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Sample records for analysis phenotype anchoring

  1. Mercury-induced hepatotoxicity in zebrafish: in vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation

    Directory of Open Access Journals (Sweden)

    Mathavan Sinnakaruppan

    2010-03-01

    Full Text Available Abstract Background Mercury is a prominent environmental contaminant that causes detrimental effects to human health. Although the liver has been known to be a main target organ, there is limited information on in vivo molecular mechanism of mercury-induced toxicity in the liver. By using transcriptome analysis, phenotypic anchoring and validation of targeted gene expression in zebrafish, mercury-induced hepatotoxicity was investigated and a number of perturbed cellular processes were identified and compared with those captured in the in vitro human cell line studies. Results Hepato-transcriptome analysis of mercury-exposed zebrafish revealed that the earliest deregulated genes were associated with electron transport chain, mitochondrial fatty acid beta-oxidation, nuclear receptor signaling and apoptotic pathway, followed by complement system and proteasome pathway, and thereafter DNA damage, hypoxia, Wnt signaling, fatty acid synthesis, gluconeogenesis, cell cycle and motility. Comparative meta-analysis of microarray data between zebrafish liver and human HepG2 cells exposed to mercury identified some common toxicological effects of mercury-induced hepatotoxicity in both models. Histological analyses of liver from mercury-exposed fish revealed morphological changes of liver parenchyma, decreased nucleated cell count, increased lipid vesicles, glycogen and apoptotic bodies, thus providing phenotypic evidence for anchoring of the transcriptome analysis. Validation of targeted gene expression confirmed deregulated gene-pathways from enrichment analysis. Some of these genes responding to low concentrations of mercury may serve as toxicogenomic-based markers for detection and health risk assessment of environmental mercury contaminations. Conclusion Mercury-induced hepatotoxicity was triggered by oxidative stresses, intrinsic apoptotic pathway, deregulation of nuclear receptor and kinase activities including Gsk3 that deregulates Wnt signaling

  2. The Analysis Stability of Anchor Retaining Wall

    International Nuclear Information System (INIS)

    The construction of anchored retaining walls reach every day in the field of Civil Engineering especially in public works. Their dimensioning and stability are the axes of research for geotechnical. The rule is to reduce the active forces of the slide and increase the effective normal stress on the rupture surface. So that, we anchored tied-back (constituted by steel cables) in the stable ground located under the failure surface and we apply at the top a traction force. This effort can be distributed over the ground surface by means of small plates or massive reinforced concrete. The study of the stability of anchored retaining wall was also performed by using software GEO4. Many cases can be solved using analytical solutions available in the group GEO4 program, but for our standard model solution studied analytically proved unsatisfactory so we used a numerical analysis based on the method of finite element in this program. The results obtained by numerical study were interpreted to identify the precision numerical predictions. Moreover these methods were useful and economics in the realization of reinforced slopes by tied-buck. (author)

  3. ANCHORING EFFECT ANALYSIS OF TENSIONED BOLTS

    Institute of Scientific and Technical Information of China (English)

    夏建中

    1997-01-01

    The paper analyses quantitatively the anchoring effect of tensioned bolts on surrounding rock strength, and defines two concepts: one is the surrounding rock strength increased amount △τ13 and the other is the strength influence factor k. The anchoring effect of tensioned bolts is considered to increase a strength increased amount △τ13 where △τ13 is the product k and tensioned load p, i. e. △τ13= kp, where k is a function of two variables x and y. The distributive properties both △τ13 and k are also discussed in the paper, obtaining some useful results for designing bolting support parameters.

  4. Proteomic analysis of GPI-anchored membrane proteins

    DEFF Research Database (Denmark)

    Jung, Hye Ryung; Jensen, Ole Nørregaard

    2006-01-01

    humans. GPI-APs confer important cellular functions as receptors, enzymes and scaffolding molecules. Specific enzymes and detergent extraction methods combined with separation technologies and mass spectrometry permit proteomic analysis of GPI-APs from plasma membrane preparations to reveal cell......Glycosyl-phosphatidyl-inositol-anchored proteins (GPI-APs) represent a subset of post-translationally modified proteins that are tethered to the outer leaflet of the plasma membrane via a C-terminal GPI anchor. GPI-APs are found in a variety of eukaryote species, from pathogenic microorganisms to...

  5. Analysis of Glenoid Inter-anchor Distance with an All-Suture Anchor System

    Science.gov (United States)

    Kramer, Jonathan; Robinson, Sean; Dutton, Pascual; Dickinson, Ephraim; Rodriguez, John Paul; Camisa, William; Leasure, Jeremi M.; Montgomery, William H.

    2016-01-01

    Objectives: Arthroscopic shoulder stabilization using suture anchors are commonly used techniques. More recently developed all-suture systems employ smaller diameter anchors, which increase repair contact area and allow greater placement density on narrow surfaces such as the glenoid. Our goal is investigate the strength characteristics of various inter-anchor distances in a human glenoid model. Methods: Twelve fresh-frozen human cadaveric glenoids were potted after the labrum was excised. The glenoids were then implanted with 1.4 mm all-suture anchors (Juggerknot, Biomet, Warsaw, IN) at varying inter-anchor distances. Anchors were implanted adjacent to one another or at 2 mm, 3 mm, or 5 mm distances using a template with pre-drilled holes. The glenoids were then underwent single cycle pullout testing using a test frame (Instron 8521, Instron Inc., Norwood, MA). A 5 N preload was applied to the construct and the actuator was driven away from the shoulder at a rate of 12.5mm/s as seen in Figure 1. Force and displacement were collected from the test frame actuator at a rate of 500 Hz. The primary outcomes were failure strength and stiffness. Stiffness was calculated from the initial linear region of the force displacement curve. Failure strength was defined as the first local maximum inflection point in the force displacement curve. Results: During load to fail testing, all but three of the specimens had both anchors pull out of the glenoid. The other mode of failure included one or both of the sutures failing. Stiffness was 13.52 ± 3.8, 17.97 ± 5.02, 17.59 ± 4.65 and 18.95 ± 4.67 N/mm for the adjacent, 2 mm, 3 mm and 5 mm treatment groups as shown Table 1. The adjacent group had a significantly lower stiffness compared to the other treatment groups. Failure strength was 48.68 ± 20.64, 76.16 ± 23.78, 73.19 ± 35.83 and 87.04 ± 34.67 N for the adjacent, 2 mm, 3 mm and 5 mm treatment groups as shown in Table 1. The adjacent group had a significantly lower

  6. Knowledge-based analysis of phenotypes

    KAUST Repository

    Hoendorf, Robert

    2016-01-27

    Phenotypes are the observable characteristics of an organism, and they are widely recorded in biology and medicine. To facilitate data integration, ontologies that formally describe phenotypes are being developed in several domains. I will describe a formal framework to describe phenotypes. A formalized theory of phenotypes is not only useful for domain analysis, but can also be applied to assist in the diagnosis of rare genetic diseases, and I will show how our results on the ontology of phenotypes is now applied in biomedical research.

  7. Multivariate Analysis of Genotype-Phenotype Association.

    Science.gov (United States)

    Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

    2016-04-01

    With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

  8. Proteomic analysis of glycosylphosphatidylinositol-anchored membrane proteins

    DEFF Research Database (Denmark)

    Elortza, Felix; Nühse, Thomas S; Foster, Leonard J;

    2003-01-01

    Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are a functionally and structurally diverse family of post-translationally modified membrane proteins found mostly in the outer leaflet of the plasma membrane in a variety of eukaryotic cells. Although the general role of GPI-APs remains...... unclear, they have attracted attention because they act as enzymes and receptors in cell adhesion, differentiation, and host-pathogen interactions. GPI-APs may represent potential diagnostic and therapeutic targets in humans and are interesting in plant biotechnology because of their key role in root...... and 44 GPI-APs in an Arabidopsis thaliana membrane preparation, representing the largest experimental dataset of GPI-anchored proteins to date....

  9. Mechanical Analysis of Stress Distribution in a Carbon Fiber-Reinforced Polymer Rod Bonding Anchor

    Directory of Open Access Journals (Sweden)

    Peng Feng

    2014-04-01

    Full Text Available This paper presents an elastic shear stress distribution theoretical model at the carbon fiber-reinforced polymer (CFRP-adhesive interface of a single-rod and a multi-rod straight-pipe bonding anchor. A comparison between theoretical and finite element analysis results reveals that the accuracy of the theory can be used to guide the preliminary design of CFRP rod bonding anchors. The mechanical performance of the inner cone bonding anchor for multi-rods are evaluated within different coefficients of friction and inner inclined angles. Numerical results indicate that the straight-parabolic inner cone bonding anchor has a significant effect on reducing the shear force at the loading end.

  10. Transcriptome and biochemical analysis reveals that suppression of GPI-anchor synthesis leads to autophagy and possible necroptosis in Aspergillus fumigatus.

    Directory of Open Access Journals (Sweden)

    Jianghong Yan

    Full Text Available Previously, it has been shown that GPI proteins are required for cell wall synthesis and organization in Aspergillus fumigatus, a human opportunistic pathogen causing life-threatening invasive aspergillosis (IA in immunocompromised patients. Blocking GPI anchor synthesis leads to severe phenotypes such as cell wall defects, increased cell death, and attenuated virulence. However, the mechanism by which these phenotypes are induced is unclear. To gain insight into global effects of GPI anchoring in A. fumigatus, in this study a conditional expression mutant was constructed and a genome wide transcriptome analysis was carried out. Our results suggested that suppression of GPI anchor synthesis mainly led to activation of phosphatidylinositol (PtdIns signaling and ER stress. Biochemical and morphological evidence showed that autophagy was induced in response to suppression of the GPI anchor synthesis, and also an increased necroptosis was observed. Based on our results, we propose that activation of PtdIns3K and increased cytosolic Ca(2+, which was induced by both ER stress and PtdIns signaling, acted as the main effectors to induce autophagy and possible necroptosis.

  11. A development of numerical analysis model for tensile capacity evaluation of cast-in-place anchor

    International Nuclear Information System (INIS)

    Numerical analysis is carried out to identify the appropriateness of the design codes that is available for the tensile design of fastening system at Nuclear Power Plant (NPP) in this study. This study is intended for the cast-in-place anchor that is widely used for the fastening of equipment in Korean NPPs. The microplane model and the elastic-perfectly plastic model are employed for the quasi-brittle material like concrete and for the ductile material like anchor bolt as constitutive model for numerical analysis and smeared crack model is employed for the crack and damage phenomena. The developed numerical model is verified on a basis of the various test data of cast-in-place anchor. The appropriateness of both ACI 349 Code and CCD approach of CEB-FIP Code is evaluated for the tensile design of cast-in-place anchor and it is proved that both design codes give a conservative results compared with real tensile capacity of cast-in-place anchor

  12. Analysis of Cracking Mode of Anchor Structure of Underground Engineering Induced by Reinforcement Corrosion

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    Wantao Ding

    2014-02-01

    Full Text Available Based on elastic theory and assumption of maximum tensile-stress failure criterion, together with construction process of anchor structure and rust expansion critical process, this study proposed a simplified reinforcement rust expansion mechanical model of anchor structure system. Elastic criterion of different initial cracking mode was rewarded under different stress ratios. According to analysis of critical cracking mode of different medium, cracking order of mortar and surrounding rock depended on their material parameters, in-situ stress and thickness of mortar cover. Critical cracking conditions of different medium without effect of in-situ stress was the same as that of considering in-situ stress while k is equal to 3 or 1/3. And engineering example shows that three different cracking modes exist under different stress ratios. The result provides a useful reference for analysis of mechanical deterioration mechanism of anchor structure and design of support structure of underground engineering.

  13. Mechanical mechanism analysis of tension type anchor based on shear displacement method

    Institute of Scientific and Technical Information of China (English)

    XIAO Shu-jun; CHEN Chang-fu

    2008-01-01

    Based on the fact that the shear stress along anchorage segment is neither linearly nor uniformly distributed, the load transfer mechanism of the tension type anchor was studied and the mechanical characteristic of anchorage segment was analyzed. Shear stress-strain relationship of soil surrounding anchorage body was simplified into three-folding-lines model consisting of elastic phase, elasto-plastic phase and residual phase considering its softening eharaeteristic. Meanwhile, shear displacement method that has been extensively used in the analysis of pile foundation was introduced. Based on elasto-plastic theory, the distributions of displacement, shear stress and axial force along the anchorage segment of tension type anchor were obtained, and the formula for calculating the elastic limit load was also developed accordingly. Finally, an example was given to discuss the variation of stress and displacement in the anchorage segment with the loads exerted on the anchor, and a program was worked out to calculate the anchor maximum bearing capacity. The influence of some parameters on the anchor bearing capacity was discussed, and effective anchorage length was obtained simultaneously. The results show that the shear stress first increases and then decreases and finally trends to theresidual strength with increase of distance from bottom of the anchorage body, the displacement increases all the time with theincrease of distance from bottom of the anchorage body, and the increase of velocity gradually becomes greater.

  14. MPHASYS: a mouse phenotype analysis system

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    Mian I

    2007-06-01

    Full Text Available Abstract 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.

  15. Hierarchical genetic clusters for phenotypic analysis

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    Luiza Barbosa da Matta

    2015-10-01

    Full Text Available Methods to obtain phenotypic information were evaluated to help breeders choosing the best methodology for analysis of genetic diversity in backcross populations. Phenotypes were simulated for 13 characteristics generated in 10 populations with 100 individuals each. Genotypic information was generated from 100 loci of which 20 were taken at random to determine the characteristics expressing two alleles. Dissimilarity measures were calculated, and genetic diversity was analyzed through hierarchical clustering and graphic projection of the distances. A backcross was performed from the two most divergent populations. A set of characteristics with variable heritability was taken into account. The environmental effect was simulated assuming . For hierarchical clusters, the following methods were used: Gower Method, average linkage within the cluster, average linkage among clusters, the furthest neighbor method, the nearest neighbor method, Ward’s method, and the median method. The environmental effect and heritability of the analyzed variables had an influence on the pattern of hierarchical clustering populations according to the backcrossed generations. The nearest neighbor method was the most efficient in reconstructing the system of backcrossing, and it presented the highest cophenetic correlation. The efficiency of the nearest neighbor method was the highest when the analysis involved characteristics of high heritability.

  16. Anchor reinforcements

    Energy Technology Data Exchange (ETDEWEB)

    Levkovich, P.Ye.; Sal' nikov, V.K.; Savich, N.S.

    1980-11-30

    An anchor reinforcement includes an anchor shaft, an elastic jig with a separator wall having compartments placed parallely along it and filled with reinforcement material and a device for destroying the jig wall separator. To quickly put the anchor in place and increase the reliability of the reinforcement by mixing the reinforcement material components better, the device for destroying the jig separator wall was made in the shape of a shovel, fastened to the anchor shaft and the separator wall has a longitudinal hollow for holding the anchor shaft/shovel.

  17. Advanced phenotyping and phenotype data analysis for the study of plant growth and development.

    Science.gov (United States)

    Rahaman, Md Matiur; Chen, Dijun; Gillani, Zeeshan; Klukas, Christian; Chen, Ming

    2015-01-01

    Due to an increase in the consumption of food, feed, fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to breed high yielding crops that can adapt to the future climate changes, particularly in developing countries. To solve these global challenges, novel approaches are required to identify quantitative phenotypes and to explain the genetic basis of agriculturally important traits. These advances will facilitate the screening of germplasm with high performance characteristics in resource-limited environments. Recently, plant phenomics has offered and integrated a suite of new technologies, and we are on a path to improve the description of complex plant phenotypes. High-throughput phenotyping platforms have also been developed that capture phenotype data from plants in a non-destructive manner. In this review, we discuss recent developments of high-throughput plant phenotyping infrastructure including imaging techniques and corresponding principles for phenotype data analysis. PMID:26322060

  18. Analysis of Anchors and Bracing Configurations for Personal Fall Arrest Systems in Residential Construction

    OpenAIRE

    Morris, Justin Collins

    2013-01-01

    AbstractAnalysis of Anchors and Bracing Configurations with Personal Fall Arrest Systems in Residential ConstructionJustin Collins Morris    Falls continue to be a major problem in the residential construction industry and account for a large number of injuries and fatalities each year (US Department of Labor, 2012).  The effects of a fall are catastrophic to the workers and their families as well as the construction company and surrounding community.  Prevention of these incidents has been t...

  19. Analysis on the anchor mechanism of the full length resin bolt

    Institute of Scientific and Technical Information of China (English)

    宋彦波; 刘洪涛

    2003-01-01

    The purpose of this paper is to reveal the stress distribution characteristic along the full length anchor bolt. Based on the mechanic model set up, the author calculated the anchor mechanism of the full length resin rock-bolt. The stress distribution characteristic is different according to different type of surrounding-rock. The conclusion is important to optimize the roadway bolt support design.

  20. Latent cluster analysis of ALS phenotypes identifies prognostically differing groups.

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    Jeban Ganesalingam

    Full Text Available BACKGROUND: Amyotrophic lateral sclerosis (ALS is a degenerative disease predominantly affecting motor neurons and manifesting as several different phenotypes. Whether these phenotypes correspond to different underlying disease processes is unknown. We used latent cluster analysis to identify groupings of clinical variables in an objective and unbiased way to improve phenotyping for clinical and research purposes. METHODS: Latent class cluster analysis was applied to a large database consisting of 1467 records of people with ALS, using discrete variables which can be readily determined at the first clinic appointment. The model was tested for clinical relevance by survival analysis of the phenotypic groupings using the Kaplan-Meier method. RESULTS: The best model generated five distinct phenotypic classes that strongly predicted survival (p<0.0001. Eight variables were used for the latent class analysis, but a good estimate of the classification could be obtained using just two variables: site of first symptoms (bulbar or limb and time from symptom onset to diagnosis (p<0.00001. CONCLUSION: The five phenotypic classes identified using latent cluster analysis can predict prognosis. They could be used to stratify patients recruited into clinical trials and generating more homogeneous disease groups for genetic, proteomic and risk factor research.

  1. Pipe-anchor discontinuity analysis utilizing power series solutions, Bessel functions, and Fourier series

    International Nuclear Information System (INIS)

    One of the paradigmatic classes of problems that frequently arise in piping stress analysis discipline is the effect of local stresses created by supports and restraints attachments. Over the past 20 years, concerns have been identified by both regulatory agencies in the nuclear power industry and others in the process and chemicals industries concerning the effect of various stiff clamping arrangements on the expected life of the pipe and its various piping components. In many of the commonly utilized geometries and arrangements of pipe clamps, the elasticity problem becomes the axisymmetric stress and deformation determination in a hollow cylinder (pipe) subjected to the appropriate boundary conditions and respective loads per se. One of the geometries that serve as a pipe anchor is comprised of two pipe clamps that are bolted tightly to the pipe and affixed to a modified shoe-type arrangement. The shoe is employed for the purpose of providing an immovable base that can be easily attached either by bolting or welding to a structural steel pipe rack. Over the past 50 years, the computational tools available to the piping analyst have changed dramatically and thereby have caused the implementation of solutions to the basic problems of elasticity to change likewise. The need to obtain closed form elasticity solutions, however, has always been a driving force in engineering. The employment of symbolic calculus that is currently available through numerous software packages makes closed form solutions very economical. This paper briefly traces the solutions over the past 50 years to a variety of axisymmetric stress problems involving hollow circular cylinders employing a Fourier series representation. In the present example, a properly chosen Fourier series represent the mathematical simulation of the imposed axial displacements on the outside diametrical surface. A general solution technique is introduced for the axisymmetric discontinuity stresses resulting from an

  2. Arrows as anchors: An analysis of the material features of electric field vector arrows

    Science.gov (United States)

    Gire, Elizabeth; Price, Edward

    2014-12-01

    Representations in physics possess both physical and conceptual aspects that are fundamentally intertwined and can interact to support or hinder sense making and computation. We use distributed cognition and the theory of conceptual blending with material anchors to interpret the roles of conceptual and material features of representations in students' use of representations for computation. We focus on the vector-arrows representation of electric fields and describe this representation as a conceptual blend of electric field concepts, physical space, and the material features of the representation (i.e., the physical writing and the surface upon which it is drawn). In this representation, spatial extent (e.g., distance on paper) is used to represent both distances in coordinate space and magnitudes of electric field vectors. In conceptual blending theory, this conflation is described as a clash between the input spaces in the blend. We explore the benefits and drawbacks of this clash, as well as other features of this representation. This analysis is illustrated with examples from clinical problem-solving interviews with upper-division physics majors. We see that while these intermediate physics students make a variety of errors using this representation, they also use the geometric features of the representation to add electric field contributions and to organize the problem situation productively.

  3. Arrows as Anchors: An Analysis of the Material Features of Electric Field Vector Arrows

    Science.gov (United States)

    Gire, Elizabeth; Price, Edward

    2014-01-01

    Representations in physics possess both physical and conceptual aspects that are fundamentally intertwined and can interact to support or hinder sense making and computation. We use distributed cognition and the theory of conceptual blending with material anchors to interpret the roles of conceptual and material features of representations in…

  4. Parameter analysis of anchor bolt support for large-span and jointed rock mass

    Institute of Scientific and Technical Information of China (English)

    LI Xi-bing; ZHOU Zi-long; LI Qi-yue; HU Liu-qing

    2005-01-01

    In order to obtain the optimal parameters of anchor bolt supporting system for large-span and jointed rock mass in Kaiyang Phosphor Mine, it is expensive and unavailable with the method of in-situ experiments. This paper describes a numerical modeling with discrete element method for the supporting effects of different type of anchor bolts. The anchor bolts with variant length of 0.5 m, 0.8 m, 1.0 m, diameter of 10 mm, 15 mm, 20 mm, setting spacing of 3.0 m, 2.5 m, 2.0 m, and setting angle of 10°, 20°, 30°, are simulated respectively. The results show that there exist optimal parameters of anchor bolt support for large-span and jointed rock mass. For the bolt support of the concerning, the optimal length is 2.5-3.5 m, the diameter is 25-35 mm, the spacing is 0.5-0.6 m, and the setting angle is 105°.

  5. COPD phenotype description using principal components analysis

    DEFF Research Database (Denmark)

    Roy, Kay; Smith, Jacky; Kolsum, Umme;

    2009-01-01

    BACKGROUND: Airway inflammation in COPD can be measured using biomarkers such as induced sputum and Fe(NO). This study set out to explore the heterogeneity of COPD using biomarkers of airway and systemic inflammation and pulmonary function by principal components analysis (PCA). SUBJECTS AND METH...

