET epithelium. In addition, the colonial opacity of S. pneumoniae during the disease course was examined. The opaque phenotype was predominant among the pneumococcus isolates from the middle-ear fluid in the cohort infected with the both pathogens. Together, these data suggest that the synergic effect of influenza A virus and S. pneumoniae on the changes of the carbohydrate moieties in the ET epithelium and that the selection of the opaque variant may facilitate the pneumococcal invasion of the middle ear.

  14. Finding our way through phenotypes.

    PubMed

    Deans, Andrew R; Lewis, Suzanna E; Huala, Eva; Anzaldo, Salvatore S; Ashburner, Michael; Balhoff, James P; Blackburn, David C; Blake, Judith A; Burleigh, J Gordon; Chanet, Bruno; Cooper, Laurel D; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E; Dumontier, Michel; Franz, Nico M; Friedrich, Frank; Gkoutos, George V; Haendel, Melissa; Harmon, Luke J; Hayamizu, Terry F; He, Yongqun; Hines, Heather M; Ibrahim, Nizar; Jackson, Laura M; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J; Le Novère, Nicolas; Lundberg, John G; Macklin, James; Mast, Austin R; Midford, Peter E; Mikó, István; Mungall, Christopher J; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J; Richter, Stefan; Robinson, Peter N; Ruttenberg, Alan; Schulz, Katja S; Segerdell, Erik; Seltmann, Katja C; Sharkey, Michael J; Smith, Aaron D; Smith, Barry; Specht, Chelsea D; Squires, R Burke; Thacker, Robert W; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D; Vogt, Lars; Wall, Christine E; Walls, Ramona L; Westerfeld, Monte; Wharton, Robert A; Wirkner, Christian S; Woolley, James B; Yoder, Matthew J; Zorn, Aaron M; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

  15. Finding Our Way through Phenotypes

    PubMed Central

    Deans, Andrew R.; Lewis, Suzanna E.; Huala, Eva; Anzaldo, Salvatore S.; Ashburner, Michael; Balhoff, James P.; Blackburn, David C.; Blake, Judith A.; Burleigh, J. Gordon; Chanet, Bruno; Cooper, Laurel D.; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T. Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E.; Dumontier, Michel; Franz, Nico M.; Friedrich, Frank; Gkoutos, George V.; Haendel, Melissa; Harmon, Luke J.; Hayamizu, Terry F.; He, Yongqun; Hines, Heather M.; Ibrahim, Nizar; Jackson, Laura M.; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J.; Le Novère, Nicolas; Lundberg, John G.; Macklin, James; Mast, Austin R.; Midford, Peter E.; Mikó, István; Mungall, Christopher J.; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J.; Richter, Stefan; Robinson, Peter N.; Ruttenberg, Alan; Schulz, Katja S.; Segerdell, Erik; Seltmann, Katja C.; Sharkey, Michael J.; Smith, Aaron D.; Smith, Barry; Specht, Chelsea D.; Squires, R. Burke; Thacker, Robert W.; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D.; Vogt, Lars; Wall, Christine E.; Walls, Ramona L.; Westerfeld, Monte; Wharton, Robert A.; Wirkner, Christian S.; Woolley, James B.; Yoder, Matthew J.; Zorn, Aaron M.; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

  16. Finding our way through phenotypes.

    PubMed

    Deans, Andrew R; Lewis, Suzanna E; Huala, Eva; Anzaldo, Salvatore S; Ashburner, Michael; Balhoff, James P; Blackburn, David C; Blake, Judith A; Burleigh, J Gordon; Chanet, Bruno; Cooper, Laurel D; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E; Dumontier, Michel; Franz, Nico M; Friedrich, Frank; Gkoutos, George V; Haendel, Melissa; Harmon, Luke J; Hayamizu, Terry F; He, Yongqun; Hines, Heather M; Ibrahim, Nizar; Jackson, Laura M; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J; Le Novère, Nicolas; Lundberg, John G; Macklin, James; Mast, Austin R; Midford, Peter E; Mikó, István; Mungall, Christopher J; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J; Richter, Stefan; Robinson, Peter N; Ruttenberg, Alan; Schulz, Katja S; Segerdell, Erik; Seltmann, Katja C; Sharkey, Michael J; Smith, Aaron D; Smith, Barry; Specht, Chelsea D; Squires, R Burke; Thacker, Robert W; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D; Vogt, Lars; Wall, Christine E; Walls, Ramona L; Westerfeld, Monte; Wharton, Robert A; Wirkner, Christian S; Woolley, James B; Yoder, Matthew J; Zorn, Aaron M; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