  6. Genotypic and Phenotypic Analysis of Fasciola Isolates

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    SN Mosavinasab

    2009-07-01

    Full Text Available "nBackground: To identify the fasciolid species by morphometric and molecular methods in Zanjan, north­west of Iran. "nMethods: Adult Fasciola worms (n=584 were obtained from cattle and sheep in Zanjan slaughterhouse in 2007. Living flukes were washed, then worms' images were taken by 3CCD camera and finally apical zone of each worm was obtained. Morphometric values such as body length, body width, body area, body pe­rimeter and the distance between ventral sucker and posterior end of body were obtained using Auto­CAD image analysis software. Total gDNA was extracted from individual flukes by modified phenol-chloroform method. PCR amplification of ITS2 fragment was performed the isolated DNA samples and the amplicons were consequently subjected to RFLP assay and nucleotide sequencing to distinguish be­tween fasciolid species. "nResults: Mean of morphometric values in flukes from sheep was greater than those of cattle. Accordingly, the identified species included 31% F. hepatica-like, 7% F. gigantica-like and 62% intermediate forms. How­ever, ITS2 fragment of 535 amplified specimens, showed no variation at the species-specific nucleo­tide sites 230, 340 and 341. The amplified fragment composed of partial 5.8S sequence (62bp, the com­plete ITS2 sequence (361bp and partial 28S sequence (34bp. The nucleotide contents of ITS2 region were 69 A, 116 T, 81 C and 95 G and the average G+C content was approximately 49%. Comparing of ITS2 sequences with the BLAST GenBank database, also confirmed that all specimens were F. hepatica. "nConclusion: A simple and rapid PCR-RFLP assay can be used for distinguishing between these species.

  7. Morphometric analysis of treatment effects of bone-anchored maxillary protraction in growing Class III patients

    OpenAIRE

    Baccetti, T.; Clerck, H.J. de; Cevidanes, L. H.; Franchi, L

    2010-01-01

    The aim of the present morphometric investigation was to evaluate the effects of bone-anchored maxillary protraction (BAMP) in the treatment of growing patients with Class III malocclusion. The shape and size changes in the craniofacial configuration of a sample of 26 children with Class III malocclusions consecutively treated with the BAMP protocol were compared with a matched sample of 15 children with untreated Class III malocclusions. All subjects in the two groups were at a prepubertal s...

  8. Geometric Nonlinear Analysis of Self-Anchored Cable-Stayed Suspension Bridges

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    Wang Hui-Li

    2013-01-01

    Full Text Available Geometric nonlinearity of self-anchored cable-stayed suspension bridges is studied in this paper. The repercussion of shrinkage and creep of concrete, rise-to-span ratio, and girder camber on the system is discussed. A self-anchored cable-stayed suspension bridge with a main span of 800 m is analyzed with linear theory, second-order theory, and nonlinear theory, respectively. In the condition of various rise-to-span ratios and girder cambers, the moments and displacements of both the girder and the pylon under live load are acquired. Based on the results it is derived that the second-order theory can be adopted to analyze a self-anchored cable-stayed suspension bridge with a main span of 800 m, and the error is less than 6%. The shrinkage and creep of concrete impose a conspicuous impact on the structure. And it outmatches suspension bridges for system stiffness. As the rise-to-span ratio increases, the axial forces of the main cable and the girder decline. The system stiffness rises with the girder camber being employed.

  9. Geometric nonlinear analysis of self-anchored cable-stayed suspension bridges.

    Science.gov (United States)

    Hui-Li, Wang; Yan-Bin, Tan; Si-Feng, Qin; Zhe, Zhang

    2013-01-01

    Geometric nonlinearity of self-anchored cable-stayed suspension bridges is studied in this paper. The repercussion of shrinkage and creep of concrete, rise-to-span ratio, and girder camber on the system is discussed. A self-anchored cable-stayed suspension bridge with a main span of 800 m is analyzed with linear theory, second-order theory, and nonlinear theory, respectively. In the condition of various rise-to-span ratios and girder cambers, the moments and displacements of both the girder and the pylon under live load are acquired. Based on the results it is derived that the second-order theory can be adopted to analyze a self-anchored cable-stayed suspension bridge with a main span of 800 m, and the error is less than 6%. The shrinkage and creep of concrete impose a conspicuous impact on the structure. And it outmatches suspension bridges for system stiffness. As the rise-to-span ratio increases, the axial forces of the main cable and the girder decline. The system stiffness rises with the girder camber being employed. PMID:24282388

  10. GBM heterogeneity characterization by radiomic analysis of phenotype anatomical planes

    Science.gov (United States)

    Chaddad, Ahmad; Desrosiers, Christian; Toews, Matthew

    2016-03-01

    Glioblastoma multiforme (GBM) is the most common malignant primary tumor of the central nervous system, characterized among other traits by rapid metastatis. Three tissue phenotypes closely associated with GBMs, namely, necrosis (N), contrast enhancement (CE), and edema/invasion (E), exhibit characteristic patterns of texture heterogeneity in magnetic resonance images (MRI). In this study, we propose a novel model to characterize GBM tissue phenotypes using gray level co-occurrence matrices (GLCM) in three anatomical planes. The GLCM encodes local image patches in terms of informative, orientation-invariant texture descriptors, which are used here to sub-classify GBM tissue phenotypes. Experiments demonstrate the model on MRI data of 41 GBM patients, obtained from the cancer genome atlas (TCGA). Intensity-based automatic image registration is applied to align corresponding pairs of fixed T1˗weighted (T1˗WI) post-contrast and fluid attenuated inversion recovery (FLAIR) images. GBM tissue regions are then segmented using the 3D Slicer tool. Texture features are computed from 12 quantifier functions operating on GLCM descriptors, that are generated from MRI intensities within segmented GBM tissue regions. Various classifier models are used to evaluate the effectiveness of texture features for discriminating between GBM phenotypes. Results based on T1-WI scans showed a phenotype classification accuracy of over 88.14%, a sensitivity of 85.37% and a specificity of 96.1%, using the linear discriminant analysis (LDA) classifier. This model has the potential to provide important characteristics of tumors, which can be used for the sub-classification of GBM phenotypes.

  11. Comprehensive behavioral analysis of voltage-gated calcium channel beta-anchoring and -regulatory protein knockout mice

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    Takafumi Miki

    2015-06-01

    Full Text Available Calcium (Ca2+ influx through voltage-gated Ca2+ channels (VGCCs induces numerous intracellular events such as neuronal excitability, neurotransmitter release, synaptic plasticity, and gene regulation. It has been shown that genes related to Ca2+ signaling, such as the CACNA1C, CACNB2, and CACNA1I genes that encode VGCC subunits, are associated with schizophrenia and other psychiatric disorders. Recently, VGCC beta-anchoring and -regulatory protein (BARP was identified as a novel regulator of VGCC activity via the interaction of VGCC β subunits. To examine the role of the BARP in higher brain functions, we generated BARP knockout (KO mice and conducted a comprehensive battery of behavioral tests. BARP KO mice exhibited greatly reduced locomotor activity, as evidenced by decreased vertical activity, stereotypic counts in the open field test, and activity level in the home cage, and longer latency to complete a session in spontaneous T-maze alteration test, which reached “study-wide significance”. Acoustic startle response was also reduced in the mutants. Interestingly, they showed multiple behavioral phenotypes that are seemingly opposite to those seen in the mouse models of schizophrenia and its related disorders, including increased working memory, flexibility, prepulse inhibition, and social interaction, and decreased locomotor activity, though many of these phenotypes are statistically weak and require further replications. These results demonstrate that BARP is involved in the regulation of locomotor activity and, possibly, emotionality. The possibility was also suggested that BARP KO mice may serve as a unique tool for investigating the pathogenesis/pathophysiology of schizophrenia and related disorders. Further evaluation of the molecular and physiological phenotypes of the mutant mice would provide new insights into the role of BARP in higher brain functions.

  12. Genetic association analysis of complex diseases incorporating intermediate phenotype information.

    Directory of Open Access Journals (Sweden)

    Yafang Li

    Full Text Available Genetic researchers often collect disease related quantitative traits in addition to disease status because they are interested in understanding the pathophysiology of disease processes. In genome-wide association (GWA studies, these quantitative phenotypes may be relevant to disease development and serve as intermediate phenotypes or they could be behavioral or other risk factors that predict disease risk. Statistical tests combining both disease status and quantitative risk factors should be more powerful than case-control studies, as the former incorporates more information about the disease. In this paper, we proposed a modified inverse-variance weighted meta-analysis method to combine disease status and quantitative intermediate phenotype information. The simulation results showed that when an intermediate phenotype was available, the inverse-variance weighted method had more power than did a case-control study of complex diseases, especially in identifying susceptibility loci having minor effects. We further applied this modified meta-analysis to a study of imputed lung cancer genotypes with smoking data in 1154 cases and 1137 matched controls. The most significant SNPs came from the CHRNA3-CHRNA5-CHRNB4 region on chromosome 15q24-25.1, which has been replicated in many other studies. Our results confirm that this CHRNA region is associated with both lung cancer development and smoking behavior. We also detected three significant SNPs--rs1800469, rs1982072, and rs2241714--in the promoter region of the TGFB1 gene on chromosome 19 (p = 1.46×10(-5, 1.18×10(-5, and 6.57×10(-6, respectively. The SNP rs1800469 is reported to be associated with chronic obstructive pulmonary disease and lung cancer in cigarette smokers. The present study is the first GWA study to replicate this result. Signals in the 3q26 region were also identified in the meta-analysis. We demonstrate the intermediate phenotype can potentially enhance the power of complex

  13. Computational fluid dynamic analysis of flutter characteristics for self-anchored suspension bridges

    Institute of Scientific and Technical Information of China (English)

    Zhiwen ZHU; Zhaoxiang WANG; Zhengqing CHEN

    2008-01-01

    This paper outlines the essentials and proce-dures of computational fluid dynamics (CFD) simulation applicable to evaluating flutter derivatives of bridge decks. An arbitrary Lagrangian-Eulerian (ALE) description of the flow around the moving rigid box girder combined with the finite volume discretization and multi-grid algorithm is pre-sented. The proposed methods are employed to identify flutter derivatives of the bridge deck of the Sanchaji Self-anchored Suspension Bridge. The results agree well with ones from wind tunnel tests. It demonstrates accuracy and efficiency of the present method.

  14. Analysis of Genotype-Phenotype Correlations in Human Holoprosencephaly

    OpenAIRE

    Solomon, Benjamin D.; Mercier, Sandra; Vélez, Jorge I.; Pineda-Alvarez, Daniel E.; Wyllie, Adrian; Zhou, Nan; Dubourg, Christèle; David, Veronique; Odent, Sylvie; Roessler, Erich; Muenke, Maximilian

    2010-01-01

    Since the discovery of the first gene causing holoprosencephaly (HPE), over 500 patients with mutations in genes associated with non-chromosomal, non-syndromic HPE have been described, with detailed descriptions available in over 300. Comprehensive clinical analysis of these individuals allows examination for the presence of genotype-phenotype correlations. These correlations allow a degree of differentiation between patients with mutations in different HPE-associated genes and for the applic...

  15. Transcriptomic Analysis of Phenotypic Changes in Birch (Betula platyphylla Autotetraploids

    Directory of Open Access Journals (Sweden)

    Gui-Feng Liu

    2012-10-01

    Full Text Available Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and transcriptomes of these autotetraploid individuals were compared with those of diploid trees. Autotetraploids were generally superior in breast-height diameter, volume, leaf, fruit and stoma and were generally inferior in height compared to diploids. Transcriptome data revealed numerous changes in gene expression attributable to autotetraploidization, which resulted in the upregulation of 7052 unigenes and the downregulation of 3658 unigenes. Pathway analysis revealed that the biosynthesis and signal transduction of indoleacetate (IAA and ethylene were altered after genome duplication, which may have contributed to phenotypic changes. These results shed light on variations in birch autotetraploidization and help identify important genes for the genetic engineering of birch trees.

  16. Stress Analysis of Building Curtain Wall Post Embedment Anchor Bolt%建筑幕墙后置埋件锚栓受力分析

    Institute of Scientific and Technical Information of China (English)

    陆新鑫; 吴强

    2014-01-01

    本文根据JGJ 145—2013《混凝土结构后锚固技术规程》第5.2.2条,对后置埋件在双向受弯矩、双向受剪力、以及扭矩、拉力的共同作用下进行的锚栓受力做了分析,提出了复合力作用下后置埋件锚栓的计算公式。%This paper, according to article 5.2.2 of JGJ 145 -2013 “technical specification for concrete structure of anch-oring force”, made an analysis of the force analysis of post anchor bolt under the interaction of bi-directional torque, shear force, bending, put ing forward the calculation formula of posts anchor bolt under composite force.

  17. Inconspicuous anchoring effects generated by false information

    Institute of Scientific and Technical Information of China (English)

    Chen Qu; Jun Wang; Yuejia Luo

    2008-01-01

    The impact of false information on numerical judgments was examined on young normal subjects by an event-related potential (ERP) experiment. To imitate the judgments in real world, we ensured the subjects acknowledged of the target task. The behavioral results found that both uncertain information and false information assimilated the final estimates: higher after higher anchors and lower after lower anchors; and false information caused a weaker anchoring bias than uncertain information. ERP results provided further electrophysiological evidence for the mechanism of anchoring. In the early phrase, it was an accessibility-dominated process in which two kinds of anchors elicited an N300 component related to the accessibility of anchors propositions. The knowledge relevant to targets joined the process in the late phrase, which caused a larger amplitude of late positive component (LPC) for implausible lower anchors than that for plausible higher anchors. Source analysis showed that medial frontal gyrus, whose activity was suggested to signal the need of adjustment, was more reliable to explain the LPC elicited by implausible lower anchors. Therefore, we suggest that accessibility is facilitated when the external anchor is consistent with the world knowledge, and adjustment is initiated when the external anchor is inconsistent.

  18. [Audiological analysis and peri-and postoperative complications in bone-anchored hearing aid surgery].

    Science.gov (United States)

    Noguchi, Yoshihiro; Takahashi, Masatoki; Kitamura, Ken

    2011-07-01

    The bone-anchored hearing aid (BAHA) has advantages over conventional hearing aids in sound quality and speech reception in silence, but requires surgery and may have peri-and postoperative complications. We evaluated audiological findings and complications in 12 subjects (13 ears)-8 men and 4 women aged 20-71--undergoing BAHA surgery from September 2001 to October 2005. Surgery was for single-sided deafness in one subject. Mean warble tone thresholds with BAHA were 29.9dB and 65.2dB without. Functional gains ranged from 16 to 52dB (mean: 35.3dB). Dural exposure or venous hemorrhage was seen in 4 ears, and mastoid cells opened and a skin flap was damaged in 1 ear each. No severe complications occurred perioperatively. Skin reactions categorized into grade 1 or more were recognized in nearly 70% of ears during the first postoperative year but most were a grade 1 reaction and skin reactions decreased with time. Skin overgrowth occurred in 1 ear immediately after an abutment separated accidentally from the fixture. All complications were treated in outpatient clinics. No fixture extrusion occurred. The decision to proceed with BAHA surgery thus required fully informed consent based on knowledge of peri-and postoperative complications. PMID:21838056

  19. Analysis of genotype-phenotype correlations in human holoprosencephaly.

    Science.gov (United States)

    Solomon, Benjamin D; Mercier, Sandra; Vélez, Jorge I; Pineda-Alvarez, Daniel E; Wyllie, Adrian; Zhou, Nan; Dubourg, Christèle; David, Veronique; Odent, Sylvie; Roessler, Erich; Muenke, Maximilian

    2010-02-15

    Since the discovery of the first gene causing holoprosencephaly (HPE), over 500 patients with mutations in genes associated with non-chromosomal, non-syndromic HPE have been described, with detailed descriptions available in over 300. Comprehensive clinical analysis of these individuals allows examination for the presence of genotype-phenotype correlations. These correlations allow a degree of differentiation between patients with mutations in different HPE-associated genes and for the application of functional studies to determine intragenic correlations. These early correlations are an important advance in the understanding of the clinical aspects of this disease, and in general argue for continued analysis of the genetic and clinical findings of large cohorts of patients with rare diseases in order to better inform both basic biological insight and care and counseling for affected patients and families. PMID:20104608

  20. Indexing and Analysis of Fungal Phenotypes Using Morphology and Spectrometry

    DEFF Research Database (Denmark)

    Hansen, Michael Adsetts Edberg

    2005-01-01

    is therefore important. By rapid and correct identification it is possible to investigate the food e.g. to evaluate the quality, as well as to eliminate already known isolates from drug-discovery screening programs, and perhaps even predict the presence of new drug candidates. Unfortunately, detection...... to evaluate the visual phenotypic characters, a method for visual clone identification of Penicillium commune { the most widespread and most frequently occurring spoilage fungus on cheese { was developed (Papers A, B and C). The method was based on images of fungal colonies acquired after growth on a standard...... medium and involves a high degree of objectivity. On a data set from 137 isolates we obtained a leave-one-out cross-validation identification rate of approximately 93% A fully automated data processing approach for qualitative comparison of a large number of mass spectra from the direct infusion analysis...

  1. Surgical repair of central slip avulsion injuries with Mitek bone anchor--retrospective analysis of a case series.

    LENUS (Irish Health Repository)

    Chan, Jeffrey C Y

    2007-01-01

    The purpose of this study is to describe our technique of central slip repair using the Mitek bone anchor and to evaluate the treatment outcome. Eight digits in eight patients were reconstructed using the bone anchor: three little fingers, two middle fingers, two index fingers and one ring finger. There were two immediate and six delayed repairs (range from one day to eight months). Four patients had pre-operative intensive splinting and physiotherapy to restore passive extension of the proximal interphalangeal joint prior to central slip reconstruction. All patients have made good progress since surgery. No patient requires a second procedure and none of the bone anchors have dislodged or loosened. We conclude that the Mitek bone anchor is a reliable technique to achieve soft tissue to bone fixation in central slip avulsion injuries. We recommend that this technique be considered as a treatment option for patients requiring surgical repair.

  2. Advanced phenotyping and phenotype data analysis for the study of plant growth and development

    OpenAIRE

    Rahaman, Md. Matiur; Chen, Dijun; Gillani, Zeeshan; Klukas, Christian; Chen, Ming

    2015-01-01

    Due to an increase in the consumption of food, feed, fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to breed high yielding crops that can adapt to the future climate changes, particularly in developing countries. To solve these global challenges, novel approaches are required to identify quantitative phenotypes and to explain the genetic basis of agriculturally important traits. These advances will facilitate the screening of germpla...

  3. Analysis on anchoring plate retaining wall of Shanxi Science and Technology Museum%山西省科技馆锚定板挡土墙分析

    Institute of Scientific and Technical Information of China (English)

    张波

    2015-01-01

    介绍了锚定板式挡土墙的受力原理及适用条件,结合工程实例,从参数设计、土压力计算、锚定板抗拔力计算、稳定性分析等方面,阐述了锚定板挡土墙的具体设计方法,指出锚定板挡土墙具有施工速度快、造价低等优势。%This paper introduced the force principle and applicable conditions of anchoring plate retaining wall,combining with the engineering examples,from the parameter design,soil pressure calculation,anchor plate pulling force calculation,stability analysis and other aspects,elabo-rated the specific design method of anchoring plate retaining wall,pointed out that the anchoring plate retaining wall had quick construction speed,low cost and other advantages.

  4. Systematic analysis of experimental phenotype data reveals gene functions.

    Directory of Open Access Journals (Sweden)

    Robert Hoehndorf

    Full Text Available High-throughput phenotyping projects in model organisms have the potential to improve our understanding of gene functions and their role in living organisms. We have developed a computational, knowledge-based approach to automatically infer gene functions from phenotypic manifestations and applied this approach to yeast (Saccharomyces cerevisiae, nematode worm (Caenorhabditis elegans, zebrafish (Danio rerio, fruitfly (Drosophila melanogaster and mouse (Mus musculus phenotypes. Our approach is based on the assumption that, if a mutation in a gene [Formula: see text] leads to a phenotypic abnormality in a process [Formula: see text], then [Formula: see text] must have been involved in [Formula: see text], either directly or indirectly. We systematically analyze recorded phenotypes in animal models using the formal definitions created for phenotype ontologies. We evaluate the validity of the inferred functions manually and by demonstrating a significant improvement in predicting genetic interactions and protein-protein interactions based on functional similarity. Our knowledge-based approach is generally applicable to phenotypes recorded in model organism databases, including phenotypes from large-scale, high throughput community projects whose primary mode of dissemination is direct publication on-line rather than in the literature.

  5. A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

    Directory of Open Access Journals (Sweden)

    Doherty Kathleen M

    2011-12-01

    Full Text Available Abstract Background Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs that are effective against historically multi-PI-resistant HIV-1 variants. Nevertheless, mutation patterns that confer decreasing susceptibility to available PIs continue to arise within the population. Understanding the phenotypic and genotypic patterns responsible for multi-PI resistance is necessary for developing PIs that are active against clinically-relevant PI-resistant HIV-1 variants. Results In this work, we use globally optimal integer programming-based clustering techniques to elucidate multi-PI phenotypic resistance patterns using a data set of 398 HIV-1 protease sequences that have each been phenotyped for susceptibility toward the nine clinically-approved HIV-1 PIs. We validate the information content of the clusters by evaluating their ability to predict the level of decreased susceptibility to each of the available PIs using a cross validation procedure. We demonstrate the finding that as a result of phenotypic cross resistance, the considered clinical HIV-1 protease isolates are confined to ~6% or less of the clinically-relevant phenotypic space. Clustering and feature selection methods are used to find representative sequences and mutations for major resistance phenotypes to elucidate their genotypic signatures. We show that phenotypic similarity does not imply genotypic similarity, that different PI-resistance mutation patterns can give rise to HIV-1 isolates with similar phenotypic profiles. Conclusion Rather than characterizing HIV-1 susceptibility toward each PI individually, our study offers a unique perspective on the phenomenon of PI class resistance by uncovering major multidrug-resistant phenotypic patterns and their often diverse genotypic determinants, providing a methodology that can be applied to understand clinically-relevant phenotypic patterns to aid in the

  6. Application of a stand-alone anchored spacer in noncontiguous anterior cervical arthrodesis with radiologic analysis of the intermediate segment.