  17. Characterization of systemic metabolic phenotypes associated with subclinical atherosclerosis.

    PubMed

    Würtz, Peter; Soininen, Pasi; Kangas, Antti J; Mäkinen, Ville-Petteri; Groop, Per-Henrik; Savolainen, Markku J; Juonala, Markus; Viikari, Jorma S; Kähönen, Mika; Lehtimäki, Terho; Raitakari, Olli T; Ala-Korpela, Mika

    2011-02-01

    Detailed molecular phenotyping gives insight into disease mechanisms and can individualize medical practice for improved risk assessment and treatment. We show in an epidemiological study (n = 4309) that the multi-metabolic profiles obtained by serum NMR metabonomics inherently associate with the extent of atherosclerosis already in preclinical stages. Data-driven analysis of the spectral profiles of healthy, young adults revealed three distinct metabolic phenotypes associated with high carotid intima-media thickness (IMT), a surrogate marker of cardiovascular disease. The phenotypes were characterized by varying combinations of well-known metabolic disturbances like elevated VLDL and LDL and low HDL levels. Low IMT was also associated with distinct metabolic phenotypes with lipoprotein as well as other biochemical characteristics partly opposing those found for the high IMT phenotypes. Profiles of low-molecular-weight metabolites quantified from the experimentation were also characteristic for the metabolic phenotypes and substantiate developments toward the use of multi-metabolic risk phenotypes. The methodology can be taken as a direct extension for the routine analytics used for the risk assessment of atherosclerosis; quantification of metabolites will complement and might even replace conventional lipid measurements. Serum NMR metabonomics is therefore anticipated as a rational option for comprehensive cardiovascular risk assessment.

  18. Regulatory mechanisms link phenotypic plasticity to evolvability

    PubMed Central

    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

  19. The Evolutionary Potential of Phenotypic Mutations

    PubMed Central

    Yanagida, Hayato; Gispan, Ariel; Kadouri, Noam; Rozen, Shelly; Sharon, Michal; Barkai, Naama; Tawfik, Dan S.

    2015-01-01

    Errors in protein synthesis, so-called phenotypic mutations, are orders-of-magnitude more frequent than genetic mutations. Here, we provide direct evidence that alternative protein forms and phenotypic variability derived from translational errors paved the path to genetic, evolutionary adaptations via gene duplication. We explored the evolutionary origins of Saccharomyces cerevisiae IDP3 - an NADP-dependent isocitrate dehydrogenase mediating fatty acids ß-oxidation in the peroxisome. Following the yeast whole genome duplication, IDP3 diverged from a cytosolic ancestral gene by acquisition of a C-terminal peroxisomal targeting signal. We discovered that the pre-duplicated cytosolic IDPs are partially localized to the peroxisome owing to +1 translational frameshifts that bypass the stop codon and unveil cryptic peroxisomal targeting signals within the 3’-UTR. Exploring putative cryptic signals in all 3’-UTRs of yeast genomes, we found that other enzymes related to NADPH production such as pyruvate carboxylase 1 (PYC1) might be prone to peroxisomal localization via cryptic signals. Using laboratory evolution we found that these translational frameshifts are rapidly imprinted via genetic single base deletions occurring within the very same gene location. Further, as exemplified here, the sequences that promote translational frameshifts are also more prone to genetic deletions. Thus, genotypes conferring higher phenotypic variability not only meet immediate challenges by unveiling cryptic 3’-UTR sequences, but also boost the potential for future genetic adaptations. PMID:26244544

  20. The Evolutionary Potential of Phenotypic Mutations.

    PubMed

    Yanagida, Hayato; Gispan, Ariel; Kadouri, Noam; Rozen, Shelly; Sharon, Michal; Barkai, Naama; Tawfik, Dan S

    2015-08-01

    Errors in protein synthesis, so-called phenotypic mutations, are orders-of-magnitude more frequent than genetic mutations. Here, we provide direct evidence that alternative protein forms and phenotypic variability derived from translational errors paved the path to genetic, evolutionary adaptations via gene duplication. We explored the evolutionary origins of Saccharomyces cerevisiae IDP3 - an NADP-dependent isocitrate dehydrogenase mediating fatty acids ß-oxidation in the peroxisome. Following the yeast whole genome duplication, IDP3 diverged from a cytosolic ancestral gene by acquisition of a C-terminal peroxisomal targeting signal. We discovered that the pre-duplicated cytosolic IDPs are partially localized to the peroxisome owing to +1 translational frameshifts that bypass the stop codon and unveil cryptic peroxisomal targeting signals within the 3'-UTR. Exploring putative cryptic signals in all 3'-UTRs of yeast genomes, we found that other enzymes related to NADPH production such as pyruvate carboxylase 1 (PYC1) might be prone to peroxisomal localization via cryptic signals. Using laboratory evolution we found that these translational frameshifts are rapidly imprinted via genetic single base deletions occurring within the very same gene location. Further, as exemplified here, the sequences that promote translational frameshifts are also more prone to genetic deletions. Thus, genotypes conferring higher phenotypic variability not only meet immediate challenges by unveiling cryptic 3'-UTR sequences, but also boost the potential for future genetic adaptations.