    Science.gov (United States)

    Shi, Sheng; Liu, Zu-De; You, Wen-Jie; Ouyang, Yue-Ping; Li, Xin-Feng; Qian, Lie; Zhong, Gui-Bin

    2016-03-01

    The purpose of this study was to describe the clinical features of noncontiguous cervical degenerative disc disease (cDDD), investigate the efficacy and complications of a stand-alone anchored spacer (SAAS) for patients with noncontiguous cDDD, and present radiologic analysis of the intermediate segment (IS) after skip-level fusion. Nineteen consecutive patients with noncontiguous cDDD who underwent skip-level anterior cervical discectomy and fusion (ACDF) with SAAS from January 2010 to December 2012 were enrolled in this study. Clinical outcomes were assessed preoperatively and at 24 months postoperatively using the Japanese Orthopaedic Association score, Neck Disability Index, and Visual Analog Scale. Overall cervical alignment (OCA) of the cervical spine, and the range of motion (ROM), intervertebral disc height (IDH), disc signal intensity and disc protrusion of IS were measured and compared before and after surgery. Clinical outcomes significantly improved compared to preoperative scores. The OCA was corrected and maintained at 24 months postoperatively compared with preoperative values (p0.05). However, decreased signal intensity on T2-weighted MRI was evidenced in three mobile IS at final follow-up (20.0%). Skip-level ACDF with SAAS may be an efficacious option for the treatment of noncontiguous cDDD. PMID:26597607

  7. Application of Mass Cytometry (CyTOF) for Functional and Phenotypic Analysis of Natural Killer Cells.

    Science.gov (United States)

    Kay, Alexander W; Strauss-Albee, Dara M; Blish, Catherine A

    2016-01-01

    Mass cytometry is a novel platform for high-dimensional phenotypic and functional analysis of single cells. This system uses elemental metal isotopes conjugated to monoclonal antibodies to evaluate up to 42 parameters simultaneously on individual cells with minimal overlap between channels. The platform can be customized for analysis of both phenotypic and functional markers. Here, we will describe methods to stain, collect, and analyze intracellular functional markers and surface phenotypic markers on natural killer cells. PMID:27177653

  8. Comparative Metabolomic and Lipidomic Analysis of Phenotype Stratified Prostate Cells.

    Directory of Open Access Journals (Sweden)

    Tanya C Burch

    Full Text Available Prostate cancer (PCa is the most prevalent cancer amongst men and the second most common cause of cancer related-deaths in the USA. Prostate cancer is a heterogeneous disease ranging from indolent asymptomatic cases to very aggressive life threatening forms. The goal of this study was to identify differentially expressed metabolites and lipids in prostate cells with different tumorigenic phenotypes. We have used mass spectrometry metabolomic profiling, lipidomic profiling, bioinformatic and statistical methods to identify, quantify and characterize differentially regulated molecules in five prostate derived cell lines. We have identified potentially interesting species of different lipid subclasses including phosphatidylcholines (PCs, phosphatidylethanolamines (PEs, glycerophosphoinositols (PIs and other metabolites that are significantly upregulated in prostate cancer cells derived from distant metastatic sites. Transcriptomic and biochemical analysis of key enzymes that are involved in lipid metabolism demonstrate the significant upregulation of choline kinase alpha in the metastatic cells compared to the non-malignant and non-metastatic cells. This suggests that different de novo lipogenesis and other specific signal transduction pathways are activated in aggressive metastatic cells as compared to normal and non-metastatic cells.

  9. A Penalized Mixture Model Approach in Genotype/Phenotype Association Analysis for Quantitative Phenotypes

    Directory of Open Access Journals (Sweden)

    Lang Li

    2010-04-01

    Full Text Available A mixture normal model has been developed to partition genotypes in predicting quantitative phenotypes. Its estimation and inference are performed through an EM algorithm. This approach can conduct simultaneous genotype clustering and hypothesis testing. It is a valuable method for predicting the distribution of quantitative phenotypes among multi-locus genotypes across genes or within a gene. This mixture model’s performance is evaluated in data analyses for two pharmacogenetics studies. In one example, thirty five CYP2D6 genotypes were partitioned into three groups to predict pharmacokinetics of a breast cancer drug, Tamoxifen, a CYP2D6 substrate (p-value = 0.04. In a second example, seventeen CYP2B6 genotypes were categorized into three clusters to predict CYP2B6 protein expression (p-value = 0.002. The biological validities of both partitions are examined using established function of CYP2D6 and CYP2B6 alleles. In both examples, we observed genotypes clustered in the same group to have high functional similarities. The power and recovery rate of the true partition for the mixture model approach are investigated in statistical simulation studies, where it outperforms another published method.

  10. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis.

    Science.gov (United States)

    Paux, Etienne; Legeai, Fabrice; Guilhot, Nicolas; Adam-Blondon, Anne-Françoise; Alaux, Michaël; Salse, Jérôme; Sourdille, Pierre; Leroy, Philippe; Feuillet, Catherine

    2008-02-01

    Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective tool to support physical mapping in large genomes. PMID:18038165

  11. Genetic Association Analysis of Complex Diseases Incorporating Intermediate Phenotype Information

    OpenAIRE

    Li, Yafang; Huang, Jian; Amos, Christopher I.

    2012-01-01

    Genetic researchers often collect disease related quantitative traits in addition to disease status because they are interested in understanding the pathophysiology of disease processes. In genome-wide association (GWA) studies, these quantitative phenotypes may be relevant to disease development and serve as intermediate phenotypes or they could be behavioral or other risk factors that predict disease risk. Statistical tests combining both disease status and quantitative risk factors should ...

  12. Hypersensitivity to Suture Anchors

    Directory of Open Access Journals (Sweden)

    Masafumi Goto

    2013-01-01

    Full Text Available Hypersensitivity to suture anchor is extremely rare. Herein, we present a case in which hypersensitivity to suture anchor was strongly suspected. The right rotator cuff of a 50-year-old woman was repaired with a metal suture anchor. Three weeks after the surgery, she developed erythema around her face, trunk, and hands, accompanied by itching. Infection was unlikely because no abnormalities were detected by blood testing or by medical examination. Suspicious of a metallic allergy, a dermatologist performed a patch testing 6 months after the first surgery. The patient had negative reactions to tests for titanium, aluminum, and vanadium, which were the principal components of the suture anchor. The anchor was removed 7 months after the first surgery, and the erythema disappeared immediately. When allergic symptoms occur and persist after the use of a metal anchor, removal should be considered as a treatment option even if the patch test result is negative.

  13. Genetic Analysis of Low BMI Phenotype in the Utah Population Database

    OpenAIRE

    Yates, William R.; Johnson, Craig; McKee, Patrick; Cannon-Albright, Lisa A.

    2013-01-01

    The low body mass index (BMI) phenotype of less than 18.5 has been linked to medical and psychological morbidity as well as increased mortality risk. Although genetic factors have been shown to influence BMI across the entire BMI, the contribution of genetic factors to the low BMI phenotype is unclear. We hypothesized genetic factors would contribute to risk of a low BMI phenotype. To test this hypothesis, we conducted a genealogy data analysis using height and weight measurements from driver...

  14. Structural analysis of the contacts anchoring moenomycin to peptidoglycan glycosyltransferases and implications for antibiotic design

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Y.; Fuse, S.; Ostash, B.; Sliz, P.; Kahne, D.; Walker, S. (Harvard-Med); (Harvard)

    2008-08-20

    Peptidoglycan glycosyltransferases (PGTs), enzymes that catalyze the formation of the glycan chains of the bacterial cell wall, have tremendous potential as antibiotic targets. The moenomycins, a potent family of natural product antibiotics, are the only known active site inhibitors of the PGTs and serve as blueprints for the structure-based design of new antibacterials. A 2.8 {angstrom} structure of a Staphylococcus aureus PGT with moenomycin A bound in the active site appeared recently, potentially providing insight into substrate binding; however, the protein-ligand contacts were not analyzed in detail and the implications of the structure for inhibitor design were not addressed. We report here the 2.3 {angstrom} structure of a complex of neryl-moenomycin A bound to the PGT domain of Aquifex aeolicus PBP1A. The structure allows us to examine protein-ligand contacts in detail and implies that six conserved active site residues contact the centrally located F-ring phosphoglycerate portion of neryl-moenomycin A. A mutational analysis shows that all six residues play important roles in enzymatic activity. We suggest that small scaffolds that maintain these key contacts will serve as effective PGT inhibitors. To test this hypothesis, we have prepared, via heterologous expression of a subset of moenomycin biosynthetic genes, a novel moenomycin intermediate that maintains these six contacts but does not contain the putative minimal pharmacophore. This compound has comparable biological activity to the previously proposed minimal pharmacophore. The results reported here may facilitate the design of antibiotics targeted against peptidoglycan glycosyltransferases.

  15. Experimental analysis of multi-attribute decision-making based on Atanassov intuitionistic fuzzy sets: a discussion of anchor dependency and accuracy functions

    Science.gov (United States)

    Chen, Ting-Yu

    2012-06-01

    This article presents a useful method for relating anchor dependency and accuracy functions to multiple attribute decision-making (MADM) problems in the context of Atanassov intuitionistic fuzzy sets (A-IFSs). Considering anchored judgement with displaced ideals and solution precision with minimal hesitation, several auxiliary optimisation models have proposed to obtain the optimal weights of the attributes and to acquire the corresponding TOPSIS (the technique for order preference by similarity to the ideal solution) index for alternative rankings. Aside from the TOPSIS index, as a decision-maker's personal characteristics and own perception of self may also influence the direction in the axiom of choice, the evaluation of alternatives is conducted based on distances of each alternative from the positive and negative ideal alternatives, respectively. This article originates from Li's [Li, D.-F. (2005), 'Multiattribute Decision Making Models and Methods Using Intuitionistic Fuzzy Sets', Journal of Computer and System Sciences, 70, 73-85] work, which is a seminal study of intuitionistic fuzzy decision analysis using deduced auxiliary programming models, and deems it a benchmark method for comparative studies on anchor dependency and accuracy functions. The feasibility and effectiveness of the proposed methods are illustrated by a numerical example. Finally, a comparative analysis is illustrated with computational experiments on averaging accuracy functions, TOPSIS indices, separation measures from positive and negative ideal alternatives, consistency rates of ranking orders, contradiction rates of the top alternative and average Spearman correlation coefficients.

  16. Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution.

    Science.gov (United States)

    Khang, Tsung Fei; Soo, Oi Yoon Michelle; Tan, Wooi Boon; Lim, Lee Hong Susan

    2016-01-01

    Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. When combined with morphological and molecular data, analysis of anchor morphometry can potentially answer a wide range of biological questions. Materials and Methods. We used data from anchor morphometry, body size and morphology of 13 Ligophorus (Monogenea: Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts: Moolgarda buchanani (Bleeker) and Liza subviridis (Valenciennes) from Malaysia. Anchor shape and size data (n = 530) were generated using methods of geometric morphometrics. We used 28S rRNA, 18S rRNA, and ITS1 sequence data to infer a maximum likelihood phylogeny. We discriminated species using principal component and cluster analysis of shape data. Adams's K mult was used to detect phylogenetic signal in anchor shape. Phylogeny-correlated size and shape changes were investigated using continuous character mapping and directional statistics, respectively. We assessed morphological constraints in anchor morphometry using phylogenetic regression of anchor shape against body size and anchor size. Anchor morphological integration was studied using partial least squares method. The association between copulatory organ morphology and anchor shape and size in phylomorphospace was used to test the Rohde-Hobbs hypothesis. We created monogeneaGM, a new R package that integrates analyses of monogenean anchor geometric morphometric data with morphological and phylogenetic data. Results. We discriminated 12 of the 13 Ligophorus species using anchor shape data. Significant phylogenetic signal was detected in anchor shape. Thus, we discovered new morphological characters based on anchor shaft shape, the length between the inner root point and the outer root

  17. Influence of Anchoring on Burial Depth of Submarine Pipelines

    Science.gov (United States)

    Zhuang, Yuan; Li, Yang; Su, Wei

    2016-01-01

    Since the beginning of the twenty-first century, there has been widespread construction of submarine oil-gas transmission pipelines due to an increase in offshore oil exploration. Vessel anchoring operations are causing more damage to submarine pipelines due to shipping transportation also increasing. Therefore, it is essential that the influence of anchoring on the required burial depth of submarine pipelines is determined. In this paper, mathematical models for ordinary anchoring and emergency anchoring have been established to derive an anchor impact energy equation for each condition. The required effective burial depth for submarine pipelines has then been calculated via an energy absorption equation for the protection layer covering the submarine pipelines. Finally, the results of the model calculation have been verified by accident case analysis, and the impact of the anchoring height, anchoring water depth and the anchor weight on the required burial depth of submarine pipelines has been further analyzed. PMID:27166952

  18. Influence of Anchoring on Burial Depth of Submarine Pipelines.

    Science.gov (United States)

    Zhuang, Yuan; Li, Yang; Su, Wei

    2016-01-01

    Since the beginning of the twenty-first century, there has been widespread construction of submarine oil-gas transmission pipelines due to an increase in offshore oil exploration. Vessel anchoring operations are causing more damage to submarine pipelines due to shipping transportation also increasing. Therefore, it is essential that the influence of anchoring on the required burial depth of submarine pipelines is determined. In this paper, mathematical models for ordinary anchoring and emergency anchoring have been established to derive an anchor impact energy equation for each condition. The required effective burial depth for submarine pipelines has then been calculated via an energy absorption equation for the protection layer covering the submarine pipelines. Finally, the results of the model calculation have been verified by accident case analysis, and the impact of the anchoring height, anchoring water depth and the anchor weight on the required burial depth of submarine pipelines has been further analyzed. PMID:27166952

  19. Download - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available The Rice Growth Monitoring for The Phenotypic Functional Analysis Download First of all, please read the lic... Download - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  20. Susceptibility to anchoring effects

    Directory of Open Access Journals (Sweden)

    Todd McElroy

    2007-02-01

    Full Text Available Previous research on anchoring has shown this heuristic to be a very robust psychological phenomenon ubiquitous across many domains of human judgment and decision-making. Despite the prevalence of anchoring effects, researchers have only recently begun to investigate the underlying factors responsible for how and in what ways a person is susceptible to them. This paper examines how one such factor, the Big-Five personality trait of openness-to-experience, influences the effect of previously presented anchors on participants' judgments. Our findings indicate that participants high in openness-to-experience were significantly more influenced by anchoring cues relative to participants low in this trait. These findings were consistent across two different types of anchoring tasks providing convergent evidence for our hypothesis.

  1. Exhaled breath analysis discriminates phenotypes of acute lung injury (ALI)

    OpenAIRE

    Bos, L.D.J.; Hemmes, S.N.T.; Nijsen, T.M.E.; P. J. Sterk; Schultz, M.J

    2012-01-01

    Introduction It has been postulated that the pathophysiology and clinical presentation of ALI based on pulmonary and non-pulmonary etiology represent different phenotypes1. Until now, little biological evidence on the molecular level has been presented to support this hypothesis. Exhaled air contains volatile organic compounds (VOCs), metabolites of systemic or respiratory origin. Exhaled air metabolites may differ between diseases2. Molecular profiling of exhaled air of intubated and mechani...

  2. Cultural Anchors and the Organization of Differences: A Multi-method Analysis of LGBT Marches on Washington.

    Science.gov (United States)

    Ghaziani, Amin; Baldassarri, Delia

    2011-04-01

    Social scientists describe culture as either coherent or incoherent and political dissent as either unifying or divisive. This article moves beyond such dichotomies. Content, historical, and network analyses of public debates on how to organize four lesbian, gay, bisexual, and transgender (LGBT) Washington marches provide evidence for an integrative position. Rather than just describe consistencies or contradictions, we contend that the key analytic challenge is to explain the organization of differences. We propose one way of doing this using the mechanism of a cultural anchor. Within and across marches, a small collection of ideas remains fixed in the national conversation, yet in a way that allows activists to address their internal diversity and respond to unfolding historical events. These results suggest that activists do not simply organize around their similarities but, through cultural anchors, they use their commonalities to build a thinly coherent foundation that can also support their differences. Situated at the nexus of culture, social movements, sexualities, and networks, this article demonstrates how the anchoring mechanism works in the context of LGBT political organizing. PMID:23661809

  3. Anchoring visions in organizations

    DEFF Research Database (Denmark)

    Simonsen, Jesper

    1999-01-01

    This paper introduces the term 'anchoring' within systems development: Visions, developed through early systems design within an organization, need to be deeply rooted in the organization. A vision's rationale needs to be understood by those who decide if the vision should be implemented as well as...... anchoring is considered to be a main activity, is outlined. The task of anchoring visions is described, and techniques and activities are suggested with respect to those actors that have to act on the visions and the recommendations from a design proposal. The paper concludes that obtaining appropriate...

  4. The anchor of the frameless intrauterine device does not migrate over time: an analysis in over 300 women

    Directory of Open Access Journals (Sweden)

    Wildemeersch D

    2014-12-01

    Full Text Available Dirk Wildemeersch,1 Ansgar Pett,2 Sohela Jandi,2 Kilian Nolte,3 Wolfgang Albrecht4 1Gynecological Outpatient Clinic and IUD Training Centre, Ghent, Belgium; 2Gynecological Outpatient Clinic, Berlin, Germany; 3Gynecological Outpatient Clinic, Uetze, Germany; 4Gynecological Outpatient Clinic, Feldkirchen, Austria Objective: To evaluate the correct position of the anchor at insertion and follow-up and assess if migration of the anchor occurs over time. Materials and methods: This was an insertion-related, prospective, postmarketing study in 309 women. Following insertion, women were followed up at 4–6 weeks, 6 months, and yearly thereafter. The position of the visualized anchor in the fundus of the uterus was evaluated using ultrasound by measuring its distance from the serosal surface of the uterus (SA-distance. Results: A total of 309 parous (n=115 and nulliparous (n=194 women were fitted with the frameless GyneFix 200 or the GyneFix 330 intrauterine device for contraception. The mean SA-distance in 306 parous and nulliparous women was 6.0 mm (range 2.0–24.0 mm at insertion in the parous group and 5.4 mm (range 1.3–11.0 mm in the nulliparous group. At the first follow-up in 281 women, the SA-distance was 6.0 mm (range 2.0–12.0 mm in the parous group and 5.5 mm (range 1.1–11.0 mm in the nulliparous group. The SA-distance was not significantly different. One patient had an exceptionally large SA-distance of 24 mm, probably due to insertion in the posterior wall. No follow-up could be done in this patient. In 77 women, the SA-distance was measured up to 42 months. The mean SA-distance at insertion in the parous group was 5.2 mm (range 3.0–8.5 mm and 4.8 mm (range 1.3–7.0 mm in the nulliparous group. At the last follow-up up to 36 months or longer, the SA-distance was 5.1 mm (range 3.0–8.5 mm in the parous group and 4.9 mm (range 1.3–7.0 mm in the nulliparous group. The SA-distance was not significantly different. The visualized

  5. Peax: interactive visual analysis and exploration of complex clinical phenotype and gene expression association.

    Science.gov (United States)

    Hinterberg, Michael A; Kao, David P; Bristow, Michael R; Hunter, Lawrence E; Port, J David; Görg, Carsten

    2015-01-01

    Increasing availability of high-dimensional clinical data, which improves the ability to define more specific phenotypes, as well as molecular data, which can elucidate disease mechanisms, is a driving force and at the same time a major challenge for translational and personalized medicine. Successful research in this field requires an approach that ties together specific disease and health expertise with understanding of molecular data through statistical methods. We present PEAX (Phenotype-Expression Association eXplorer), built upon open-source software, which integrates visual phenotype model definition with statistical testing of expression data presented concurrently in a web-browser. The integration of data and analysis tasks in a single tool allows clinical domain experts to obtain new insights directly through exploration of relationships between multivariate phenotype models and gene expression data, showing the effects of model definition and modification while also exploiting potential meaningful associations between phenotype and miRNA-mRNA regulatory relationships. We combine the web visualization capabilities of Shiny and D3 with the power and speed of R for backend statistical analysis, in order to abstract the scripting required for repetitive analysis of sub-phenotype association. We describe the motivation for PEAX, demonstrate its utility through a use case involving heart failure research, and discuss computational challenges and observations. We show that our visual web-based representations are well-suited for rapid exploration of phenotype and gene expression association, facilitating insight and discovery by domain experts. PMID:25592601

  6. Phenotypic and Functional Analysis of Porcine T Lymphocytes

    Institute of Scientific and Technical Information of China (English)

    李华; 陈应华

    2001-01-01

    Porcine and other higher mammals express clusters of differentiation (CD) antigens on the surface of T lymphocytes, such as CD2, CD3, CD4, CD8, etc. However, in porcine, a high percentage of the CD4+ CD8-T lymphocyte subpopulation exist in the peripheral blood and the ratio of the CD4+ and CD8+ T lymphocyte subpopulations is reversed. These differences bring new challenges to better understanding of the phenotype and function of porcine T lymphocytes in antigen recognition and immune response.

  7. Cluster analysis in severe emphysema subjects using phenotype and genotype data: an exploratory investigation

    Directory of Open Access Journals (Sweden)

    Martinez Fernando J

    2010-03-01

    Full Text Available Abstract Background Numerous studies have demonstrated associations between genetic markers and COPD, but results have been inconsistent. One reason may be heterogeneity in disease definition. Unsupervised learning approaches may assist in understanding disease heterogeneity. Methods We selected 31 phenotypic variables and 12 SNPs from five candidate genes in 308 subjects in the National Emphysema Treatment Trial (NETT Genetics Ancillary Study cohort. We used factor analysis to select a subset of phenotypic variables, and then used cluster analysis to identify subtypes of severe emphysema. We examined the phenotypic and genotypic characteristics of each cluster. Results We identified six factors accounting for 75% of the shared variability among our initial phenotypic variables. We selected four phenotypic variables from these factors for cluster analysis: 1 post-bronchodilator FEV1 percent predicted, 2 percent bronchodilator responsiveness, and quantitative CT measurements of 3 apical emphysema and 4 airway wall thickness. K-means cluster analysis revealed four clusters, though separation between clusters was modest: 1 emphysema predominant, 2 bronchodilator responsive, with higher FEV1; 3 discordant, with a lower FEV1 despite less severe emphysema and lower airway wall thickness, and 4 airway predominant. Of the genotypes examined, membership in cluster 1 (emphysema-predominant was associated with TGFB1 SNP rs1800470. Conclusions Cluster analysis may identify meaningful disease subtypes and/or groups of related phenotypic variables even in a highly selected group of severe emphysema subjects, and may be useful for genetic association studies.

  8. Susceptibility to anchoring effects

    OpenAIRE

    Todd McElroy; Keith Dowd

    2007-01-01

    Previous research on anchoring has shown this heuristic to be a very robust psychological phenomenon ubiquitous across many domains of human judgment and decision-making. Despite the prevalence of anchoring effects, researchers have only recently begun to investigate the underlying factors responsible for how and in what ways a person is susceptible to them. This paper examines how one such factor, the Big-Five personality trait of openness-to-experience, influences the effect of previously p...

  9. License - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available The Rice Growth Monitoring for The Phenotypic Functional Analysis License License to Use This Database Last ...be sure attribute this database as follows: The Rice Growth Monitoring for the Phenotypic Functional...e History of This Database Site Policy | Contact Us License - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  10. Auditory hedonic phenotypes in dementia: A behavioural and neuroanatomical analysis.

    Science.gov (United States)

    Fletcher, Phillip D; Downey, Laura E; Golden, Hannah L; Clark, Camilla N; Slattery, Catherine F; Paterson, Ross W; Schott, Jonathan M; Rohrer, Jonathan D; Rossor, Martin N; Warren, Jason D

    2015-06-01

    Patients with dementia may exhibit abnormally altered liking for environmental sounds and music but such altered auditory hedonic responses have not been studied systematically. Here we addressed this issue in a cohort of 73 patients representing major canonical dementia syndromes (behavioural variant frontotemporal dementia (bvFTD), semantic dementia (SD), progressive nonfluent aphasia (PNFA) amnestic Alzheimer's disease (AD)) using a semi-structured caregiver behavioural questionnaire and voxel-based morphometry (VBM) of patients' brain MR images. Behavioural responses signalling abnormal aversion to environmental sounds, aversion to music or heightened pleasure in music ('musicophilia') occurred in around half of the cohort but showed clear syndromic and genetic segregation, occurring in most patients with bvFTD but infrequently in PNFA and more commonly in association with MAPT than C9orf72 mutations. Aversion to sounds was the exclusive auditory phenotype in AD whereas more complex phenotypes including musicophilia were common in bvFTD and SD. Auditory hedonic alterations correlated with grey matter loss in a common, distributed, right-lateralised network including antero-mesial temporal lobe, insula, anterior cingulate and nucleus accumbens. Our findings suggest that abnormalities of auditory hedonic processing are a significant issue in common dementias. Sounds may constitute a novel probe of brain mechanisms for emotional salience coding that are targeted by neurodegenerative disease. PMID:25929717

  11. The Analysis of Force State and Emphasis of Health Monitoring about the Anchor of Existing Bridge and Tunnel%既有桥梁隧道锚受力状态分析及健康监测重点

    Institute of Scientific and Technical Information of China (English)

    吕曹炯; 黄贵明; 张望胜; 叶梦君

    2015-01-01

    采用有限元软件对坝陵河大桥隧道锚进行受力状态分析,表明隧道锚整体是稳定的,需对局部区域加强监控。根据应力计算结果,需加强监控的区域是前锚室空腔上部、后锚室空腔上部和支墩远离锚体一侧的下部;根据位移计算结果,需加强监控的区域是支墩及前锚室区域处围岩、主缆护室和后锚室围岩。根据计算结果确定隧道锚运营期健康监测测点的布设,并指导实测数据分析。%Numerical analysis about force state of the anchor of Balinghe Bridge and tunnel by using fi-nite element software has been performed in this paper.The results show that the anchor of tunnel is stable and partial location needs strengthening monitoring.According to the stress calculating results, the parts which need strengthening monitoring are the upside of former anchor chamber and behind anchor chamber and one side of lower part of buttress which is far from anchor.According to the dis-placement calculating results,the parts which need strengthening monitoring are the surrounding rock around buttress and former anchor chamber and behind anchor chamber,the protection chamber of main cable.The results of this paper have guiding significance to the measuring point arrangement of health monitoring in operation period and the analysis of measured data of tunnel anchor.

  12. Recent Study of Drag Embedment Plate Anchors in China

    Institute of Scientific and Technical Information of China (English)

    Haixiao Liu

    2012-01-01

    Experimental and theoretical studies of drag embedment plate anchors recently carried out in Tianjin University are summarized in this research paper,which involve a series of important topics relevant to the study of drag anchors.The techniques for measuring the trajectory and movement direction of drag anchors in soils,the techniques for measuring the moving embedment point and reverse catenary shape of the embedded drag line,the penetration mechanism and kinematic behavior of drag anchors,the ultimate embedment depth of drag anchors,the movement direction of the anchor with an arbitrary fluke section,the reverse catenary properties of the embedded drag line,the interactional properties between drag anchor and installation line,the kinematic model of drag anchors in seabed soils,and the analytical method for predicting the anchor trajectory in soils will all be examined.The present work remarkably reduces the uncertainties in design and analysis of drag embedment plate anchors,and is beneficial to improving the application of this new type of drag anchor in offshore engineering.

  13. Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases

    Science.gov (United States)

    Hoehndorf, Robert; Schofield, Paul N.; Gkoutos, Georgios V.

    2015-06-01

    Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together, and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.

  14. Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases

    KAUST Repository

    Hoehndorf, Robert

    2015-06-08

    Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together, and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.

  15. FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A glycosylphosphatidylinositol (GPI) anchor is a common but complex C-terminal post-translational modification of extracellular proteins in eukaryotes. Here we investigate the problem of correctly annotating GPI-anchored proteins for the growing number of sequences in public databases. We developed a computational system, called FragAnchor, based on the tandem use of a neural network (NN) and a hidden Markov model (HMM). Firstly, NN selects potential GPI-anchored proteins in a dataset, then HMM parses these potential GPI signals and refines the prediction by qualitative scoring. FragAnchor correctly predicted 91% of all the GPI-anchored proteins annotated in the Swiss-Prot database.In a large-scale analysis of 29 eukaryote proteomes, FragAnchor predicted that the percentage of highly probable GPI-anchored proteins is between 0.21% and 2.01%. The distinctive feature of FragAnchor, compared with other systems,is that it targets only the C-terminus of a protein, making it less sensitive to the background noise found in databases and possible incomplete protein sequences. Moreover, FragAnchor can be used to predict GPI-anchored proteins in all eukaryotes. Finally, by using qualitative scoring, the predictions combine both sensitivity and information content. The predictor is publicly available at http: // navet. ics. hawaii.edu/~fraganchor/NNHMM/NNHMM.html.

  16. Simplified Analytical Method for Optimized Initial Shape Analysis of Self-Anchored Suspension Bridges and Its Verification

    Directory of Open Access Journals (Sweden)

    Myung-Rag Jung

    2015-01-01

    Full Text Available A simplified analytical method providing accurate unstrained lengths of all structural elements is proposed to find the optimized initial state of self-anchored suspension bridges under dead loads. For this, equilibrium equations of the main girder and the main cable system are derived and solved by evaluating the self-weights of cable members using unstrained cable lengths and iteratively updating both the horizontal tension component and the vertical profile of the main cable. Furthermore, to demonstrate the validity of the simplified analytical method, the unstrained element length method (ULM is applied to suspension bridge models based on the unstressed lengths of both cable and frame members calculated from the analytical method. Through numerical examples, it is demonstrated that the proposed analytical method can indeed provide an optimized initial solution by showing that both the simplified method and the nonlinear FE procedure lead to practically identical initial configurations with only localized small bending moment distributions.

  17. Degradation theories of concrete and development of a new deviatoric model in incremental tangent formulation: limit analysis applied to case of anchor bolts embedded in concrete

    International Nuclear Information System (INIS)

    This research is achieved in the general framework of the study of the concrete behaviour. It has for objective the development of a new behaviour model satisfying to the particular requirements for an industrial exploitation. After the analysis of different existent models, a first development has concerned models based on the smeared crack theory. A new formulation of the theory permitted to overcome the stress locking problem. However, the analysis showed the persistence of some limits inert to this approach in spite of this improvement. Then, an analysis of the physical mechanisms of the concrete degradation has been achieved and permitted to develop the new damage model MODEV. The general formulation of this model is based on the theory of the thermodynamics and applied to the case of the heterogeneous and brittle materials. The MODEV model considers two damage mechanisms: extension and sliding. The model considers also that the relative tangent displacement between microcracks lips is responsible of the strain irreversibility. Thus, the rate of inelastic strain becomes function of the damage and the heterogeneity index of the material. The unilateral effect is taken in account as an elastic hardening or softening process according to re-closing or reopening of cracks. The model is written within the framework of non standard generalised materials in incremental tangent formulation and implemented in the general finite element code SYMPHONIE. The validation of the model has been achieved on the basis of several tests issued from the literature. The second part of this research has concerned the development of the CHEVILAB software. This simulation tool based on the limit analysis approach permit the evaluation of the ultimate load capacity of anchors bolts. The kinematics approach of the limit analysis has been adapted to the problem of anchors while considering several specific failure mechanisms. This approach has been validated then by comparison with the

  18. Image analysis and platform development for automated phenotyping in cytomics

    NARCIS (Netherlands)

    Yan, Kuan

    2013-01-01

    This thesis is dedicated to the empirical study of image analysis in HT/HC screen study. Often a HT/HC screening produces extensive amounts that cannot be manually analyzed. Thus, an automated image analysis solution is prior to an objective understanding of the raw image data. Compared to general a

  19. Trisomy 2p: Analysis of unusual phenotypic findings

    Energy Technology Data Exchange (ETDEWEB)

    Lurie, I.W.; Ilyina, H.G.; Gurevich, D.B. [Belorussian Research Institute of Hereditary Disease, Minsk (Russian Federation)] [and others

    1995-01-16

    We present three probands with partial trisomies 2p21-23 due to ins(4;2)(q21;p21p23) pat, 2p23-pter due to t(2;4)(p23;q35)mat, and 2p21-pter due to t(2;11)(p21;q23.3)mat. More than 50 cases of partial trisomy 2p have been reviewed and some abnormalities, unusual for most other types of structural autosomal imbalance, have been found in patients with inherited forms of 2p trisomy and in their non-karyotyped sibs. Neural tube defects (anencephaly, occipital encephalocele, and spina bifida) were found in five probands and 4/6 affected non-karyotyped sibs. The only triplicated segment common to all was 2p24. Different forms of {open_quotes}broncho-pulmonary a/hypoplasia{close_quotes} (including two cases of lung agenesis) were described in four patients (overlapping triplicated segment was 2p21-p25). Three patients (with overlapping triplicated segment 2p23-p25) had diaphragmatic hernia. Abnormal rotation of the heart or L-transposition of large vessels (with or without visceral heterotaxia) was found in two infants (overlapping triplicated segment 2p23-p24). In two patients with common triplicated segment 2p22.3-p25, neuroblastoma has been described. The occurrence of all these defects may be explained either by the action of the same gene(s) mapped to 2p24 or by action of some independent factors located in different segments of the short arm. Although the latter hypothesis is much less probable, it can not be rejected at the present time. We propose the existence of a genetic system controlling surveillance of an abnormal embryo to explain the phenotypic differences between patients with the same imbalance within a family. In some {open_quotes}restrictive{close_quotes} combinations the abnormal embryos will die, although in {open_quotes}permissive{close_quotes} combinations they can survive. 47 refs., 2 figs., 3 tabs.

  20. Anchoring the Deficit of the Anchor Deficit: Dyslexia or Attention?

    Science.gov (United States)

    Willburger, Edith; Landerl, Karin

    2010-01-01

    In the anchoring deficit hypothesis of dyslexia ("Trends Cogn. Sci.", 2007; 11: 458-465), it is proposed that perceptual problems arise from the lack of forming a perceptual anchor for repeatedly presented stimuli. A study designed to explicitly test the specificity of the anchoring deficit for dyslexia is presented. Four groups, representing all…

  1. Intra-familiar discordant PKU phenotype explained by mutation analysis in three pedigrees.

    Science.gov (United States)

    Trunzo, Roberta; Santacroce, Rosa; D'Andrea, Giovanna; Longo, Vittoria; De Girolamo, Giuseppe; Dimatteo, Claudia; Leccese, Angelica; Lillo, Vincenza; Papadia, Francesco; Margaglione, Maurizio

    2014-02-01

    Classical phenylketonuria (PKU) and mild hyperphenylalaninemia (MHP) are two phenotypes of phenylalanine hydroxylase (PAH) deficiency with different degrees of severity. We have analyzed three families in which classical PKU, MHP and a normal phenotype occurred within each family due to the different combinations of three mutations segregating within the family. Indeed, sequence PAH analysis revealed three different alleles segregating in each family. This report suggests that when discordant phenotypes occur in a family, complete analysis of the PAH gene may be performed in order to support the diagnosis and assist in accurate genetic counseling and patient management. We further support the marked heterogeneity of hyperphenylalaninemia primarily due to allelic heterogeneity at the PAH locus. PMID:24296287

  2. Frailty phenotypes in the elderly based on cluster analysis

    DEFF Research Database (Denmark)

    Dato, Serena; Montesanto, Alberto; Lagani, Vincenzo;

    2012-01-01

    genetic background on the frailty status is still questioned. We investigated the applicability of a cluster analysis approach based on specific geriatric parameters, previously set up and validated in a southern Italian population, to two large longitudinal Danish samples. In both cohorts, we identified...

  3. WormScan: a technique for high-throughput phenotypic analysis of Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Mark D Mathew

    Full Text Available BACKGROUND: There are four main phenotypes that are assessed in whole organism studies of Caenorhabditis elegans; mortality, movement, fecundity and size. Procedures have been developed that focus on the digital analysis of some, but not all of these phenotypes and may be limited by expense and limited throughput. We have developed WormScan, an automated image acquisition system that allows quantitative analysis of each of these four phenotypes on standard NGM plates seeded with E. coli. This system is very easy to implement and has the capacity to be used in high-throughput analysis. METHODOLOGY/PRINCIPAL FINDINGS: Our system employs a readily available consumer grade flatbed scanner. The method uses light stimulus from the scanner rather than physical stimulus to induce movement. With two sequential scans it is possible to quantify the induced phototactic response. To demonstrate the utility of the method, we measured the phenotypic response of C. elegans to phosphine gas exposure. We found that stimulation of movement by the light of the scanner was equivalent to physical stimulation for the determination of mortality. WormScan also provided a quantitative assessment of health for the survivors. Habituation from light stimulation of continuous scans was similar to habituation caused by physical stimulus. CONCLUSIONS/SIGNIFICANCE: There are existing systems for the automated phenotypic data collection of C. elegans. The specific advantages of our method over existing systems are high-throughput assessment of a greater range of phenotypic endpoints including determination of mortality and quantification of the mobility of survivors. Our system is also inexpensive and very easy to implement. Even though we have focused on demonstrating the usefulness of WormScan in toxicology, it can be used in a wide range of additional C. elegans studies including lifespan determination, development, pathology and behavior. Moreover, we have even adapted the

  4. Molecular Analysis Expands the Spectrum of Phenotypes Associated with GLI3 Mutations

    NARCIS (Netherlands)

    J.J. Johnston; J.C. Sapp; J.T. Turner; D. Amor; S. Aftimos; K.A. Aleck; M. Bocian; J.N. Bodurtha; G.F. Cox; C.J. Curry; R. Day; D. Donnai; M. Field; I. Fujiwara; M. Gabbett; M. Gal; J.M. Graham Jr; P. Hedera; R.C.M. Hennekam; J.H. Hersh; R.J. Hopkin; H. Kayserili; A.M.J. Kidd; V. Kimonis; A.E. Lin; S.A. Lynch; M. Maisenbacher; S. Mansour; J. McGaughran; L. Mehta; H. Murphy; M. Raygada; N.H. Robin; A.F. Rope; K.N. Rosenbaum; G.B. Schaefer; A. Shealy; W. Smith; M. Soller; A Sommer; H.J. Stalker; B. Steiner; M.J. Stephan; D. Tilstra; S. Tomkins; P. Trapane; A.C.H. Tsai; M.I. van Allen; P.C. Vasudevan; B. Zabel; J. Zunich; G.C.M. Black; L.G. Biesecker

    2010-01-01

    A range of phenotypes including Greig cephalopolysyndactyly and Pallister-Hall syndromes (GCPS, PHS) are caused by pathogenic mutation of the GLI3 gene. To characterize the clinical variability of GLI3 mutations, we present a subset of a cohort of 174 probands referred for GLI3 analysis. Eighty-one

  5. Markov chain Monte Carlo linkage analysis of a complex qualitative phenotype.

    Science.gov (United States)

    Hinrichs, A; Lin, J H; Reich, T; Bierut, L; Suarez, B K

    1999-01-01

    We tested a new computer program, LOKI, that implements a reversible jump Markov chain Monte Carlo (MCMC) technique for segregation and linkage analysis. Our objective was to determine whether this software, designed for use with continuously distributed phenotypes, has any efficacy when applied to the discrete disease states of the simulated data from the Mordor data from GAW Problem 1. Although we were able to identify the genomic location for two of the three quantitative trait loci by repeated application of the software, the MCMC sampler experienced significant mixing problems indicating that the method, as currently formulated in LOKI, was not suitable for the discrete phenotypes in this data set. PMID:10597502

  6. Condensing Raman spectrum for single-cell phenotype analysis

    KAUST Repository

    Sun, Shiwei

    2015-12-09

    Background In recent years, high throughput and non-invasive Raman spectrometry technique has matured as an effective approach to identification of individual cells by species, even in complex, mixed populations. Raman profiling is an appealing optical microscopic method to achieve this. To fully utilize Raman proling for single-cell analysis, an extensive understanding of Raman spectra is necessary to answer questions such as which filtering methodologies are effective for pre-processing of Raman spectra, what strains can be distinguished by Raman spectra, and what features serve best as Raman-based biomarkers for single-cells, etc. Results In this work, we have proposed an approach called rDisc to discretize the original Raman spectrum into only a few (usually less than 20) representative peaks (Raman shifts). The approach has advantages in removing noises, and condensing the original spectrum. In particular, effective signal processing procedures were designed to eliminate noise, utilising wavelet transform denoising, baseline correction, and signal normalization. In the discretizing process, representative peaks were selected to signicantly decrease the Raman data size. More importantly, the selected peaks are chosen as suitable to serve as key biological markers to differentiate species and other cellular features. Additionally, the classication performance of discretized spectra was found to be comparable to full spectrum having more than 1000 Raman shifts. Overall, the discretized spectrum needs about 5storage space of a full spectrum and the processing speed is considerably faster. This makes rDisc clearly superior to other methods for single-cell classication.

  7. Undiagnosed genetic muscle disease in the north of England: an in depth phenotype analysis.

    Science.gov (United States)

    Harris, Elizabeth; Laval, Steve; Hudson, Judith; Barresi, Rita; De Waele, Liesbeth; Straub, Volker; Lochmüller, Hanns; Bushby, Kate; Sarkozy, Anna

    2013-01-01

    Advances in the molecular characterisation of genetic muscle disease has been rapid, as demonstrated by a recent analysis of these conditions in the north of England by Norwood et al (2009), in which a genetic diagnosis was achieved for 75.7% of patients. However, there remain many patients with suspected genetic muscle disease in who a diagnosis is not obtained, often despite considerable diagnostic effort, and these patients are now being considered for the application of new technologies such as next generation sequencing. This study aimed to provide an in-depth phenotype analysis of undiagnosed patients referred to the Northern region muscle clinic with suspected genetic muscle disease, with the intention of gaining insight into these conditions, identifing cases with a shared phenotype who may be amenable to collective diagnostic testing or research, and evaluating the strengths and limitations of our current diagnostic strategy. We used two approaches: a review of clinical findings in patients with undiagnosed muscle disease, and a hierarchical cluster analysis to provide an unbiased interpretation of the phenotype data. These joint approaches identified a correlation of phenotypic features according to the age of disease onset and also delineated several interesting groups of patients, as well as highlighting areas of frequent diagnostic difficulty that could benefit from the use of new high-throughput diagnostic techniques. Correspondence to: anna.sarkozy@ncl.ac.uk. PMID:23788081

  8. Hair Analysis for Determination of Isoniazid Concentrations and Acetylator Phenotype during Antituberculous Treatment

    OpenAIRE

    Michael Eisenhut; Detlef Thieme; Dagmar Schmid; Sybille Fieseler; Hans Sachs

    2012-01-01

    Background. Analysis of isoniazid (INH) uptake has been based on measurement of plasma concentrations providing a short-term and potentially biased view. Objectives. To establish hair analysis as a tool to measure long-term uptake of INH and to assess whether acetylator phenotype in hair reflects N-acetyltransferase-2 (NAT2) genotype. Design and Methods. INH and acetyl-INH concentrations in hair were determined in patients on INH treatment for M. tuberculosis infection using high pressure liq...