  1. Genetic and Phenotypic Characterization of a Salmonella enterica serovar Enteritidis Emerging Strain with Superior Intra-macrophage Replication Phenotype

    PubMed Central

    Shomer, Inna; Avisar, Alon; Desai, Prerak; Azriel, Shalhevet; Smollan, Gill; Belausov, Natasha; Keller, Nathan; Glikman, Daniel; Maor, Yasmin; Peretz, Avi; McClelland, Michael; Rahav, Galia; Gal-Mor, Ohad

    2016-01-01

    Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the ubiquitous Salmonella serovars worldwide and a major cause of food-born outbreaks, which are often associated with poultry and poultry derivatives. Here we report a nation-wide S. Enteritidis clonal outbreak that occurred in Israel during the last third of 2015. Pulsed field gel electrophoresis and whole genome sequencing identified genetically related strains that were circulating in Israel as early as 2008. Global comparison linked this outbreak strain to several clinical and marine environmental isolates that were previously isolated in California and Canada, indicating that similar strains are prevalent outside of Israel. Phenotypic comparison between the 2015 outbreak strain and other clinical and reference S. Enteritidis strains showed only limited intra-serovar phenotypic variation in growth in rich medium, invasion into Caco-2 cells, uptake by J774.1A macrophages, and host cell cytotoxicity. In contrast, significant phenotypic variation was shown among different S. Enteritidis isolates when biofilm-formation, motility, invasion into HeLa cells and uptake by THP-1 human macrophages were studied. Interestingly, the 2015 outbreak clone was found to possess superior intra-macrophage replication ability within both murine and human macrophages in comparison to the other S. Enteritidis strains studied. This phenotype is likely to play a role in the virulence and host-pathogen interactions of this emerging clone. PMID:27695450

  2. Genetic and Phenotypic Characterization of a Salmonella enterica serovar Enteritidis Emerging Strain with Superior Intra-macrophage Replication Phenotype

    PubMed Central

    Shomer, Inna; Avisar, Alon; Desai, Prerak; Azriel, Shalhevet; Smollan, Gill; Belausov, Natasha; Keller, Nathan; Glikman, Daniel; Maor, Yasmin; Peretz, Avi; McClelland, Michael; Rahav, Galia; Gal-Mor, Ohad

    2016-01-01

    Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the ubiquitous Salmonella serovars worldwide and a major cause of food-born outbreaks, which are often associated with poultry and poultry derivatives. Here we report a nation-wide S. Enteritidis clonal outbreak that occurred in Israel during the last third of 2015. Pulsed field gel electrophoresis and whole genome sequencing identified genetically related strains that were circulating in Israel as early as 2008. Global comparison linked this outbreak strain to several clinical and marine environmental isolates that were previously isolated in California and Canada, indicating that similar strains are prevalent outside of Israel. Phenotypic comparison between the 2015 outbreak strain and other clinical and reference S. Enteritidis strains showed only limited intra-serovar phenotypic variation in growth in rich medium, invasion into Caco-2 cells, uptake by J774.1A macrophages, and host cell cytotoxicity. In contrast, significant phenotypic variation was shown among different S. Enteritidis isolates when biofilm-formation, motility, invasion into HeLa cells and uptake by THP-1 human macrophages were studied. Interestingly, the 2015 outbreak clone was found to possess superior intra-macrophage replication ability within both murine and human macrophages in comparison to the other S. Enteritidis strains studied. This phenotype is likely to play a role in the virulence and host-pathogen interactions of this emerging clone.