  9. Automated local bright feature image analysis of nuclear protein distribution identifies changes in tissue phenotype

    International Nuclear Information System (INIS)

    The organization of nuclear proteins is linked to cell and tissue phenotypes. When cells arrest proliferation, undergo apoptosis, or differentiate, the distribution of nuclear proteins changes. Conversely, forced alteration of the distribution of nuclear proteins modifies cell phenotype. Immunostaining and fluorescence microscopy have been critical for such findings. However, there is an increasing need for quantitative analysis of nuclear protein distribution to decipher epigenetic relationships between nuclear structure and cell phenotype, and to unravel the mechanisms linking nuclear structure and function. We have developed imaging methods to quantify the distribution of fluorescently-stained nuclear protein NuMA in different mammary phenotypes obtained using three-dimensional cell culture. Automated image segmentation of DAPI-stained nuclei was generated to isolate thousands of nuclei from three-dimensional confocal images. Prominent features of fluorescently-stained NuMA were detected using a novel local bright feature analysis technique, and their normalized spatial density calculated as a function of the distance from the nuclear perimeter to its center. The results revealed marked changes in the distribution of the density of NuMA bright features as non-neoplastic cells underwent phenotypically normal acinar morphogenesis. In contrast, we did not detect any reorganization of NuMA during the formation of tumor nodules by malignant cells. Importantly, the analysis also discriminated proliferating non-neoplastic cells from proliferating malignant cells, suggesting that these imaging methods are capable of identifying alterations linked not only to the proliferation status but also to the malignant character of cells. We believe that this quantitative analysis will have additional applications for classifying normal and pathological tissues

  10. Automated local bright feature image analysis of nuclear proteindistribution identifies changes in tissue phenotype

    Energy Technology Data Exchange (ETDEWEB)

    Knowles, David; Sudar, Damir; Bator, Carol; Bissell, Mina

    2006-02-01

    The organization of nuclear proteins is linked to cell and tissue phenotypes. When cells arrest proliferation, undergo apoptosis, or differentiate, the distribution of nuclear proteins changes. Conversely, forced alteration of the distribution of nuclear proteins modifies cell phenotype. Immunostaining and fluorescence microscopy have been critical for such findings. However, there is an increasing need for quantitative analysis of nuclear protein distribution to decipher epigenetic relationships between nuclear structure and cell phenotype, and to unravel the mechanisms linking nuclear structure and function. We have developed imaging methods to quantify the distribution of fluorescently-stained nuclear protein NuMA in different mammary phenotypes obtained using three-dimensional cell culture. Automated image segmentation of DAPI-stained nuclei was generated to isolate thousands of nuclei from three-dimensional confocal images. Prominent features of fluorescently-stained NuMA were detected using a novel local bright feature analysis technique, and their normalized spatial density calculated as a function of the distance from the nuclear perimeter to its center. The results revealed marked changes in the distribution of the density of NuMA bright features as non-neoplastic cells underwent phenotypically normal acinar morphogenesis. In contrast, we did not detect any reorganization of NuMA during the formation of tumor nodules by malignant cells. Importantly, the analysis also discriminated proliferating non-neoplastic cells from proliferating malignant cells, suggesting that these imaging methods are capable of identifying alterations linked not only to the proliferation status but also to the malignant character of cells. We believe that this quantitative analysis will have additional applications for classifying normal and pathological tissues.

  11. Graph of growth data - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available The Rice Growth Monitoring for The Phenotypic Functional Analysis Graph of growth data Data detail Data name...ense Update History of This Database Site Policy | Contact Us Graph of growth data - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  12. Behavioral Analysis of Dopaminergic Activation in Zebrafish and Rats Reveals Similar Phenotypes.

    Science.gov (United States)

    Ek, Fredrik; Malo, Marcus; Åberg Andersson, Madelene; Wedding, Christoffer; Kronborg, Joel; Svensson, Peder; Waters, Susanna; Petersson, Per; Olsson, Roger

    2016-05-18

    Zebrafish is emerging as a complement to mammals in behavioral studies; however, there is a lack of comparative studies with rodents and humans to establish the zebrafish as a predictive translational model. Here we present a detailed phenotype evaluation of zebrafish larvae, measuring 300-3000 variables and analyzing them using multivariate analysis to identify the most important ones for further evaluations. The dopamine agonist apomorphine has previously been shown to have a complex U-shaped dose-response relationship in the variable distance traveled. In this study, we focused on breaking down distance traveled into more detailed behavioral phenotypes for both zebrafish and rats and identified in the multivariate analysis low and high dose phenotypes with characteristic behavioral features. Further analysis of single parameters also identified an increased activity at the lowest concentration indicative of a U-shaped dose-response. Apomorphine increased the distance of each swim movement (bout) at both high and low doses, but the underlying behavior of this increase is different; at high dose, both bout duration and frequency increased whereas bout max speed was higher at low dose. Larvae also displayed differences in place preference. The low dose phenotype spent more time in the center, indicative of an anxiolytic effect, while the high-dose phenotype had a wall preference. These dose-dependent effects corroborated findings in a parallel rat study and previous observations in humans. The translational value of pharmacological zebrafish studies was further evaluated by comparing the amino acid sequence of the dopamine receptors (D1-D4), between zebrafish, rats and humans. Humans and zebrafish share 100% of the amino acids in the binding site for D1 and D3 whereas D2 and D4 receptors share 85-95%. Molecular modeling of dopamine D2 and D4 receptors indicated that nonconserved amino acids have limited influence on important ligand-receptor interactions. PMID

  13. PULLOUT CAPACITY OF HORIZONTAL AND INCLINED PLATE ANCHORS IN CLAYEY SOILS

    Directory of Open Access Journals (Sweden)

    BALESHWAR SINGH

    2011-11-01

    Full Text Available Soil anchors are required to withstand uplift or lateral forces acting on the foundations of structures constructed both in land and offshore sites. Plate anchoring system is being increasingly used to moor floating structures for the exploration and development of oil and gas fields. In this study, various experimental,theoretical and numerical approaches for estimation of pullout capacity of horizontal and inclined plate anchors in clayey soils are reviewed. A comparative analysis of the ultimate capacity is then carried out for plate anchors embedded in clayey soils by varying embedment ratio for horizontal anchors and by varying inclination angle for inclined plate anchors.

  14. The Anchoring Concept

    DEFF Research Database (Denmark)

    Simonsen, Jesper

    1998-01-01

    This paper introduces the term 'anchoring' within systems development: Visions, developed through early systems design within an organization, need to be deeply rooted in the organization. A vision's rationale needs to be understood by those who decide if the vision should be implemented as well as...... by those involved in the actual implementation. A model depicting a recent trend within systems development is presented: Organizations rely on purchasing generic software products and/or software development outsourced to external contractors. A contemporary method for participatory design, where...

  15. Novel Meta-Analysis-Derived Type 2 Diabetes Risk Loci Do Not Determine Prediabetic Phenotypes

    OpenAIRE

    Staiger, Harald; Machicao, Fausto; Kantartzis, Konstantinos; Schäfer, Silke A.; Kirchhoff, Kerstin; Guthoff, Martina; Silbernagel, Günther; Stefan, Norbert; Fritsche, Andreas; Häring, Hans-Ulrich

    2008-01-01

    Background Genome-wide association (GWA) studies identified a series of novel type 2 diabetes risk loci. Most of them were subsequently demonstrated to affect insulin secretion of pancreatic β-cells. Very recently, a meta-analysis of GWA data revealed nine additional risk loci with still undefined roles in the pathogenesis of type 2 diabetes. Using our thoroughly phenotyped cohort of subjects at an increased risk for type 2 diabetes, we assessed the association of the nine latest genetic vari...

  16. Analysis of multiple phenotypes in genome-wide genetic mapping studies

    OpenAIRE

    Suo, C.; Toulopoulou, T; Bramon, E.; Walshe, M; Picchioni, M.; Murray, R.; Ott, J

    2013-01-01

    BACKGROUND: Complex traits may be defined by a range of different criteria. It would result in a loss of information to perform analyses simply on the basis of a final clinical dichotomized affected / unaffected variable. RESULTS: We assess the performance of four alternative approaches for the analysis of multiple phenotypes in genetic association studies. We describe the four methods in detail and discuss their relative theoretical merits and disadvantages. Using simulation we demonstrate t...

  17. Surprisal Analysis of Glioblastoma Multiform (GBM) MicroRNA Dynamics Unveils Tumor Specific Phenotype

    OpenAIRE

    Zadran, Sohila; Remacle, Françoise; Levine, R. D.

    2014-01-01

    Gliomablastoma multiform (GBM) is the most fatal form of all brain cancers in humans. Currently there are limited diagnostic tools for GBM detection. Here, we applied surprisal analysis, a theory grounded in thermodynamics, to unveil how biomolecule energetics, specifically a redistribution of free energy amongst microRNAs (miRNAs), results in a system deviating from a non-cancer state to the GBM cancer –specific phenotypic state. Utilizing global miRNA microarray expression data of normal an...

  18. META-ANALYSIS OF CYP2D6 METABOLIZER PHENOTYPE AND METOPROLOL PHARMACOKINETICS

    OpenAIRE

    Blake, CM; Kharasch, ED; Schwab, M.; Nagele, P.

    2013-01-01

    Metoprolol, a commonly prescribed beta-blocker, is primarily metabolized by cytochrome P450 2D6 (CYP2D6), an enzyme with substantial genetic heterogeneity. Several smaller studies have shown that metoprolol pharmacokinetics is influenced by CYP2D6 genotype and metabolizer phenotype. To increase robustness of metoprolol pharmacokinetic estimates, a systematic review and meta-analysis of pharmacokinetic studies that administered a single oral dose of immediate release metoprolol was performed. ...

  19. Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma

    OpenAIRE

    Hansmann, Leo; Blum, Lisa; Ju, Chia-Hsin; Liedtke, Michaela; Robinson, William H; Davis, Mark M.

    2015-01-01

    It would be very beneficial if the status of cancers could be determined from a blood specimen. However, peripheral blood leukocytes are very heterogeneous between individuals and thus high resolution technologies are likely required. We used cytometry by time-of-flight (CyTOF) and next generation sequencing to ask whether a plasma cell cancer (multiple myeloma) and related pre-cancerous states had any consistent effect on the peripheral blood mononuclear cell phenotypes of patients. Analysis...

  20. Approximative methods for the stability analysis of anchored liquid storage tanks under earthquake excitation; Naeherungsmethoden zur Stabilitaetsuntersuchung von erdbebenerregten verankerten Fluessigkeitsbehaeltern

    Energy Technology Data Exchange (ETDEWEB)

    Seiler, C.

    2001-07-01

    This doctoral thesis presents approximative methods for the stability analysis of anchored liquid storage tanks under earthquake excitation. By first introducing a quasistatic model well known phenomena of collapse are analysed with little numerical effort and the underlying mechanisms of collapse are explained. Subsequently, a more detailed analysis of the structural behavior in the time domain is obtained by a complete interactive model and by employing a suitable time integration method. In this context, the dynamic stability behavior is calculated by defining a problem oriented criterion. Performing an extensive parameter study the approximative methods are discussed and the results lead to a new empirical design concept which may be implemented in the current draft of Eurocode 8, part 4 for stability verifications. (orig.) [German] In der vorliegenden Arbeit wird das Stabilitaetsverhalten von verankerten Fluessigkeitsbehaeltern unter seismischer Einwirkung mit Hilfe unterschiedlicher Naeherungsmethoden behandelt. Die Einfuehrung eines quasistatischen Ersatzmodells bietet zunaechst die Moeglichkeit, bekannte Versagensphaenomene mit geringem numerischen Aufwand zu berechnen und die zugrundeliegenden Versagensmechanismen zu erklaeren. Zu einer genaueren Analyse des Tragverhaltens im Zeitbereich wird anschliessend ein vollstaendiges Interaktionsmodell in Verbindung mit einem geeigneten Zeitintegrationsverfahren herangezogen. Das dynamische Stabilitaetsverhalten wird dabei mit einem Kriterium beurteilt, das problemorientiert definiert wird. Eine umfangreiche Parameterstudie stellt die vorgestellten Naeherungsverfahren gegenueber und dient als Datenbasis fuer ein neu entwickeltes empirisches Bemessungskonzept, das in die aktuelle Normengebung des EC 8, Teil 4 in bezug auf die erforderlichen Stabilitaetsnachweise aufgenommen werden koennte. (orig.)

  1. 小行星着陆器锚系统及其实验研究%Development and Experimental Analysis of Anchoring System for Asteroid Lander

    Institute of Scientific and Technical Information of China (English)

    赵志军; 赵京东; 刘宏

    2013-01-01

    The lander is easy to rebound and flow away when landing on an asteroid.To solve this problem,an anchoring system which could anchor the lander to the surface of the asteroid is designed.The related characteristics of the asteroid constraining the design of the anchoring system are analyzed.The anchoring system is designed according to the "cord connecting mode" after analyzing the design alternatives of the anchoring system.It consists of anchoring unit,winding unit,unlocking unit,wire unit and electric/control unit.The penetration depth of the conic anchor tip is also studied.The penetrating/anchoring capability and dragging capability under microgravity of the anchoring system are tested.Experiments show that the anchoring system could penetrate/anchor in the frozen medium and drag the lander to the landing slope under microgravity environment.%针对小行星表面着陆器容易反弹及飘走的难题,设计了一种将着陆器锚固在小行星表面的锚系统.基于小行星特点,对锚系统设计方案进行了分析,选择“链式锚固方式”作为本研究的锚系统方案.基于该方案对锚系统进行了设计,其包括锚固单元、缠绕单元、解锁单元、线绳单元及电气控制单元.对锥形锚尖的侵彻深度进行了研究.经过在冻土介质中的侵彻/锚固实验及气浮微重力环境下的拖拽实验,证明该锚系统具有微重力环境下对小行星着陆器进行锚固及拖拽的基本功能.

  2. Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

    Science.gov (United States)

    Zhao, S; Tyson, G H; Chen, Y; Li, C; Mukherjee, S; Young, S; Lam, C; Folster, J P; Whichard, J M; McDermott, P F

    2016-01-01

    The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2')-If, aph(2″)-Ig, aph(2″)-Ih, aac(6')-Ie-aph(2″)-Ia, aac(6')-Ie-aph(2″)-If, aac(6')-Im, aadE, sat4, ant(6'), aad9, aph(3')-Ic, and aph(3')-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs. PMID:26519386

  3. Phenotypic Analysis Reveals that the 2010 Haiti Cholera Epidemic Is Linked to a Hypervirulent Strain.

    Science.gov (United States)

    Satchell, Karla J F; Jones, Christopher J; Wong, Jennifer; Queen, Jessica; Agarwal, Shivani; Yildiz, Fitnat H

    2016-09-01

    Vibrio cholerae O1 El Tor strains have been responsible for pandemic cholera since 1961. These strains have evolved over time, spreading globally in three separate waves. Wave 3 is caused by altered El Tor (AET) variant strains, which include the strain with the signature ctxB7 allele that was introduced in 2010 into Haiti, where it caused a devastating epidemic. In this study, we used phenotypic analysis to compare an early isolate from the Haiti epidemic to wave 1 El Tor isolates commonly used for research. It is demonstrated that the Haiti isolate has increased production of cholera toxin (CT) and hemolysin, increased motility, and a reduced ability to form biofilms. This strain also outcompetes common wave 1 El Tor isolates for colonization of infant mice, indicating that it has increased virulence. Monitoring of CT production and motility in additional wave 3 isolates revealed that this phenotypic variation likely evolved over time rather than in a single genetic event. Analysis of available whole-genome sequences and phylogenetic analyses suggested that increased virulence arose from positive selection for mutations found in known and putative regulatory genes, including hns and vieA, diguanylate cyclase genes, and genes belonging to the lysR and gntR regulatory families. Overall, the studies presented here revealed that V. cholerae virulence potential can evolve and that the currently prevalent wave 3 AET strains are both phenotypically distinct from and more virulent than many El Tor isolates. PMID:27297393

  4. Proteomic analysis of human norepinephrine transporter complexes reveals associations with protein phosphatase 2A anchoring subunit and 14-3-3 proteins

    International Nuclear Information System (INIS)

    The norepinephrine transporter (NET) terminates noradrenergic signals by clearing released NE at synapses. NET regulation by receptors and intracellular signaling pathways is supported by a growing list of associated proteins including syntaxin1A, protein phosphatase 2A (PP2A) catalytic subunit (PP2A-C), PICK1, and Hic-5. In the present study, we sought evidence for additional partnerships by mass spectrometry-based analysis of proteins co-immunoprecipitated with human NET (hNET) stably expressed in a mouse noradrenergic neuroblastoma cell line. Our initial proteomic analyses reveal multiple peptides derived from hNET, peptides arising from the mouse PP2A anchoring subunit (PP2A-Ar) and peptides derived from 14-3-3 proteins. We verified physical association of NET with PP2A-Ar via co-immunoprecipitation studies using mouse vas deferens extracts and with 14-3-3 via a fusion pull-down approach, implicating specifically the hNET NH2-terminus for interactions. The transporter complexes described likely support mechanisms regulating transporter activity, localization, and trafficking

  5. Update History of This Database - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available The Rice Growth Monitoring for The Phenotypic Functional Analysis Update History of This Database Date Updat...The Rice Growth Monitoring for the Phenotypic Functional Analysis English archive... site is opened. 2003/10/01 The Rice Growth Monitoring System for the Phenotypic Functional Analysis ( http:...date History of This Database - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  6. Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy

    Directory of Open Access Journals (Sweden)

    Claudia Gonzaga-Jauregui

    2015-08-01

    Full Text Available Charcot-Marie-Tooth (CMT disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ∼45% (17/37 of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.

  7. Phenotypic characterization of Corynebacterium glutamicum under osmotic stress conditions using elementary mode analysis.

    Science.gov (United States)

    Rajvanshi, Meghna; Venkatesh, K V

    2011-09-01

    Corynebacterium glutamicum, a soil bacterium, is used to produce amino acids such as lysine and glutamate. C. glutamicum is often exposed to osmolality changes in its medium, and the bacterium has therefore evolved several adaptive response mechanisms to overcome them. In this study we quantify the metabolic response of C. glutamicum under osmotic stress using elementary mode analysis (EMA). Further, we obtain the optimal phenotypic space for the synthesis of lysine and formation of biomass. The analysis demonstrated that with increasing osmotic stress, the flux towards trehalose formation and energy-generating pathways increased, while the flux of anabolic reactions diminished. Nodal analysis indicated that glucose-6-phosphate, phosphoenol pyruvate, and pyruvate nodes were capable of adapting to osmotic stress, whereas the oxaloacetic acid node was relatively unresponsive. Fewer elementary modes were active under stress indicating the rigid behavior of the metabolism in response to high osmolality. Optimal phenotypic space analysis revealed that under normal conditions the organism optimized growth during the initial log phase and lysine and trehalose formation during the stationary phase. However, under osmotic stress, the analysis demonstrated that the organism operates under suboptimal conditions for growth, and lysine and trehalose formation. PMID:21132515

  8. Coupled thermo-fluid stress analysis of Kambara Reactor with various anchors in the stirring of molten iron at extremely high temperatures

    International Nuclear Information System (INIS)

    Kambara Reactors (KR) are commonly used to reduce sulfur content in steel making, achieving efficiency levels exceeding 85% at 1300 °C. Unfortunately, the operational lifespan of the KR impeller is somewhat limited due to fracturing of the refractory material via thermal shock, resulting in the penetration of molten iron into the inner core. Few studies have investigated the coupled thermo-fluid stress of KR impellers at extremely high temperatures. This study employed CFX and FEM to simulate and analyze the molten iron and the resulting thermal stress imposed on the KR impeller. Simulation results including flow field, temperature, and thermal stress under extremely high temperatures are in strong agreement with empirical data. V-type anchors for the KR impeller outperformed Y-type anchors. - Highlights: • A thermo-fluid coupling approach is proposed to analyze the thermal stress. • The temperature and stress of the impeller are 790 °C and 744 MPa at the final stage. • The highest temperatures occur at the tip of anchors, which causes material crack. • The thermal stress in impellers with Y-type anchors is greater than V-type anchors

  9. Network Based Integrated Analysis of Phenotype-Genotype Data for Prioritization of Candidate Symptom Genes

    Directory of Open Access Journals (Sweden)

    Xing Li

    2014-01-01

    Full Text Available Background. Symptoms and signs (symptoms in brief are the essential clinical manifestations for individualized diagnosis and treatment in traditional Chinese medicine (TCM. To gain insights into the molecular mechanism of symptoms, we develop a computational approach to identify the candidate genes of symptoms. Methods. This paper presents a network-based approach for the integrated analysis of multiple phenotype-genotype data sources and the prediction of the prioritizing genes for the associated symptoms. The method first calculates the similarities between symptoms and diseases based on the symptom-disease relationships retrieved from the PubMed bibliographic database. Then the disease-gene associations and protein-protein interactions are utilized to construct a phenotype-genotype network. The PRINCE algorithm is finally used to rank the potential genes for the associated symptoms. Results. The proposed method gets reliable gene rank list with AUC (area under curve 0.616 in classification. Some novel genes like CALCA, ESR1, and MTHFR were predicted to be associated with headache symptoms, which are not recorded in the benchmark data set, but have been reported in recent published literatures. Conclusions. Our study demonstrated that by integrating phenotype-genotype relationships into a complex network framework it provides an effective approach to identify candidate genes of symptoms.

  10. An integrated analysis of phenotypic selection on insect body size and development time.

    Science.gov (United States)

    Eck, Daniel J; Shaw, Ruth G; Geyer, Charles J; Kingsolver, Joel G

    2015-09-01

    Most studies of phenotypic selection do not estimate selection or fitness surfaces for multiple components of fitness within a unified statistical framework. This makes it difficult or impossible to assess how selection operates on traits through variation in multiple components of fitness. We describe a new generation of aster models that can evaluate phenotypic selection by accounting for timing of life-history transitions and their effect on population growth rate, in addition to survival and reproductive output. We use this approach to estimate selection on body size and development time for a field population of the herbivorous insect, Manduca sexta (Lepidoptera: Sphingidae). Estimated fitness surfaces revealed strong and significant directional selection favoring both larger adult size (via effects on egg counts) and more rapid rates of early larval development (via effects on larval survival). Incorporating the timing of reproduction and its influence on population growth rate into the analysis resulted in larger values for size in early larval development at which fitness is maximized, and weaker selection on size in early larval development. These results illustrate how the interplay of different components of fitness can influence selection on size and development time. This integrated modeling framework can be readily applied to studies of phenotypic selection via multiple fitness components in other systems. PMID:26257167

  11. Spectrum of mutations and genotype-phenotype analysis in Currarino syndrome.

    Science.gov (United States)

    Köchling, J; Karbasiyan, M; Reis, A

    2001-08-01

    The triad of a presacral tumour, sacral agenesis and anorectal malformation constitutes the Currarino syndrome which is caused by dorsal-ventral patterning defects during embryonic development. The syndrome occurs in the majority of patients as an autosomal dominant trait associated with mutations in the homeobox gene HLXB9 which encodes the nuclear protein HB9. However, genotype-phenotype analyses have been performed only in a few families and there are no reports about the specific impact of HLXB9 mutations on HB9 function. We performed a mutational analysis in 72 individuals from nine families with Currarino syndrome. We identified a total of five HLXB9 mutations, four novel and one known mutation, in four out of four families and one out of five sporadic cases. Highly variable phenotypes and a low penetrance with half of all carriers being clinically asymptomatic were found in three families, whereas affected members of one family showed almost identical phenotypes. However, an obvious genotype-phenotype correlation was not found. While HLXB9 mutations were diagnosed in 23 patients, no mutation or microdeletion was detected in four sporadic patients with Currarino syndrome. The distribution pattern of here and previously reported HLXB9 mutations indicates mutational predilection sites within exon 1 and the homeobox. Furthermore, sequence homology to Drosophila homeobox genes suggest that some of these mutations located within the homeobox may alter the DNA-binding specificity of HB9 while those in sequences homologous to a recently identified NLS motif of the human homeobox gene PDX-1 may impair nuclear translocation of the mutated protein. PMID:11528505

  12. Factor analysis demonstrates a common schizoidal phenotype within autistic and schizotypal tendency: Implications for neuroscientific studies

    Directory of Open Access Journals (Sweden)

    Talitha Caitlyn Ford

    2014-08-01

    Full Text Available Behavioural and cognitive dysfunction, particularly social and communication impairments are shared between autism and schizophrenia spectrum disorders, while evidence for a diametric autism-positive schizophrenia symptom profile is inconsistent. We investigated the shared phenotype at a personality trait level, particularly its resemblance to schizoid personality disorder, as well as differential aspects of the autism-schizophrenia model.Items of the Autism Spectrum Quotient (AQ and Schizotypal Personality Questionnaire (SPQ were pseudo-randomly combined, and were completed by 449 (162 male, 287 female non-clinical participants aged 18-40. A Factor Analysis revealed three factors; the first represented a shared social disorganization phenotype, the second reflected perceptual oddities specific to schizotypy while the third reflected social rigidity specific to autism. The AQ and SPQ were strongly correlated with Factor 1 (AQ: r=.75, p<.001; SPQ: r=.96, p<.001, SPQ score was correlated with Factor 2 (r=.51, p<.001, particularly in Cognitive-Perceptual features (r=.66, p<.001, and AQ score was strongly correlated with Factor 3 (r=.76, p<.001. Furthermore, there was no relationship between Factor 1 and Factor 2.Thus, there is robust evidence for a shared social disorganization phenotype in autistic and schizotypal tendency, which reflects the schizoid phenotype. Discriminating and independent dimensions of schizotypal and autistic tendency exist in Factors 2 and 3 respectively. Current diagnostic protocols could result in different diagnoses depending on the instrument used, suggesting the need for neuromarkers that objectively differentiate autistic and schizotypal traits and resolve the question of commonality versus comorbidity.