  3. The digital revolution in phenotyping

    PubMed Central

    Oellrich, Anika; Collier, Nigel; Groza, Tudor; Rebholz-Schuhmann, Dietrich; Shah, Nigam; Bodenreider, Olivier; Boland, Mary Regina; Georgiev, Ivo; Liu, Hongfang; Livingston, Kevin; Luna, Augustin; Mallon, Ann-Marie; Manda, Prashanti; Robinson, Peter N.; Rustici, Gabriella; Simon, Michelle; Wang, Liqin; Winnenburg, Rainer; Dumontier, Michel

    2016-01-01

    Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, defined as observable characteristics of organisms, can be seen as one of the bridges that lead to a translation of experimental findings into clinical applications and thereby support ‘bench to bedside’ efforts. However, to build this translational bridge, a common and universal understanding of phenotypes is required that goes beyond domain-specific definitions. To achieve this ambitious goal, a digital revolution is ongoing that enables the encoding of data in computer-readable formats and the data storage in specialized repositories, ready for integration, enabling translational research. While phenome research is an ongoing endeavor, the true potential hidden in the currently available data still needs to be unlocked, offering exciting opportunities for the forthcoming years. Here, we provide insights into the state-of-the-art in digital phenotyping, by means of representing, acquiring and analyzing phenotype data. In addition, we provide visions of this field for future research work that could enable better applications of phenotype data. PMID:26420780

  4. Toward composite molecular signatures in the phenotyping of asthma.

    PubMed

    Wagener, Ariane H; Yick, Ching Yong; Brinkman, Paul; van der Schee, Marc P; Fens, Niki; Sterk, Peter J

    2013-12-01

    The complex biology of respiratory diseases such as asthma is feeding the discovery of various disease phenotypes. Although the clinical management of asthma phenotypes by using a single biomarker (e.g., sputum eosinophils) is successful, emerging evidence shows the requirement of multiscale, high-dimensional biological and clinical measurements to capture the complexity of various asthma phenotypes. High-throughput "omics" technologies, including transcriptomics, proteomics, lipidomics, and metabolomics, are increasingly standardized for biomarker discovery in asthma. The leading principle is obeying available guidelines on omics analysis, thereby strictly limiting false discovery. In this review we address the concept of transcriptomics using microarrays or next-generation RNA sequencing and their applications in asthma, highlighting the strengths and limitations of both techniques, and review metabolomics in exhaled air (breathomics) as a noninvasive alternative for sampling the airways directly. These developments will inevitably lead to the integration of molecular signatures in the phenotyping of asthma and other diseases.

  5. Variation in Plasmodium falciparum Erythrocyte Invasion Phenotypes and Merozoite Ligand Gene Expression across Different Populations in Areas of Malaria Endemicity

    PubMed Central

    Bowyer, Paul W.; Stewart, Lindsay B.; Aspeling-Jones, Harvey; Mensah-Brown, Henrietta E.; Ahouidi, Ambroise D.; Amambua-Ngwa, Alfred; Awandare, Gordon A.

    2015-01-01

    Plasmodium falciparum merozoites use diverse alternative erythrocyte receptors for invasion and variably express cognate ligands encoded by the erythrocyte binding antigen (eba) and reticulocyte binding-like homologue (Rh) gene families. Previous analyses conducted on parasites from single populations in areas of endemicity revealed a wide spectrum of invasion phenotypes and expression profiles, although comparisons across studies have been limited by the use of different protocols. For direct comparisons within and among populations, clinical isolates from three different West African sites of endemicity (in Ghana, Guinea, and Senegal) were cryopreserved and cultured ex vivo after thawing in a single laboratory to assay invasion of target erythrocytes pretreated with enzymes affecting receptor subsets. Complete invasion assay data from 67 isolates showed no differences among the populations in the broad range of phenotypes measured by neuraminidase treatment (overall mean, 40.6% inhibition) or trypsin treatment (overall mean, 83.3% inhibition). The effects of chymotrypsin treatment (overall mean, 79.2% inhibition) showed heterogeneity across populations (Kruskall-Wallis P = 0.023), although the full phenotypic range was seen in each. Schizont-stage transcript data for a panel of 8 invasion ligand genes (eba175, eba140, eba181, Rh1, Rh2a, Rh2b, Rh4, and Rh5) were obtained for 37 isolates, showing similar ranges of variation in each population except that eba175 levels tended to be higher in parasites from Ghana than in those from Senegal (whereas levels of eba181 and Rh2b were lower in parasites from Ghana). The broad diversity in invasion phenotypes and gene expression seen within each local population, with minimal differences among them, is consistent with a hypothesis of immune selection maintaining parasite variation. PMID:25870227

  6. Variation in Plasmodium falciparum erythrocyte invasion phenotypes and merozoite ligand gene expression across different populations in areas of malaria endemicity.

    PubMed

    Bowyer, Paul W; Stewart, Lindsay B; Aspeling-Jones, Harvey; Mensah-Brown, Henrietta E; Ahouidi, Ambroise D; Amambua-Ngwa, Alfred; Awandare, Gordon A; Conway, David J

    2015-06-01

    Plasmodium falciparum merozoites use diverse alternative erythrocyte receptors for invasion and variably express cognate ligands encoded by the erythrocyte binding antigen (eba) and reticulocyte binding-like homologue (Rh) gene families. Previous analyses conducted on parasites from single populations in areas of endemicity revealed a wide spectrum of invasion phenotypes and expression profiles, although comparisons across studies have been limited by the use of different protocols. For direct comparisons within and among populations, clinical isolates from three different West African sites of endemicity (in Ghana, Guinea, and Senegal) were cryopreserved and cultured ex vivo after thawing in a single laboratory to assay invasion of target erythrocytes pretreated with enzymes affecting receptor subsets. Complete invasion assay data from 67 isolates showed no differences among the populations in the broad range of phenotypes measured by neuraminidase treatment (overall mean, 40.6% inhibition) or trypsin treatment (overall mean, 83.3% inhibition). The effects of chymotrypsin treatment (overall mean, 79.2% inhibition) showed heterogeneity across populations (Kruskall-Wallis P = 0.023), although the full phenotypic range was seen in each. Schizont-stage transcript data for a panel of 8 invasion ligand genes (eba175, eba140, eba181, Rh1, Rh2a, Rh2b, Rh4, and Rh5) were obtained for 37 isolates, showing similar ranges of variation in each population except that eba175 levels tended to be higher in parasites from Ghana than in those from Senegal (whereas levels of eba181 and Rh2b were lower in parasites from Ghana). The broad diversity in invasion phenotypes and gene expression seen within each local population, with minimal differences among them, is consistent with a hypothesis of immune selection maintaining parasite variation.

  7. Refined Phenotyping of Modic Changes

    PubMed Central

    Määttä, Juhani H.; Karppinen, Jaro; Paananen, Markus; Bow, Cora; Luk, Keith D.K.; Cheung, Kenneth M.C.; Samartzis, Dino

    2016-01-01

    . The strength of the associations increased with the number of MC. This large-scale study is the first to definitively note MC types and specific morphologies to be independently associated with prolonged severe LBP and back-related disability. This proposed refined MC phenotype may have direct implications in clinical decision-making as to the development and management of LBP. Understanding of these imaging biomarkers can lead to new preventative and personalized therapeutics related to LBP. PMID:27258491

  8. Glaucoma: genes, phenotypes, and new directions for therapy

    PubMed Central

    Fan, Bao Jian; Wiggs, Janey L.

    2010-01-01

    Glaucoma, a leading cause of blindness worldwide, is characterized by progressive optic nerve damage, usually associated with intraocular pressure. Although the clinical progression of the disease is well defined, the molecular events responsible for glaucoma are currently poorly understood and current therapeutic strategies are not curative. This review summarizes the human genetics and genomic approaches that have shed light on the complex inheritance of glaucoma genes and the potential for gene-based and cellular therapies that this research makes possible. PMID:20811162

  9. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes

    PubMed Central

    2012-01-01

    Ontologies are widely used in the biomedical community for annotation and integration of databases. Formal definitions can relate classes from different ontologies and thereby integrate data across different levels of granularity, domains and species. We have applied this methodology to the Ascomycete Phenotype Ontology (APO), enabling the reuse of various orthogonal ontologies and we have converted the phenotype associated data found in the SGD following our proposed patterns. We have integrated the resulting data in the cross-species phenotype network PhenomeNET, and we make both the cross-species integration of yeast phenotypes and a similarity-based comparison of yeast phenotypes across species available in the PhenomeBrowser. Furthermore, we utilize our definitions and the yeast phenotype annotations to suggest novel functional annotations of gene products in yeast. PMID:23046642

  10. Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes.

    PubMed

    Gkoutos, Georgios V; Hoehndorf, Robert

    2012-09-21

    Ontologies are widely used in the biomedical community for annotation and integration of databases. Formal definitions can relate classes from different ontologies and thereby integrate data across different levels of granularity, domains and species. We have applied this methodology to the Ascomycete Phenotype Ontology (APO), enabling the reuse of various orthogonal ontologies and we have converted the phenotype associated data found in the SGD following our proposed patterns. We have integrated the resulting data in the cross-species phenotype network PhenomeNET, and we make both the cross-species integration of yeast phenotypes and a similarity-based comparison of yeast phenotypes across species available in the PhenomeBrowser. Furthermore, we utilize our definitions and the yeast phenotype annotations to suggest novel functional annotations of gene products in yeast.