  13. Nif- phenotype of Azotobacter vinelandii UW97. Characterization and mutational analysis.

    Science.gov (United States)

    Pulakat, L; Hausman, B S; Lei, S; Gavini, N

    1996-01-26

    We have identified the molecular basis for the nitrogenase negative phenotype exhibited by Azotobacter vinelandii UW97. This strain was initially isolated following nitrosoguanidine mutagenesis. Recently, it was shown that this strain lacks the Fe protein activity, which results in the synthesis of a FeMo cofactor-deficient apodinitrogenase. Activation of this apodinitrogenase requires the addition of both MgATP and wild-type Fe protein to the crude extracts made by A. vinelandii UW97 (Allen, R.M., Homer, M.J., Chatterjee R., Ludden, P.W., Roberts, G.P., and Shah, V.K. (1993) J. Biol. Chem. 268 23670-23674). Earlier, we proposed the sequence of events in the MoFe protein assembly based on the biochemical and spectroscopic analysis of the purified apodinitrogenase from A. vinelandii DJ54 (Gavini, N., Ma, L., Watt, G., and Burgess, B.K. (1994) Biochemistry 33, 11842-11849). Taken together, these results imply that the assembly process of apodinitrogenase is arrested at the same step in both of these strains. Since A. vinelandii DJ54 is a delta nifH strain, this strain is not useful in identifying the features of the Fe protein involved in the MoFe protein assembly. Here, we report a systematic analysis of an A. vinelandii UW97 mutant and show that, unlike A. vinelandii DJ54, the nifH gene of A. vinelandii UW97 has no deletion in either coding sequence or the surrounding sequences. The specific mutation responsible for the Nif- phenotype of A. vinelandii UW97 is the substitution of a non-conserved serine at position 44 of the Fe protein by a phenylalanine as shown by DNA sequencing. Furthermore, oligonucleotide site-directed mutagenesis was employed to confirm that the Nif- phenotype in A. vinelandii UW97 is exclusively due to the substitution of the Fe protein residue serine 44 by phenylalanine. By contrast, replacing Ser-44 with alanine did not affect the Nif phenotype of A. vinelandii. Therefore, it seems that the Nif- phenotype of A. vinelandii UW97 is caused by a

  14. PHENOTYPIC ANALYSIS OF OsTPKb LOSS OF FUNCTION MUTANT RICE LINES

    Directory of Open Access Journals (Sweden)

    Isayenkov S. V.

    2015-08-01

    Full Text Available The results of screen and analysis of two OsTPKb rice mutant lines were described. The phenotypes and growth rate level of homozygous mutant plants of both rice lines were estimated. The electron microscopy of aleurone layer from forming seeds was performed. The OsTPKb mutant plants demonstrate lower growth rate in comparison with wild type plants. The loss of function OsTPKb mutations invariably led to (semisterile rice plants. The functional disruption of OsTPKb channel has negative impact on plant growth and development. It might completely change the cell morphology of aleurone layer.

  15. Flow cytometric analysis of Mixed phenotype acute leukemia: Experience from a tertiary oncology center

    Directory of Open Access Journals (Sweden)

    Renu Sukumaran

    2015-01-01

    Full Text Available Introduction: Mixed phenotype acute leukemia (MPAL is a rare subset of acute leukemia where the blasts exhibit lineage specific antigens of more than one lineage. Flow cytometric immunophenotyping is essential for the diagnosis of MPAL and the accurate diagnosis highly depends on the panel of markers used. The precise incidence of MPAL is uncertain as various institutions use different combinations of antibodies to assign the blasts to a particular lineage. Aim: The aim was to study the immunoprofile of acute leukemia including aberrant antigen expressions and to study the incidence, clinical features, laboratory findings, and immunophenotype of MPAL in our institution. Materials and Methods: All cases of acute leukemias in which flow cytometric analysis during 1-year period from July 2012 to July 2013 were included in this study. Results: During the study period, flow cytometric analysis of 506 cases was performed. B lymphoblastic leukemia was the most common subtype of acute leukemia. CD13 was the most common aberrant antigen expression in acute lymphoblastic leukemia and CD7 was the most common aberrant antigen expression in acute myeloid leukemia. A diagnosis of MPAL was made in 15 cases, which accounted for 2.96% of all leukemias. 9 cases were diagnosed as T/myeloid, 5 cases as B/myeloid and 1 case as B/T. Conclusion: Mixed phenotype acute leukemia is a rare subset of acute leukemia. Flow cytometry is critical in establishing a diagnosis of MPAL. The panel of antibodies used is important in the identification of the "mixed" phenotype. Cytoplasmic markers (cytoplasmic MPO, cytoplasmic 79a, cytoplasmic 22 and cytoplasmic CD3 should be included in the primary flow cytometric panel.

  16. Stress distribution of inlay-anchored adhesive fixed partial dentures: a finite element analysis of the influence of restorative materials and abutment preparation design

    OpenAIRE

    Magne, Pascal; Perakis, Nikolaos; Belser, Urs Christophe; Krejci, Ivo

    2002-01-01

    Indirect composite or ceramic fixed partial dentures (FPDs) have become an alternative to conventional metal-ceramic adhesive fixed partial dentures (AFPDs). Little information about the adequate restorative material and tooth preparation design for inlay-anchored AFPDs is available to the clinician.

  17. Recognition of the Cornelia de Lange syndrome phenotype with facial dysmorphology novel analysis.

    Science.gov (United States)

    Basel-Vanagaite, L; Wolf, L; Orin, M; Larizza, L; Gervasini, C; Krantz, I D; Deardoff, M A

    2016-05-01

    Facial analysis systems are becoming available to healthcare providers to aid in the recognition of dysmorphic phenotypes associated with a multitude of genetic syndromes. These technologies automatically detect facial points and extract various measurements from images to recognize dysmorphic features and evaluate similarities to known facial patterns (gestalts). To evaluate such systems' usefulness for supporting the clinical practice of healthcare professionals, the recognition accuracy of the Cornelia de Lange syndrome (CdLS) phenotype was examined with FDNA's automated facial dysmorphology novel analysis (FDNA) technology. In the first experiment, 2D facial images of CdLS patients with either an NIPBL or SMC1A gene mutation as well as non-CdLS patients which were assessed by dysmorphologists in a previous study were evaluated by the FDNA technology; the average detection rate of experts was 77% while the system's detection rate was 87%. In the second study, when a new set of NIPBL, SMC1A and non-CdLS patient photos was evaluated, the detection rate increased to 94%. The results from both studies indicated that the system's detection rate was comparable to that of dysmorphology experts. Therefore, utilizing such technologies may be a useful tool in a clinical setting. PMID:26663098

  18. Underestimated effect sizes in GWAS: fundamental limitations of single SNP analysis for dichotomous phenotypes.

    Directory of Open Access Journals (Sweden)

    Sven Stringer

    Full Text Available Complex diseases are often highly heritable. However, for many complex traits only a small proportion of the heritability can be explained by observed genetic variants in traditional genome-wide association (GWA studies. Moreover, for some of those traits few significant SNPs have been identified. Single SNP association methods test for association at a single SNP, ignoring the effect of other SNPs. We show using a simple multi-locus odds model of complex disease that moderate to large effect sizes of causal variants may be estimated as relatively small effect sizes in single SNP association testing. This underestimation effect is most severe for diseases influenced by numerous risk variants. We relate the underestimation effect to the concept of non-collapsibility found in the statistics literature. As described, continuous phenotypes generated with linear genetic models are not affected by this underestimation effect. Since many GWA studies apply single SNP analysis to dichotomous phenotypes, previously reported results potentially underestimate true effect sizes, thereby impeding identification of true effect SNPs. Therefore, when a multi-locus model of disease risk is assumed, a multi SNP analysis may be more appropriate.

  19. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity

    International Nuclear Information System (INIS)

    Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution

  20. Bone Anchored Hearing Treatment Procedure

    Medline Plus

    Full Text Available ... skin to allow removal of some of the soft tissue where the screwlike fixture will be anchored. The ... screen, acting as a hinge. Beneath that the soft tissue consisting of fat and some muscle is removed. ...

  1. Bone Anchored Hearing Treatment Procedure

    Medline Plus

    Full Text Available ... to allow removal of some of the soft tissue where the screwlike fixture will be anchored. The ... series of slides demonstrates the removal of the tissue beneath the skin flap. You can see in ...

  2. Bone Anchored Hearing Treatment Procedure

    Medline Plus

    Full Text Available ... The Baha system consists of a bone-anchored titanium fixture that is implanted in the mastoid bone, ... the -- great. I'm going to grab the titanium implant. And what I want you to notice ...

  3. Bone Anchored Hearing Treatment Procedure

    Medline Plus

    Full Text Available ... of the bone oscillator is superficial on the skin, the transference of that energy is less efficient, ... slides, is to mark the location in the skin where the screwlike fixture will be anchored. Subsequent ...

  4. Evaluation of phenotypic stability of cassava clones by AMMI analysis in northwestern Paraná state

    Directory of Open Access Journals (Sweden)

    Marcus Vinícius Kvitschal

    2006-01-01

    Full Text Available High yield stability and adaptability of storage root are highly desirable attributes of cassava clones. Theobjective of this study was therefore to evaluate the effect of the genotype x environment interaction (G x E and the stability ofcassava clones developed at IAC. A subset of eight cassava genotypes was chosen in trials of storage root yield, arranged ina randomized complete block design with four replications, in two counties (Araruna and Maringá, in the northwesternregion of Paraná State, over five growing seasons (1997-2001. The G x E interaction was evaluated by joint varianceanalysis and stability and adaptability by AMMI analysis. The G x E interaction was significant (P<0.05 for storage rootyield. Results indicated AMMI analysis as an efficient tool for the evaluation of phenotypic adaptability and stability of cassavaclones and IAC 190 as the most promising clone.

  5. Relationships of Campanian olive cultivars: comparative analysis of molecular and phenotypic data.

    Science.gov (United States)

    Corrado, Giandomenico; La Mura, Maurizio; Ambrosino, Orsola; Pugliano, Giuseppe; Varricchio, Paola; Rao, Rosa

    2009-08-01

    Estimation of the genetic relatedness of traditional olive cultivars with genetic markers and phenotypic data enables progress in plant breeding, management of genetic resources, and protection of both breeders' rights and certified premium products. We used amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and quantitative and qualitative morphological traits, including characteristics recommended for variety registration, to study genetic diversity and relationships in the olive at different levels. The 14 varieties analyzed, which are used for the production of Protected Denomination of Origin extra-virgin olive oil, represent the most important cultivars in the Campania region of Italy and typify a regional diversity characteristic of traditional olive cultivation. The genetic distances obtained with the two DNA marker systems were significantly correlated, as were those obtained by quantitative and qualitative traits. A lower but significant correlation was also observed between distances based on molecular markers and quantitative traits, but qualitative traits, even if sampled in high numbers, failed to describe the pattern of molecular similarity. Our data imply that the type and the number of phenotypic traits scored can greatly influence the outcome of the analysis, and care should be taken when qualitative and quantitative data are combined. Furthermore, the data indicate that the two molecular marker systems are useful for investigating genetic relationships, but they may also be used to complement and assist the traditional registration of varieties. We propose that since the information provided by molecular and morphological marker systems in olive is different, they should serve different purposes. PMID:19767899

  6. Analysis of root growth from a phenotyping data set using a density-based model.

    Science.gov (United States)

    Kalogiros, Dimitris I; Adu, Michael O; White, Philip J; Broadley, Martin R; Draye, Xavier; Ptashnyk, Mariya; Bengough, A Glyn; Dupuy, Lionel X

    2016-02-01

    Major research efforts are targeting the improved performance of root systems for more efficient use of water and nutrients by crops. However, characterizing root system architecture (RSA) is challenging, because roots are difficult objects to observe and analyse. A model-based analysis of RSA traits from phenotyping image data is presented. The model can successfully back-calculate growth parameters without the need to measure individual roots. The mathematical model uses partial differential equations to describe root system development. Methods based on kernel estimators were used to quantify root density distributions from experimental image data, and different optimization approaches to parameterize the model were tested. The model was tested on root images of a set of 89 Brassica rapa L. individuals of the same genotype grown for 14 d after sowing on blue filter paper. Optimized root growth parameters enabled the final (modelled) length of the main root axes to be matched within 1% of their mean values observed in experiments. Parameterized values for elongation rates were within ±4% of the values measured directly on images. Future work should investigate the time dependency of growth parameters using time-lapse image data. The approach is a potentially powerful quantitative technique for identifying crop genotypes with more efficient root systems, using (even incomplete) data from high-throughput phenotyping systems. PMID:26880747

  7. Identification of novel KIF11 mutations in patients with familial exudative vitreoretinopathy and a phenotypic analysis.

    Science.gov (United States)

    Li, Jia-Kai; Fei, Ping; Li, Yian; Huang, Qiu-Jing; Zhang, Qi; Zhang, Xiang; Rao, Yu-Qing; Li, Jing; Zhao, Peiquan

    2016-01-01

    KIF11 gene mutations cause a rare autosomal dominant inheritable disease called microcephaly with or without chorioretinopathy, lymphedema, or mental retardation (MCLMR). Recently, such mutations were also found to be associated with familial exudative vitreoretinopathy (FEVR). Here, we report 7 novel KIF11 mutations identified by targeted gene capture in a cohort of 142 probands with FEVR who were diagnosed in our clinic between March 2015 and November 2015. These mutations were: p.L171V, c.790-2A>C, p.Q525*, p.Q842*, p.S936*, p.L983fs and p.R1025G. Phenotypic analysis revealed that all of the affected probands had advanced FEVR (stage 4 or above). Three had microcephaly, and one had chorioretinopathy, which indicated a phenotypic overlap with MCLMR. Two mutations were also found in the families of the affected probands. One parent with a p.R1025G mutation had an avascular peripheral retina and abnormal looping vessels. However, one parent with p.L983fs had normal retina, which indicated incomplete penetration of the genotype. Our results further confirmed that KIF11 is causative of FEVR in an autosomal dominant manner. We also suggest the examination of MCLMR-like features, such as microcephaly, chorioretinopathy, for patients with FEVR and wide-field fundus photography for patients with MCLMR in future practice. PMID:27212378

  8. Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma

    Science.gov (United States)

    Hansmann, Leo; Blum, Lisa; Ju, Chia-Hsin; Liedtke, Michaela; Robinson, William H.; Davis, Mark M.

    2015-01-01

    It would be very beneficial if the status of cancers could be determined from a blood specimen. However, peripheral blood leukocytes are very heterogeneous between individuals and thus high resolution technologies are likely required. We used cytometry by time-of-flight (CyTOF) and next generation sequencing to ask whether a plasma cell cancer (multiple myeloma) and related pre-cancerous states had any consistent effect on the peripheral blood mononuclear cell phenotypes of patients. Analysis of peripheral blood samples from 13 cancer patients, 9 pre-cancer patients, and 9 healthy individuals revealed significant differences in the frequencies of the T, B, and natural killer cell compartments. Most strikingly, we identified a novel B-cell population that normally accounts for 4.0±0.7% (mean±SD) of total B cells and is up to 13-fold expanded in multiple myeloma patients with active disease. This population expressed markers previously associated with both memory (CD27+) and naïve (CD24loCD38+) phenotypes. Single-cell immunoglobulin gene sequencing showed polyclonality, indicating that these cells are not precursors to the myeloma, and somatic mutations, a characteristic of memory cells. SYK, ERK, and p38 phosphorylation responses, and the fact that most of these cells expressed isotypes other than IgM or IgD, confirmed the memory character of this population, defining it as a novel type of memory B cells. PMID:25711758

  9. Family-Based Rare Variant Association Analysis: A Fast and Efficient Method of Multivariate Phenotype Association Analysis.

    Science.gov (United States)

    Wang, Longfei; Lee, Sungyoung; Gim, Jungsoo; Qiao, Dandi; Cho, Michael; Elston, Robert C; Silverman, Edwin K; Won, Sungho

    2016-09-01

    Family-based designs have been repeatedly shown to be powerful in detecting the significant rare variants associated with human diseases. Furthermore, human diseases are often defined by the outcomes of multiple phenotypes, and thus we expect multivariate family-based analyses may be very efficient in detecting associations with rare variants. However, few statistical methods implementing this strategy have been developed for family-based designs. In this report, we describe one such implementation: the multivariate family-based rare variant association tool (mFARVAT). mFARVAT is a quasi-likelihood-based score test for rare variant association analysis with multiple phenotypes, and tests both homogeneous and heterogeneous effects of each variant on multiple phenotypes. Simulation results show that the proposed method is generally robust and efficient for various disease models, and we identify some promising candidate genes associated with chronic obstructive pulmonary disease. The software of mFARVAT is freely available at http://healthstat.snu.ac.kr/software/mfarvat/, implemented in C++ and supported on Linux and MS Windows. PMID:27312886

  10. Embedded Figures Test Performance in the Broader Autism Phenotype: A Meta-analysis.

    Science.gov (United States)

    Cribb, Serena J; Olaithe, Michelle; Di Lorenzo, Renata; Dunlop, Patrick D; Maybery, Murray T

    2016-09-01

    People with autism show superior performance to controls on the Embedded Figures Test (EFT). However, studies examining the relationship between autistic-like traits and EFT performance in neurotypical individuals have yielded inconsistent findings. To examine the inconsistency, a meta-analysis was conducted of studies that (a) compared high and low Autism-Spectrum Quotient (AQ) groups, and (b) treated AQ as a continuous variable. Outcomes are consistent with superior visual search forming part of the broader autism phenotype, but in existing literature, this is evident only when comparing extreme groups. Reanalysis of data from previous studies suggests findings are unlikely to be driven by a small number of high scorers. Monte Carlo simulations are used to illustrate the effect of methodological differences on results. PMID:27312717

  11. Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms

    Directory of Open Access Journals (Sweden)

    Li Yongle

    2011-10-01

    Full Text Available Abstract Background Frost is an important abiotic stress that limits cereal production in the temperate zone. As the most frost tolerant small grain cereal, rye (Secale cereale L. is an ideal cereal model for investigating the genetic basis of frost tolerance (FT, a complex trait with polygenic inheritance. Using 201 genotypes from five Eastern and Middle European winter rye populations, this study reports a multi-platform candidate gene-based association analysis in rye using 161 single nucleotide polymorphisms (SNPs and nine insertion-deletion (Indel polymorphisms previously identified from twelve candidate genes with a putative role in the frost responsive network. Results Phenotypic data analyses of FT in three different phenotyping platforms, controlled, semi-controlled and field, revealed significant genetic variations in the plant material under study. Statistically significant (P ScCbf15 and one in ScCbf12, all leading to amino acid exchanges, were significantly associated with FT over all three phenotyping platforms. Distribution of SNP effect sizes expressed as percentage of the genetic variance explained by individual SNPs was highly skewed towards zero with a few SNPs obtaining large effects. Two-way epistasis was found between 14 pairs of candidate genes. Relatively low to medium empirical correlations of SNP-FT associations were observed across the three platforms underlining the need for multi-level experimentation for dissecting complex associations between genotypes and FT in rye. Conclusions Candidate gene based-association studies are a powerful tool for investigating the genetic basis of FT in rye. Results of this study support the findings of bi-parental linkage mapping and expression studies that the Cbf gene family plays an essential role in FT.

  12. Anchor Plates in Two-Layered Cohesion Less Soils

    Directory of Open Access Journals (Sweden)

    Hamed Niroumand

    2010-01-01

    Full Text Available Problem statement: During the past few years a great number of experimental model and numerical analysis results on the uplift resistance of anchor plate embedded in homogeneous cohesion less soil has been reported by many researchers. A review of related literature shows that not much research has been done to analyze the performance of anchor plates in layered soils a problem, which is often encountered by the professional engineers in the field. Approach: This study presented the performance of the anchor plates in the cohesion less soil by different researchers. It was based on different previous researches, from the earliest till the most recent ones. The main aim of this research was focused on the prediction of the anchor plates behavior and the force in the layered cohesion less soils. Few laboratory studies were conducted to investigate the uplift capacity behavior of cohesion less soil by previous researchers. Results: The experimental and numerical investigation included uplift test on cohesion less soil by last researchers. The embedment ratio and the effect of density on uplift response were evaluated. This analysis was investigated experimentally and numerically behavior of anchor plates buried in two layered cohesion less soil. Although earlier researchers developed experimentally expressions to estimate the uplift capacity of irregular anchor plates in layered cohesion less soils. Conclusion: The study observed that the ultimate uplift capacity is dependent on the relative strength of the two layers, the depth ratio of embedment and the upper layer thickness ratio.