  11. Phenotype-environment matching in sand fleas.

    PubMed

    Stevens, Martin; Broderick, Annette C; Godley, Brendan J; Lown, Alice E; Troscianko, Jolyon; Weber, Nicola; Weber, Sam B

    2015-08-01

    Camouflage is perhaps the most widespread anti-predator strategy in nature, found in numerous animal groups. A long-standing prediction is that individuals should have camouflage tuned to the visual backgrounds where they live. However, while several studies have demonstrated phenotype-environment associations, few have directly shown that this confers an improvement in camouflage, particularly with respect to predator vision. Here, we show that an intertidal crustacean, the sand flea (Hippa testudinaria), has coloration tuned to the different substrates on which it occurs when viewed by potential avian predators. Individual sand fleas from a small, oceanic island (Ascension) matched the colour and luminance of their own beaches more closely than neighbouring beaches to a model of avian vision. Based on past work, this phenotype-environment matching is likely to be driven through ontogenetic changes rather than genetic adaptation. Our work provides some of the first direct evidence that animal coloration is tuned to provide camouflage to prospective predators against a range of visual backgrounds, in a population of animals occurring over a small geographical range. PMID:26268993

  12. In pursuit of taste phenotypes.

    PubMed

    Green, Barry G

    2013-05-01

    Notable progress has been made relating individual differences in bitter taste sensitivity to specific alleles and TAS2R receptors, but psychophysical evidence of reliable phenotypes for other tastes has been more elusive. In this issue, Wise and Breslin report a study of individual differences in threshold sensitivity to sour and salty taste, which, though failing to find clear phenotypes, exemplifies the type of approach and analysis necessary to disentangle sources of variance inherent in the psychophysical measures applied from those attributable to true differences in sensitivity. Methodological and theoretical lessons that can be taken from this work are discussed in the context of the early and dramatic evidence of chemosensory phenotypes that belied the complexity of taste receptor genetics and focused attention solely on peripheral determinants of sensitivity.

  13. Optofluidic Detection for Cellular Phenotyping

    PubMed Central

    Tung, Yi-Chung; Huang, Nien-Tsu; Oh, Bo-Ram; Patra, Bishnubrata; Pan, Chi-Chun; Qiu, Teng; Paul, K. Chu; Zhang, Wenjun; Kurabayashi, Katsuo

    2012-01-01

    Quantitative analysis of the output of processes and molecular interactions within a single cell is highly critical to the advancement of accurate disease screening and personalized medicine. Optical detection is one of the most broadly adapted measurement methods in biological and clinical assays and serves cellular phenotyping. Recently, microfluidics has obtained increasing attention due to several advantages, such as small sample and reagent volumes, very high throughput, and accurate flow control in the spatial and temporal domains. Optofluidics, which is the attempt to integrate optics with microfluidic, shows great promise to enable on-chip phenotypic measurements with high precision, sensitivity, specificity, and simplicity. This paper reviews the most recent developments of optofluidic technologies for cellular phenotyping optical detection. PMID:22854915

  14. Phenotypic MicroRNA Microarrays

    PubMed Central

    Kwon, Yong-Jun; Heo, Jin Yeong; Kim, Hi Chul; Kim, Jin Yeop; Liuzzi, Michel; Soloveva, Veronica

    2013-01-01

    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the biology of selected cellular models. After reverse-transfection of microRNAs and siRNA, the cellular phenotype generated by microRNAs regulated NF-κB expression comparably to the siRNA. The ability to print microRNA molecules for reverse transfection into cells is opening up the wide horizon for the phenotypic high content screening of microRNA libraries using cellular disease models.

  15. Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP)

    PubMed Central

    Lin, Ko-Wei; Tharp, Melissa; Conway, Mike; Hsieh, Alexander; Ross, Mindy; Kim, Jihoon; Kim, Hyeon-Eui

    2013-01-01

    The database of Genotypes and Phenotypes (dbGaP) contains various types of data generated from genome-wide association studies (GWAS). These data can be used to facilitate novel scientific discoveries and to reduce cost and time for exploratory research. However, idiosyncrasies and inconsistencies in phenotype variable names are a major barrier to reusing these data. We addressed these challenges in standardizing phenotype variables by formalizing their descriptions using Clinical Element Models (CEM). Designed to represent clinical data, CEMs were highly expressive and thus were able to represent a majority (77.5%) of the 215 phenotype variable descriptions. However, their high expressivity also made it difficult to directly apply them to research data such as phenotype variables in dbGaP. Our study suggested that simplification of the template models makes it more straightforward to formally represent the key semantics of phenotype variables. PMID:24058713

  16. PhenoMiner: from text to a database of phenotypes associated with OMIM diseases.

    PubMed

    Collier, Nigel; Groza, Tudor; Smedley, Damian; Robinson, Peter N; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