  13. Decoding Cytoskeleton-Anchored and Non-Anchored Receptors from Single-Cell Adhesion Force Data.

    Science.gov (United States)

    Sariisik, Ediz; Popov, Cvetan; Müller, Jochen P; Docheva, Denitsa; Clausen-Schaumann, Hauke; Benoit, Martin

    2015-10-01

    Complementary to parameters established for cell-adhesion force curve analysis, we evaluated the slope before a force step together with the distance from the surface at which the step occurs and visualized the result in a two-dimensional density plot. This new tool allows detachment steps of long membrane tethers to be distinguished from shorter jumplike force steps, which are typical for cytoskeleton-anchored bonds. A prostate cancer cell line (PC3) immobilized on an atomic-force-microscopy sensor interacted with three different substrates: collagen-I (Col-I), bovine serum albumin, and a monolayer of bone marrow-derived stem cells (SCP1). To address PC3 cells' predominant Col-I binding molecules, an antibody-blocking β1-integrin was used. Untreated PC3 cells on Col-I or SCP1 cells, which express Col-I, predominantly showed jumps in their force curves, while PC3 cells on bovine-serum-albumin- and antibody-treated PC3 cells showed long membrane tethers. The probability density plots thus revealed that β1-integrin-specific interactions are predominately anchored to the cytoskeleton, while the nonspecific interactions are mainly membrane-anchored. Experiments with latrunculin-A-treated PC3 cells corroborated these observations. The plots thus reveal details of the anchoring of bonds to the cell and provide a better understanding of receptor-ligand interactions. PMID:26445433

  14. Microfluidic single-cell analysis links boundary environments and individual microbial phenotypes.

    Science.gov (United States)

    Dusny, Christian; Schmid, Andreas

    2015-06-01

    Life is based on the cell as the elementary replicative and self-sustaining biological unit. Each single cell constitutes an independent and highly dynamic system with a remarkable individuality in a multitude of physiological traits and responses to environmental fluctuations. However, with traditional population-based cultivation set-ups, it is not possible to decouple inherent stochastic processes and extracellular contributions to phenotypic individuality for two central reasons: the lack of environmental control and the occlusion of single-cell dynamics by the population average. With microfluidic single-cell analysis as a new cell assay format, these issues can now be addressed, enabling cultivation and time-resolved analysis of single cells in precisely manipulable extracellular environments beyond the bulk. In this article, we explore the interplay of cellular physiology and environment at a single-cell level. We review biological basics that govern the functional state of the cell and put them in context with physical fundamentals that shape the extracellular environment. Furthermore, the significance of single-cell growth rates as pivotal descriptors for global cellular physiology is discussed and highlighted by selected studies. These examples illustrate the unique opportunities of microfluidic single-cell cultivation in combination with growth rate analysis, addressing questions of fundamental bio(techno)logical interest. PMID:25330456

  15. Machine Learning and Computer Vision System for Phenotype Data Acquisition and Analysis in Plants

    Directory of Open Access Journals (Sweden)

    Pedro J. Navarro

    2016-05-01

    Full Text Available Phenomics is a technology-driven approach with promising future to obtain unbiased data of biological systems. Image acquisition is relatively simple. However data handling and analysis are not as developed compared to the sampling capacities. We present a system based on machine learning (ML algorithms and computer vision intended to solve the automatic phenotype data analysis in plant material. We developed a growth-chamber able to accommodate species of various sizes. Night image acquisition requires near infrared lightning. For the ML process, we tested three different algorithms: k-nearest neighbour (kNN, Naive Bayes Classifier (NBC, and Support Vector Machine. Each ML algorithm was executed with different kernel functions and they were trained with raw data and two types of data normalisation. Different metrics were computed to determine the optimal configuration of the machine learning algorithms. We obtained a performance of 99.31% in kNN for RGB images and a 99.34% in SVM for NIR. Our results show that ML techniques can speed up phenomic data analysis. Furthermore, both RGB and NIR images can be segmented successfully but may require different ML algorithms for segmentation.

  16. Machine Learning and Computer Vision System for Phenotype Data Acquisition and Analysis in Plants.

    Science.gov (United States)

    Navarro, Pedro J; Pérez, Fernando; Weiss, Julia; Egea-Cortines, Marcos

    2016-01-01

    Phenomics is a technology-driven approach with promising future to obtain unbiased data of biological systems. Image acquisition is relatively simple. However data handling and analysis are not as developed compared to the sampling capacities. We present a system based on machine learning (ML) algorithms and computer vision intended to solve the automatic phenotype data analysis in plant material. We developed a growth-chamber able to accommodate species of various sizes. Night image acquisition requires near infrared lightning. For the ML process, we tested three different algorithms: k-nearest neighbour (kNN), Naive Bayes Classifier (NBC), and Support Vector Machine. Each ML algorithm was executed with different kernel functions and they were trained with raw data and two types of data normalisation. Different metrics were computed to determine the optimal configuration of the machine learning algorithms. We obtained a performance of 99.31% in kNN for RGB images and a 99.34% in SVM for NIR. Our results show that ML techniques can speed up phenomic data analysis. Furthermore, both RGB and NIR images can be segmented successfully but may require different ML algorithms for segmentation. PMID:27164103

  17. Molecular genetic analysis in 14 Czech Kabuki syndrome patients is confirming the utility of phenotypic scoring.

    Science.gov (United States)

    Paděrová, J; Holubová, A; Simandlová, M; Puchmajerová, A; Vlčková, M; Malíková, M; Pourová, R; Vejvalková, S; Havlovicová, M; Šenkeříková, M; Ptáková, N; Drábová, J; Geryk, J; Maver, A; Křepelová, A; Macek, M

    2016-09-01

    Kabuki syndrome (KS) is a dominantly inherited disorder mainly due to de novo pathogenic variation in KMT2D or KDM6A genes. Initially, a representative cohort of 14 Czech cases with clinical features suggestive of KS was analyzed by experienced clinical geneticists in collaboration with other specialties, and observed disease features were evaluated according to the 'MLL2-Kabuki score' defined by Makrythanasis et al. Subsequently, the aforementioned genes were Sanger sequenced and copy number variation analysis was performed by MLPA, followed by genome-wide array CGH testing. Pathogenic variants in KMT2D resulting in protein truncation in 43% (6/14; of which 3 are novel) of all cases were detected, while analysis of KDM6A was negative. MLPA analysis was negative in all instances. One female patient bears a 6.6 Mb duplication of the Xp21.2-Xp21.3 region that is probably disease causing. Subjective KS phenotyping identified predictive clinical features associated with the presence of a pathogenic variant in KMT2D. We provide additional evidence that this scoring approach fosters prioritization of patients prior to KMT2D sequencing. We conclude that KMT2D sequencing followed by array CGH is a diagnostic strategy with the highest diagnostic yield. PMID:26841933

  18. Molecular analysis in true hermaphrodites with different karyotypes and similar phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Torres, L.; Cervantes, A.; Kofman-Alfaro, S. [H.G.M. Ssa. Facultad de Medicina (Mexico)] [and others

    1996-05-17

    True hermaphroditism is characterized by the development of ovarian and testicular tissue in the same individual. Muellerian and Wolffian structures are usually present, and external genitalia are often ambiguous. The most frequent karyotype in these patients is 46,XX or various forms of mosaicism, whereas 46,XY is very rarely found. The phenotype in all these subjects is similar. We studied 10 true hermaphrodites. Six of them had a 46,XX chromosomal complement: 3 had been reared as males and 3 as females. The other 4 patients were mosaics: 3 were 46,XX/46,XY and one had a 46,XX/47,XXY karyotype. One of the 46,XX/46,XY mosaics was reared as a female, whereas the other 3 mosaics were reared as males. The sex of assignment in the 10 patients depended only on labio-scrotal differentiation. Molecular studies in 46,XX subjects documented the absence of Y centromeric sequences in all cases, arguing against hidden mosaicism. One patient presented Yp sequences (ZFY+, SRY+), which contrast with South African black 46,XX true hermaphrodites in whom no Y sequences were found. Molecular analysis in the subjects with mosaicism demonstrated the presence of Y centromeric and Yp sequences confirming the presence of a Y chromosome. Gonadal development, endocrine function, and phenotype in the 10 patients did not correlate with the presence of a Y chromosome or Y-derived sequences in the genome, confirming that true hermaphroditism is a heterogeneous condition. Both Mexican and non-South African 46,XX true hermaphrodites may be SRY positive. 51 refs., 3 figs., 2 tabs.

  19. Permanent ground anchors: Nicholson design criteria

    Science.gov (United States)

    Nicholson, P. J.; Uranowski, D. D.; Wycliffe-Jones, P. T.

    1982-09-01

    The methods used by Nicholson Construction Company in the design of permanent ground anchors specifically as related to retaining walls are discussed. Basic soil parameters, design concepts, drilling and grouting methods for ground anchors are discussed. Particular emphasis is placed on anchors founded in soil rather than rock formations. Also, soil properties necessary for the proper design of anchored retaining walls are detailed. The second chapter of the report is devoted to a general discussion of retaining wall and anchor design. In addition, a design example of an anchored retaining wall is presented in a step by step manner.

  20. Geochemical and mineralogical analysis of stone anchors from west coast of India: Provenance study using thin sections, XRF and SEM-EDS

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.; Mudholkar, A.V.; Vora, K.H.; Rao, B.R.; Gaur, A.S.; Sundaresh

    of the texture and mineral characteristics of samples. 2.2. XRF studies Another part of the rock chip was powdered using the agate ball mill for non-contamination. This powder was dried in the find sites in India. Fig. 2. Stone anchors of west coast of India (a... incalcareous cement. PPL: Plane Polarised Light BXN: Between Crossed Nicols. S. Tripati et al. / Journal of Archaeological2004 oven at 110 C14 C overnight to remove the moisture. Later the same powder was heated to w1050 C14 Cforw3 h to determine the loss...

  1. Muscle contraction phenotypic analysis enabled by optogenetics reveals functional relationships of sarcomere components in Caenorhabditis elegans

    Science.gov (United States)

    Hwang, Hyundoo; Barnes, Dawn E.; Matsunaga, Yohei; Benian, Guy M.; Ono, Shoichiro; Lu, Hang

    2016-01-01

    The sarcomere, the fundamental unit of muscle contraction, is a highly-ordered complex of hundreds of proteins. Despite decades of genetics work, the functional relationships and the roles of those sarcomeric proteins in animal behaviors remain unclear. In this paper, we demonstrate that optogenetic activation of the motor neurons that induce muscle contraction can facilitate quantitative studies of muscle kinetics in C. elegans. To increase the throughput of the study, we trapped multiple worms in parallel in a microfluidic device and illuminated for photoactivation of channelrhodopsin-2 to induce contractions in body wall muscles. Using image processing, the change in body size was quantified over time. A total of five parameters including rate constants for contraction and relaxation were extracted from the optogenetic assay as descriptors of sarcomere functions. To potentially relate the genes encoding the sarcomeric proteins functionally, a hierarchical clustering analysis was conducted on the basis of those parameters. Because it assesses physiological output different from conventional assays, this method provides a complement to the phenotypic analysis of C. elegans muscle mutants currently performed in many labs; the clusters may provide new insights and drive new hypotheses for functional relationships among the many sarcomere components.

  2. GENOME-WIDE LINKAGE ANALYSIS TO IDENTIFY CHROMOSOMAL REGIONS AFFECTING PHENOTYPIC TRAITS IN THE CHICKEN. IV. SKELETAL INTEGRITY

    Science.gov (United States)

    Two unique chicken F2 populations generated from a broiler breeder male line and two genetically distinct inbred (greater than 99%) chicken lines (Leghom and Fayoumi), were used for whole genome QTL analysis. Twelve phenotypic skeletal integrity traits (6 absolute and 6 relative traits) were measure...

  3. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity

    NARCIS (Netherlands)

    Almendro, Vanessa; Cheng, Yu-Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G; Helland, Aslaug; Rye, Inga H; Borresen-Dale, Anne-Lise; Maruyama, Reo; van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia

    2014-01-01

    Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-

  4. Pain phenotype as a predictor for drug response in painful polyneuropathy A retrospective analysis of data from controlled clinical trials

    DEFF Research Database (Denmark)

    Holbech, Jakob V; Bach, Flemming W; Finnerup, Nanna B;

    2016-01-01

    better effect in patients with preserved large fiber function with a mean difference in total pain reduction 1.31 (CI: 0.15 to 2.47). No phenotype-specific effects were found for venlafaxine, escitalopram, oxcarbazepine, valproic acid, levetiracetam or St. john's wort. Thus, this post-hoc analysis of 8...

  5. Phenotype and molecular analysis of M1 generation of stylosanthes irradiated by 60Co

    International Nuclear Information System (INIS)

    The seeds of Stylosanthes guianensis SW. ‘Reyan No.13’ were irradiated by 60Co at 0, 325, 487 and 974 Gy. Phenotype and molecular variations of Stylosanthes M1 generations were studied. Germination percentage, plant height, leaf length and stem diameter of M1 seedlings were determined using SRAP-PCR. Results showed that biological character indices of treatments were significantly lower than that of control (CK). Irradiation inhibited plant growth. Growth indices of 974 Gy treatment, except leaf length, were significantly lower than CK and other two treatments. Eight effective primers selected from 24 primers combination were used for SRAP-PCR. SRAP analysis revealed that the 57 of 88 DNA fragments were amplified showing polymorphisms. The average percentage of polymorphic bands was 64.77%. The effects of 60Coγ irradiation on DNA variation of seedlings were varied from different treatments. Numbers of polymorphic bands changed after irradiation. Coefficient of variation was in direct proportion to irradiation doses. Variation rates of 325 Gy, 487 Gy and 974 Gy treatments were 22.0%, 38.1% and 41.5%, respectively. The Nei’s genetic similarity coefficient of all treatments was ranged from 0.585 to 0.780 by software NTSYSpc 2.1 based on SRAP results and the average Nei's coefficient was 0.678. The Nei’s genetic similarity coefficient of 974 Gy treatment was 0.585 and variation degree was highest among all treatments, 487 Gy treatment was second and 325 Gy treatment was the lowest one. Based on present bands, four irradiated treatments were classified into two major groups by UPGMA cluster analysis. Group 1 included CK, 325 Gy and 487 Gy treatment and group 2 included 974 Gy. SRAP analysis determined variation of Stylosanthes after irradiation and the results of SRAP analysis were consistent with their biological indexes in some extent

  6. Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum

    Directory of Open Access Journals (Sweden)

    Venkatesh KV

    2006-10-01

    Full Text Available Abstract Background Quantification of the metabolic network of an organism offers insights into possible ways of developing mutant strain for better productivity of an extracellular metabolite. The first step in this quantification is the enumeration of stoichiometries of all reactions occurring in a metabolic network. The structural details of the network in combination with experimentally observed accumulation rates of external metabolites can yield flux distribution at steady state. One such methodology for quantification is the use of elementary modes, which are minimal set of enzymes connecting external metabolites. Here, we have used a linear objective function subject to elementary modes as constraint to determine the fluxes in the metabolic network of Corynebacterium glutamicum. The feasible phenotypic space was evaluated at various combinations of oxygen and ammonia uptake rates. Results Quantification of the fluxes of the elementary modes in the metabolism of C. glutamicum was formulated as linear programming. The analysis demonstrated that the solution was dependent on the criteria of objective function when less than four accumulation rates of the external metabolites were considered. The analysis yielded feasible ranges of fluxes of elementary modes that satisfy the experimental accumulation rates. In C. glutamicum, the elementary modes relating to biomass synthesis through glycolysis and TCA cycle were predominantly operational in the initial growth phase. At a later time, the elementary modes contributing to lysine synthesis became active. The oxygen and ammonia uptake rates were shown to be bounded in the phenotypic space due to the stoichiometric constraint of the elementary modes. Conclusion We have demonstrated the use of elementary modes and the linear programming to quantify a metabolic network. We have used the methodology to quantify the network of C. glutamicum, which evaluates the set of operational elementary modes at

  7. Newcomers' cognitive development of social identification: a cross-sectional and longitudinal analysis of self-anchoring and self-stereotyping.

    Science.gov (United States)

    van Veelen, Ruth; Hansen, Nina; Otten, Sabine

    2014-06-01

    Upon joining a new social category, group members strive to establish and maintain high social identification. Thus far, we know relatively little about the cognitive underpinnings of social identification when developing from a new to a well-established group member. This research investigates the differential impact of newcomers' self-stereotyping (i.e., assimilation of the self to group stereotypes) and self-anchoring (i.e., projection of self-attributes onto the ingroup) on the development of social identification over time. Across two time points during the academic year, first year psychology students (N = 123) filled in a questionnaire on their perceptions about the self, psychology students, and social identification. Cross-sectional and longitudinal analyses confirmed our hypotheses that self-anchoring instigated new group members' social identification, while self-stereotyping instigated social identification once group membership was more well-established. This research emphasizes the interactive role of the personal and social self in the development of social identification. PMID:23675674

  8. Push Force Analysis of Anchor Block of the Oil and Gas Pipeline in a Single-Slope Tunnel Based on the Energy Balance Method.

    Science.gov (United States)

    Yan, Yifei; Zhang, Lisong; Yan, Xiangzhen

    2016-01-01

    In this paper, a single-slope tunnel pipeline was analysed considering the effects of vertical earth pressure, horizontal soil pressure, inner pressure, thermal expansion force and pipeline-soil friction. The concept of stagnation point for the pipeline was proposed. Considering the deformation compatibility condition of the pipeline elbow, the push force of anchor blocks of a single-slope tunnel pipeline was derived based on an energy method. Then, the theoretical formula for this force is thus generated. Using the analytical equation, the push force of the anchor block of an X80 large-diameter pipeline from the West-East Gas Transmission Project was determined. Meanwhile, to verify the results of the analytical method, and the finite element method, four categories of finite element codes were introduced to calculate the push force, including CAESARII, ANSYS, AutoPIPE and ALGOR. The results show that the analytical results agree well with the numerical results, and the maximum relative error is only 4.1%. Therefore, the results obtained with the analytical method can satisfy engineering requirements. PMID:26963097

  9. Hair Analysis for Determination of Isoniazid Concentrations and Acetylator Phenotype during Antituberculous Treatment

    Directory of Open Access Journals (Sweden)

    Michael Eisenhut

    2012-01-01

    Full Text Available Background. Analysis of isoniazid (INH uptake has been based on measurement of plasma concentrations providing a short-term and potentially biased view. Objectives. To establish hair analysis as a tool to measure long-term uptake of INH and to assess whether acetylator phenotype in hair reflects N-acetyltransferase-2 (NAT2 genotype. Design and Methods. INH and acetyl-INH concentrations in hair were determined in patients on INH treatment for M. tuberculosis infection using high pressure liquid chromatography/mass spectrometry. Acetyl-INH/INH ratios were correlated with NAT-2 genotype. Results. Hair concentrations of INH, determined in 40 patients, were not dependent on ethnic group or body mass index and were significantly higher in male compared to female patients (median (range 2.37 ng/mg (0.76–4.9 versus 1.11 ng/mg (0.02–7.20 (P=0.02. Acetyl-INH/INH ratios were a median of 15.2% (14.5 to 31.7 in homozygous rapid acetylator NAT-2 genotype and 37.3% (1.73 to 51.2 in the heterozygous rapid acetylator NAT-2 genotype and both significantly higher than in the slow acetylator NAT-2 genotype with 5.8% (0.53 to 14.4 (P<0.05. Conclusions. Results of hair analysis for INH showed lower concentrations in females. Acetyl-INH/INH ratios were significantly lower in patients with slow acetylator versus rapid acetylator genotypes.

  10. Genomic analysis of natural selection and phenotypic variation in high-altitude mongolians.

    Directory of Open Access Journals (Sweden)

    Jinchuan Xing

    Full Text Available Deedu (DU Mongolians, who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago, are challenged by environmental conditions similar to native Tibetan highlanders. Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment. Here we examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole-genome sequence. High-density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations, specifically in genomic regions related with adaptation to high altitude. Several selection candidate genes identified in DU Mongolians are shared with other Asian groups (e.g., EDAR, neighboring Tibetan populations (including high-altitude candidates EPAS1, PKLR, and CYP2E1, as well as genes previously hypothesized to be associated with metabolic adaptation (e.g., PPARG. Hemoglobin concentration, a trait associated with high-altitude adaptation in Tibetans, is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude. Whole-genome sequence from a DU Mongolian (Tianjiao1 shows that about 2% of the genomic variants, including more than 300 protein-coding changes, are specific to this individual. Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments.