    2015-01-01

    Analysis of scientific and clinical phenotypes reported in the experimental literature has been curated manually to build high-quality databases such as the Online Mendelian Inheritance in Man (OMIM). However, the identification and harmonization of phenotype descriptions struggles with the diversity of human expressivity. We introduce a novel automated extraction approach called PhenoMiner that exploits full parsing and conceptual analysis. Apriori association mining is then used to identify relationships to human diseases. We applied PhenoMiner to the BMC open access collection and identified 13,636 phenotype candidates. We identified 28,155 phenotype-disorder hypotheses covering 4898 phenotypes and 1659 Mendelian disorders. Analysis showed: (i) the semantic distribution of the extracted terms against linked ontologies; (ii) a comparison of term overlap with the Human Phenotype Ontology (HP); (iii) moderate support for phenotype-disorder pairs in both OMIM and the literature; (iv) strong associations of phenotype-disorder pairs to known disease-genes pairs using PhenoDigm. The full list of PhenoMiner phenotypes (S1), phenotype-disorder associations (S2), association-filtered linked data (S3) and user database documentation (S5) is available as supplementary data and can be downloaded at http://github.com/nhcollier/PhenoMiner under a Creative Commons Attribution 4.0 license. Database URL: phenominer.mml.cam.ac.uk.

  17. PhenoMiner: from text to a database of phenotypes associated with OMIM diseases

    PubMed Central

    Collier, Nigel; Groza, Tudor; Smedley, Damian; Robinson, Peter N.; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

    2015-01-01

    Analysis of scientific and clinical phenotypes reported in the experimental literature has been curated manually to build high-quality databases such as the Online Mendelian Inheritance in Man (OMIM). However, the identification and harmonization of phenotype descriptions struggles with the diversity of human expressivity. We introduce a novel automated extraction approach called PhenoMiner that exploits full parsing and conceptual analysis. Apriori association mining is then used to identify relationships to human diseases. We applied PhenoMiner to the BMC open access collection and identified 13 636 phenotype candidates. We identified 28 155 phenotype-disorder hypotheses covering 4898 phenotypes and 1659 Mendelian disorders. Analysis showed: (i) the semantic distribution of the extracted terms against linked ontologies; (ii) a comparison of term overlap with the Human Phenotype Ontology (HP); (iii) moderate support for phenotype-disorder pairs in both OMIM and the literature; (iv) strong associations of phenotype-disorder pairs to known disease-genes pairs using PhenoDigm. The full list of PhenoMiner phenotypes (S1), phenotype-disorder associations (S2), association-filtered linked data (S3) and user database documentation (S5) is available as supplementary data and can be downloaded at http://github.com/nhcollier/PhenoMiner under a Creative Commons Attribution 4.0 license. Database URL: phenominer.mml.cam.ac.uk PMID:26507285

  18. Study of the Impact of Tissue Density Heterogeneities on 3-Dimensional Abdominal Dosimetry: Comparison Between Dose Kernel Convolution and Direct Monte Carlo Methods

    PubMed Central

    Dieudonné, Arnaud; Hobbs, Robert F.; Lebtahi, Rachida; Maurel, Fabien; Baechler, Sébastien; Wahl, Richard L.; Boubaker, Ariane; Le Guludec, Dominique; Sgouros, Georges; Gardin, Isabelle

    2014-01-01

    Dose kernel convolution (DK) methods have been proposed to speed up absorbed dose calculations in molecular radionuclide therapy. Our aim was to evaluate the impact of tissue density heterogeneities (TDH) on dosimetry when using a DK method and to propose a simple density-correction method. Methods This study has been conducted on 3 clinical cases: case 1, non-Hodgkin lymphoma treated with 131I-tositumomab; case 2, a neuroendocrine tumor treatment simulated with 177Lu-peptides; and case 3, hepatocellular carcinoma treated with 90Y-microspheres. Absorbed dose calculations were performed using a direct Monte Carlo approach accounting for TDH (3D-RD), and a DK approach (VoxelDose, or VD). For each individual voxel, the VD absorbed dose, DVD, calculated assuming uniform density, was corrected for density, giving DVDd. The average 3D-RD absorbed dose values, D3DRD, were compared with DVD and DVDd, using the relative difference ΔVD/3DRD. At the voxel level, density-binned ΔVD/3DRD and ΔVDd/3DRD were plotted against ρ and fitted with a linear regression. Results The DVD calculations showed a good agreement with D3DRD. ΔVD/3DRD was less than 3.5%, except for the tumor of case 1 (5.9%) and the renal cortex of case 2 (5.6%). At the voxel level, the ΔVD/3DRD range was 0%–14% for cases 1 and 2, and −3% to 7% for case 3. All 3 cases showed a linear relationship between voxel bin-averaged ΔVD/3DRD and density, ρ: case 1 (Δ = −0.56ρ + 0.62, R2 = 0.93), case 2 (Δ = −0.91ρ + 0.96, R2 = 0.99), and case 3 (Δ = −0.69ρ + 0.72, R2 = 0.91). The density correction improved the agreement of the DK method with the Monte Carlo approach (ΔVDd/3DRD < 1.1%), but with a lesser extent for the tumor of case 1 (3.1%). At the voxel level, the ΔVDd/3DRD range decreased for the 3 clinical cases (case 1, −1% to 4%; case 2, −0.5% to 1.5%, and −1.5% to 2%). No more linear regression existed for cases 2 and 3, contrary to case 1 (Δ = 0.41ρ − 0.38, R2 = 0.88) although

  19. An automated field phenotyping pipeline for application in grapevine research.

    PubMed

    Kicherer, Anna; Herzog, Katja; Pflanz, Michael; Wieland, Markus; Rüger, Philipp; Kecke, Steffen; Kuhlmann, Heiner; Töpfer, Reinhard

    2015-01-01

    Due to its perennial nature and size, the acquisition of phenotypic data in grapevine research is almost exclusively restricted to the field and done by visual estimation. This kind of evaluation procedure is limited by time, cost and the subjectivity of records. As a consequence, objectivity, automation and more precision of phenotypic data evaluation are needed to increase the number of samples, manage grapevine repositories, enable genetic research of new phenotypic traits and, therefore, increase the efficiency in plant research. In the present study, an automated field phenotyping pipeline was setup and applied in a plot of genetic resources. The application of the PHENObot allows image acquisition from at least 250 individual grapevines per hour directly in the field without user interaction. Data management is handled by a database (IMAGEdata). The automatic image analysis tool BIVcolor (Berries in Vineyards-color) permitted the collection of precise phenotypic data of two important fruit traits, berry size and color, within a large set of plants. The application of the PHENObot represents an automated tool for high-throughput sampling of image data in the field. The automated analysis of these images facilitates the generation of objective and precise phenotypic data on a larger scale. PMID:25730485

  20. An Automated Field Phenotyping Pipeline for Application in Grapevine Research

    PubMed Central

    Kicherer, Anna; Herzog, Katja; Pflanz, Michael; Wieland, Markus; Rüger, Philipp; Kecke, Steffen; Kuhlmann, Heiner; Töpfer, Reinhard

    2015-01-01

    Due to its perennial nature and size, the acquisition of phenotypic data in grapevine research is almost exclusively restricted to the field and done by visual estimation. This kind of evaluation procedure is limited by time, cost and the subjectivity of records. As a consequence, objectivity, automation and more precision of phenotypic data evaluation are needed to increase the number of samples, manage grapevine repositories, enable genetic research of new phenotypic traits and, therefore, increase the efficiency in plant research. In the present study, an automated field phenotyping pipeline was setup and applied in a plot of genetic resources. The application of the PHENObot allows image acquisition from at least 250 individual grapevines per hour directly in the field without user interaction. Data management is handled by a database (IMAGEdata). The automatic image analysis tool BIVcolor (Berries in Vineyards-color) permitted the collection of precise phenotypic data of two important fruit traits, berry size and color, within a large set of plants. The application of the PHENObot represents an automated tool for high-throughput sampling of image data in the field. The automated analysis of these images facilitates the generation of objective and precise phenotypic data on a larger scale. PMID:25730485

  1. Application of Phenotype Microarray technology to soil microbiology

    NASA Astrophysics Data System (ADS)

    Mocali, Stefano

    2016-04-01

    It is well established that soil microorganisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Furthermore, addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological manipulation of metabolic pathways. High-throughput culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. Thus, over the last years, Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of microorganisms. However, computational tools that could directly link PM data with the gene(s) of interest followed by the extraction of information on gene-phenotype correlation are still missing. Here potential applications of phenotype arrays to soil microorganisms, use of the plates in stress response studies and for assessment of phenotype of environmental communities are described. Considerations and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting are also discussed. In particular, here we present DuctApe, a suite that allows the analysis of both genomic sequences and PM data, to find metabolic differences among PM experiments and to correlate them with KEGG pathways and gene presence/absence patterns.

  2. Strategy revealing phenotypic differences among synthetic oscillator designs.

    PubMed

    Lomnitz, Jason G; Savageau, Michael A

    2014-09-19

    Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy, we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested. PMID:25019938

  3. Synaptic E3 Ligase SCRAPPER in Contextual Fear Conditioning: Extensive Behavioral Phenotyping of Scrapper Heterozygote and Overexpressing Mutant Mice

    PubMed Central

    Yao, I