  11. The list of strains and growth conditions - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available The Rice Growth Monitoring for The Phenotypic Functional Analysis The list of strains and growth conditions ... Site Policy | Contact Us The list of strains and growth conditions - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  12. The list of growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available The Rice Growth Monitoring for The Phenotypic Functional Analysis The list of growth image files Data detail... Site Policy | Contact Us The list of growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  13. The rice growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available The Rice Growth Monitoring for The Phenotypic Functional Analysis The rice growth image files Data detail Da...e Site Policy | Contact Us The rice growth image files - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  14. Thoracic aortic stent-graft placement combined with left subclavian artery 'chimney operation': therapeutic analysis of 15 cases with insufficient proximal anchor area

    International Nuclear Information System (INIS)

    Objective: To discuss the strategies for the management of insufficient proximal anchoring area during the performance of transluminal stent-graft placement (TSGP), and to evaluate the feasibility of intentional coverage of the left subclavian artery (LSA) together with left subclavian artery stent-graft placement by using 'chimney operation' technique. Methods: A total of 15 patients with thoracic aortic diseases complicated by insufficient proximal anchoring area, who were encountered in authors' hospital during the period from Dec. 2009 to April 2011, were enrolled in this study. The clinical data were retrospectively analyzed. The thoracic aortic diseases included aortic dissection (n=6), aortic pseudoaneurysm (n=1), aortic aneurysm (n=4) and penetrating ulcer (n=4). Of the 15 patients, the distance between the lesion and LSA anchoring site 15 mm in 2. TSGP was carried out. The ostium of LSA was intentionally and completely covered by thoracic aortic stent-graft and left subclavian artery stent-graft placement was subsequently performed. The patients were kept under observation for symptoms of cerebral and upper limb ischemia. The postoperative complications such as endoleak and the patency of LSA were assessed with angiography. Results: Thoracic aortic stent-graft placement was successfully carried out in all 15 patients. In addition, one 'chimney' stent was properly implanted in LSA in each patient. After the procedure, no complications of nervous system or severe ischemia of upper extremity occurred. Follow-up examinations performed between 5 days to 3 months after the treatment revealed that the aortic stent-graft remained in stable condition and no type Ⅰ endoleak occurred, meanwhile the blood flow in 'chimney' stent was unobstructed. Conclusion: Intentional LSA coverage with 'chimney operation' can expand the applicability of TSGP with high tolerability. It is especially useful for patients with left vertebral artery blood supply dominance or with

  15. Genotype-Phenotype Analysis in Congenital Adrenal Hyperplasia due to P450 Oxidoreductase Deficiency

    NARCIS (Netherlands)

    Krone, Nils; Reisch, Nicole; Idkowiak, Jan; Dhir, Vivek; Ivison, Hannah E.; Hughes, Beverly A.; Rose, Ian T.; O'Neil, Donna M.; Vijzelaar, Raymon; Smith, Matthew J.; MacDonald, Fiona; Cole, Trevor R.; Adolphs, Nicolai; Barton, John S.; Blair, Edward M.; Braddock, Stephen R.; Collins, Felicity; Cragun, Deborah L.; Dattani, Mehul T.; Day, Ruth; Dougan, Shelley; Feist, Miriam; Gottschalk, Michael E.; Gregory, John W.; Haim, Michaela; Harrison, Rachel; Olney, Ann Haskins; Hauffa, Berthold P.; Hindmarsh, Peter C.; Hopkin, Robert J.; Jira, Petr E.; Kempers, Marlies; Kerstens, Michiel N.; Khalifa, Mohamed M.; Koehler, Birgit; Maiter, Dominique; Nielsen, Shelly; O'Riordan, Stephen M.; Roth, Christian L.; Shane, Kate P.; Silink, Martin; Stikkelbroeck, Nike M. M. L.; Sweeney, Elizabeth; Szarras-Czapnik, Maria; Waterson, John R.; Williamson, Lori; Hartmann, Michaela F.; Taylor, Norman F.; Wudy, Stefan A.; Malunowicz, Ewa M.; Shackleton, Cedric H. L.; Arlt, Wiebke; Smith, M.J.

    2012-01-01

    Context: P450 oxidoreductase deficiency (PORD) is a unique congenital adrenal hyperplasia variant that manifests with glucocorticoid deficiency, disordered sex development (DSD), and skeletal malformations. No comprehensive data on genotype-phenotype correlations in Caucasian patients are available.

  16. Phenotypic and plasmid pattern analysis of Staphylococcus epidermidis in bacterial keratitis

    Directory of Open Access Journals (Sweden)

    Nayak Niranjan

    2007-01-01

    Full Text Available Background: Staphylococcus epidermidis , a commensal of the conjunctival sac has been incriminated as the commonest etiological agent of bacterial keratitis. However, the pathogenic potential of this commensal organism is not clearly known. Aim: To determine any phenotypic, molecular markers of S. epidermidis pathogenicity in bacterial keratitis. Materials and Methods: A total of 382 corneal ulcer isolates of S. epidermidis and 87 S. epidermidis isolates from healthy eyes (controls were studied. Speciation, biotyping and antibiotic sensitivity testing were performed by conventional methods. Tube slime and adherence tests were carried out by recommended techniques. Plasmid analysis was conducted by a standard protocol. Statistical Analysis: Chi-square test was employed for calculations. Results: Out of 382 corneal ulcer isolates (Pathogens 284 (74.3% belonged to biotypes I and II. Slime was detected in 164 (42.9% of 382 pathogens vs. 21 (24.1% of 87 controls ( P < 0.001. Sixty-five (39.6% of 164 slime positive isolates were multidrug-resistant as compared to only 49 (22.4% of 218 slime negative isolates ( P < 0.001. A significantly higher number i.e., 73.1% (120/164 of slime-producers possessed a 21Kb plasmid in contrast to only 53.2% (116/218 of nonslime-producers ( P < 0.001. Presence of this plasmid had a statistical correlation of low significance with multidrug resistance ( P =0.04. One hundred and seventy-two (45.0% of 382 pathogens and 24 (27.6% of the 87 controls were adherent to artificial surfaces ( P =0.003 and the majority of the adherent organisms (99/172, 57.6% were slime producers ( P < 0.001. Conclusions: Slime was associated with multidrug resistance in corneal ulcer isolates of S. epidermidis . The 21Kb plasmid could determine virulence as it was responsible for slime production and adherence.

  17. PEAX: INTERACTIVE VISUAL ANALYSIS AND EXPLORATION OF COMPLEX CLINICAL PHENOTYPE AND GENE EXPRESSION ASSOCIATION

    OpenAIRE

    Hinterberg, Michael A.; Kao, David P; Bristow, Michael R.; Hunter, Lawrence E.; Port, J. David; Görg, Carsten

    2015-01-01

    Increasing availability of high-dimensional clinical data, which improves the ability to define more specific phenotypes, as well as molecular data, which can elucidate disease mechanisms, is a driving force and at the same time a major challenge for translational and personalized medicine. Successful research in this field requires an approach that ties together specific disease and health expertise with understanding of molecular data through statistical methods. We present PEAX (Phenotype-...

  18. CFRP加固构件锚固端加强处理的有限元分析%Finite element analysis on the anchor end enhancement processing of CFRP reinforcement member

    Institute of Scientific and Technical Information of China (English)

    李宝来; 谭果祥; 田伟新

    2009-01-01

    以梁柱角节点为例,在梁端顶部碳纤维锚固段粘贴钢板,并向外延伸在转角处向柱旋转90°包裹混凝土,并在适当位置设置钢箍或螺栓,用有限元对其进行了分析,比较了钢板厚度,钢板有无转角,锚栓位置等情况对锚固性能的影响,并给出了一些建议.%Taking the beam-column angle node as example, the author pastes steel plate on the carbon fiber anchorage section of the beam-col-umn top, prolongs to outside and parcels concrete rotating 90 degree to the column on the comer, and sets steel hoop or bolt on suitable place, gets analysis based on the finite element, compares the influences of factors on anchor performance, such as the thickness of the steel plate, steel plate angle and anchor place, and provides some suggestion.

  19. Tumor progression: analysis of the instability of the metastatic phenotype, sensitivity to radiation and chemotherapy

    International Nuclear Information System (INIS)

    The major complications for tumor therapy are 1) tumor spread (metastasis); 2) the mixed nature of tumors (heterogeneity); and 3) the capacity of tumors to evolve (progress). To study these tumor characteristics, the rat 13762NF mammary adenocarcinoma was cloned and studied for metastatic properties and sensitivities to therapy (chemotherapy, radiation and hyperthermia). The cell clones were heterogeneous and no correlation between metastatic potential and therapeutic sensitivities was observed. Further, these phenotypes were unstable during pasage in vitro; yet, the changes were clone dependent and reproducible using different cryoprotected cell stocks. To understand the phenotypic instability, subclones were isolated from low and high passage cell clones. The results demonstrated that 1) tumor cells are heterogeneous for multiple phenotypes; 2) tumor cells are unstable for multiple phenotypes; 3) the magnitude, direction and time of occurrence of phenotypic drift is clone dependent; 4) the sensitivity of cell clones to ionizing radiation (γ or heat) and chemotherapy agents is independent of their metastatic potential; 5) shifts in metastatic potential and sensitivity to therapy may occur simultaneously but are not linked; and 6) tumor cells independently diverge to form several subpopulations with unique phenotypic profiles

  20. High-throughput phenotypic profiling of gene-environment interactions by quantitative growth curve analysis in Saccharomyces cerevisiae.

    Science.gov (United States)

    Weiss, Andrew; Delproposto, James; Giroux, Craig N

    2004-04-01

    Cell-based assays are widely used in high-throughput screening to determine the effects of toxicants and drugs on their biological targets. To enable a functional genomics modeling of gene-environment interactions, quantitative assays are required both for gene expression and for the phenotypic responses to environmental challenge. To address this need, we describe an automated high-throughput methodology that provides phenotypic profiling of the cellular responses to environmental stress in Saccharomyces cerevisiae. Standardized assay conditions enable the use of a single metric value to quantify yeast microculture growth curves. This assay format allows precise control of both genetic and environmental determinants of the cellular responses to oxidative stress, a common mechanism of environmental insult. These yeast-cell-based assays are validated with hydrogen peroxide, a simple direct-acting oxidant. Phenotypic profiling of the oxidative stress response of a yap1 mutant strain demonstrates the mechanistic analysis of genetic susceptibility to oxidative stress. As a proof of concept for analysis of more complex gene-environment interactions, we describe a combinatorial assay design for phenotypic profiling of the cellular responses to tert-butyl hydroperoxide, a complex oxidant that is actively metabolized by its target cells. Thus, the yeast microculture assay format supports comprehensive applications in toxicogenomics. PMID:15033507

  1. Anchoring in numeric judgments of visual stimuli

    Directory of Open Access Journals (Sweden)

    Linda eLangeborg

    2016-02-01

    Full Text Available This article investigates effects of anchoring in age estimation and estimation of quantities, two tasks which to different extents are based on visual stimuli. The results are compared to anchoring in answers to classic general knowledge questions that rely on semantic knowledge. Cognitive load was manipulated to explore possible differences between domains. Effects of source credibility, manipulated by differing instructions regarding the selection of anchor values (no information regarding anchor selection, information that the anchors are randomly generated or information that the anchors are answers from an expert on anchoring were also investigated. Effects of anchoring were large for all types of judgments but were not affected by cognitive load or by source credibility in either one of the researched domains. A main effect of cognitive load on quantity estimations and main effects of source credibility in the two visually based domains indicate that the manipulations were efficient. Implications for theoretical explanations of anchoring are discussed. In particular, because anchoring did not interact with source credibility or cognitive load, the results imply that the process behind anchoring in visual tasks is predominantly automatic and unconscious.

  2. Anchoring in Numeric Judgments of Visual Stimuli.

    Science.gov (United States)

    Langeborg, Linda; Eriksson, Mårten

    2016-01-01

    This article investigates effects of anchoring in age estimation and estimation of quantities, two tasks which to different extents are based on visual stimuli. The results are compared to anchoring in answers to classic general knowledge questions that rely on semantic knowledge. Cognitive load was manipulated to explore possible differences between domains. Effects of source credibility, manipulated by differing instructions regarding the selection of anchor values (no information regarding anchor selection, information that the anchors are randomly generated or information that the anchors are answers from an expert) on anchoring were also investigated. Effects of anchoring were large for all types of judgments but were not affected by cognitive load or by source credibility in either one of the researched domains. A main effect of cognitive load on quantity estimations and main effects of source credibility in the two visually based domains indicate that the manipulations were efficient. Implications for theoretical explanations of anchoring are discussed. In particular, because anchoring did not interact with cognitive load, the results imply that the process behind anchoring in visual tasks is predominantly automatic and unconscious. PMID:26941684

  3. Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

    Directory of Open Access Journals (Sweden)

    Guo Zhaobiao

    2011-02-01

    Full Text Available Abstract Background The osmotic regulator OmpR in Escherichia coli regulates differentially the expression of major porin proteins OmpF and OmpC. In Yersinia enterocolitica and Y. pseudotuberculosis, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in Y. pestis are not yet fully understood. Results Y. pestis OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. The ompR mutation likely did not affect the virulence of Y. pestis strain 201 that was a human-avirulent enzootic strain. The microarray-based comparative transcriptome analysis disclosed a set of 224 genes whose expressions were affected by the ompR mutation, indicating the global regulatory role of OmpR in Y. pestis. Real-time RT-PCR or lacZ fusion reporter assay further validated 16 OmpR-dependent genes, for which OmpR consensus-like sequences were found within their upstream DNA regions. ompC, F, X, and R were up-regulated dramatically with the increase of medium osmolarity, which was mediated by OmpR occupying the target promoter regions in a tandem manner. Conclusion OmpR contributes to the resistance against phagocytosis or survival within macrophages, which is conserved in the pathogenic yersiniae. Y. pestis OmpR regulates ompC, F, X, and R directly through OmpR-promoter DNA association. There is an inducible expressions of the pore-forming proteins OmpF, C, and × at high osmolarity in Y. pestis, in contrast to the reciprocal regulation of them in E. coli. The main difference is that ompF expression is not repressed at high osmolarity in Y. pestis, which is likely due to the absence of a promoter-distal OmpR-binding site for ompF.

  4. Differential analysis of ovarian and endometrial cancers identifies a methylator phenotype.

    Directory of Open Access Journals (Sweden)

    Diana L Kolbe

    Full Text Available Despite improved outcomes in the past 30 years, less than half of all women diagnosed with epithelial ovarian cancer live five years beyond their diagnosis. Although typically treated as a single disease, epithelial ovarian cancer includes several distinct histological subtypes, such as papillary serous and endometrioid carcinomas. To address whether the morphological differences seen in these carcinomas represent distinct characteristics at the molecular level we analyzed DNA methylation patterns in 11 papillary serous tumors, 9 endometrioid ovarian tumors, 4 normal fallopian tube samples and 6 normal endometrial tissues, plus 8 normal fallopian tube and 4 serous samples from TCGA. For comparison within the endometrioid subtype we added 6 primary uterine endometrioid tumors and 5 endometrioid metastases from uterus to ovary. Data was obtained from 27,578 CpG dinucleotides occurring in or near promoter regions of 14,495 genes. We identified 36 locations with significant increases or decreases in methylation in comparisons of serous tumors and normal fallopian tube samples. Moreover, unsupervised clustering techniques applied to all samples showed three major profiles comprising mostly normal samples, serous tumors, and endometrioid tumors including ovarian, uterine and metastatic origins. The clustering analysis identified 60 differentially methylated sites between the serous group and the normal group. An unrelated set of 25 serous tumors validated the reproducibility of the methylation patterns. In contrast, >1,000 genes were differentially methylated between endometrioid tumors and normal samples. This finding is consistent with a generalized regulatory disruption caused by a methylator phenotype. Through DNA methylation analyses we have identified genes with known roles in ovarian carcinoma etiology, whereas pathway analyses provided biological insight to the role of novel genes. Our finding of differences between serous and endometrioid

  5. Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis.

    Science.gov (United States)

    Zhang, Xia; Hirsch, Candice N; Sekhon, Rajandeep S; de Leon, Natalia; Kaeppler, Shawn M

    2016-04-01

    Seed size is an important component of grain yield and a key determinant trait for crop domestication. The Krug Yellow Dent long-term selection experiment for large and small seed provides a valuable resource to dissect genetic and phenotypic changes affecting seed size within a common genetic background. In this study, inbred lines derived from Krug Large Seed (KLS) and Krug Small Seed (KSS) populations and reciprocal F1 crosses were used to investigate developmental and molecular mechanisms governing seed size. Seed morphological characteristics showed striking differences between KLS and KSS inbred lines, and the reciprocal cross experiment revealed a strong maternal influence on both seed weight and seed size. Quantification of endosperm area, starchy endosperm cell size, and kernel dry mass accumulation indicated a positive correlation between seed size, endosperm cell number, and grain filling rate, and patterns of grain filling in reciprocal crosses mirrored that of the maternal parent. Consistent with the maternal contribution to seed weight, transcriptome profiling of reciprocal F1 hybrids showed substantial similarities to the maternal parent. A set of differentially expressed genes between KLS and KSS inbreds were found, which fell into a broad number of functional categories including DNA methylation, nucleosome assembly, and heat stress response. In addition, gene co-expression network analysis of parental inbreds and reciprocal F1 hybrids identified co-expression modules enriched in ovule development and DNA methylation, implicating these two processes in seed size determination. These results expand our understanding of seed size regulation and help to uncover the developmental and molecular basis underlying maternal control of seed size in maize. PMID:26826570

  6. Analysis of phenotype array data from Biolog MicroPlatesTM

    Institute of Scientific and Technical Information of China (English)

    John Bissett; Carol Ann Nolan

    2004-01-01

    @@ Biolog MicroPlatesTM are employed to characterize Trichoderma isolates based on differential assimilation of test substrates and redox reactions in a 96-well test plate. The Biolog method is potentially advantageous in being relatively simple, fast and economical, and data acquisition can be automated using a microplate reader and applicable software. Several research applications of the Biolog system are presented: i) "monophenetic groups" from cluster analyses of phenotype array data are investigated for previously undetected new species in Trichoderma, ii) metabolic characters differentiating species are identified, and multivariate analyses performed to complement molecular data in validating new species and significant variants, and iii) phenotype array data for more than 1200 Trichoderma strains are analysed to select strains that might be exploited for bioconversions and commercial production of enzymes. Phenotype arrays are much more sensitive to strain level variation than molecular techniques, however, phenotype array data do not consistently reflect phylogenies constructed from molecular data. Nevertheless, the Biolog phenotype array is an economical alternative method for surveying biological diversity, and provides data that complements molecular data in phylogenetic studies.

  7. Theoretical model and solution for the rheological problem of anchor-grouting a soft rock tunnel

    International Nuclear Information System (INIS)

    The paper presents an analytical method for analysis of the soft rock tunnel, based on a model dividing soft rock tunnels into a region of anchor-grouting and a region of non-anchor-grouting surrounding rock. The Poynting-Thomson model and the Kelvin-Hooke model are applied to the region of non-anchor-grouting surrounding rock and the region of anchor-grouting, respectively. Stress expressions in the region of non-anchor-grouting surrounding rock and the region of anchor-grouting are obtained. Expanding the expression of displacements in the region of anchor-grouting into a Maclaurin series, and utilizing the cumulative displacement curve of the surrounding rock through observation, a theoretical model is set up. This model and its solution for the rheology problem of anchor-grouting a soft tunnel have been proved to be effective in practical engineering; according to the Mohr-Coulomb yield condition, a safe criterion for an anchor-grouting soft rock of a tunnel can be found

  8. Clustering and classical analysis of clinical and placental phenotypes in fetal growth restriction and constitutional fetal smallness.

    Science.gov (United States)

    Stanek, Jerzy; Biesiada, Jacek

    2016-06-01

    This study aims to determine whether placental examination can be used to distinguish between pathologic fetal growth restriction (FGR) and constitutional fetal smallness. Data were extracted from a clinicoplacental database of high risk pregnancies during the period 1994-2013. These data were used to compare the 590 consecutive cases having birth weights below the 10th percentile with the 5201 remaining cases having gestational ages ≥20 weeks. The authors analyzed 20 clinical and 46 placental phenotypes using classical statistics, clustering analysis, and multidimensional scaling. Of the low-birth-weight babies, the following types of cases were compared: Four categories of placental phenotypes (those with features of poor uteroplacental perfusion, postuterine placental pathology, chronic inflammation, and a mixed category) better defined the presumably true FGR than did the clinical phenotypes. Maternal smoking and oligohydramnios were associated with fewer abnormal placental phenotypes than were maternal hypertensive diseases and abnormal Dopplers. Early-onset cases of fetal smallness clustered with placental features of poor uteroplacental perfusion, whereas late onset cases did not. Placental examination helps to retrospectively distinguish constitutionally small fetuses from those that are pathologically growth restricted. The latter correlate best with the clinical risk for FGR and with early-onset FGR. This correlation may have prognostic significance for the child and for future pregnancies, since hypoxic placental lesions can occur without clinical risk factors but with a tendency to recur in future pregnancies. PMID:27238719

  9. The duplication 17p13.3 phenotype: analysis of 21 families delineates developmental, behavioral and brain abnormalities, and rare variant phenotypes.

    Science.gov (United States)

    Curry, Cynthia J; Rosenfeld, Jill A; Grant, Erica; Gripp, Karen W; Anderson, Carol; Aylsworth, Arthur S; Saad, Taha Ben; Chizhikov, Victor V; Dybose, Giedre; Fagerberg, Christina; Falco, Michelle; Fels, Christina; Fichera, Marco; Graakjaer, Jesper; Greco, Donatella; Hair, Jennifer; Hopkins, Elizabeth; Huggins, Marlene; Ladda, Roger; Li, Chumei; Moeschler, John; Nowaczyk, Malgorzata J M; Ozmore, Jillian R; Reitano, Santina; Romano, Corrado; Roos, Laura; Schnur, Rhonda E; Sell, Susan; Suwannarat, Pim; Svaneby, Dea; Szybowska, Marta; Tarnopolsky, Mark; Tervo, Raymond; Tsai, Anne Chun-Hui; Tucker, Megan; Vallee, Stephanie; Wheeler, Ferrin C; Zand, Dina J; Barkovich, A James; Aradhya, Swaroop; Shaffer, Lisa G; Dobyns, William B

    2013-08-01

    Chromosome 17p13.3 is a gene rich region that when deleted is associated with the well-known Miller-Dieker syndrome. A recently described duplication syndrome involving this region has been associated with intellectual impairment, autism and occasional brain MRI abnormalities. We report 34 additional patients from 21 families to further delineate the clinical, neurological, behavioral, and brain imaging findings. We found a highly diverse phenotype with inter- and intrafamilial variability, especially in cognitive development. The most specific phenotype occurred in individuals with large duplications that include both the YWHAE and LIS1 genes. These patients had a relatively distinct facial phenotype and frequent structural brain abnormalities involving the corpus callosum, cerebellar vermis, and cranial base. Autism spectrum disorders were seen in a third of duplication probands, most commonly in those with duplications of YWHAE and flanking genes such as CRK. The typical neurobehavioral phenotype was usually seen in those with the larger duplications. We did not confirm the association of early overgrowth with involvement of YWHAE and CRK, or growth failure with duplications of LIS1. Older patients were often overweight. Three variant phenotypes included cleft lip/palate (CLP), split hand/foot with long bone deficiency (SHFLD), and a connective tissue phenotype resembling Marfan syndrome. The duplications in patients with clefts appear to disrupt ABR, while the SHFLD phenotype was associated with duplication of BHLHA9 as noted in two recent reports. The connective tissue phenotype did not have a convincing critical region. Our experience with this large cohort expands knowledge of this diverse duplication syndrome. PMID:23813913

  10. Anchors and their use in offshore petroleum operations

    Energy Technology Data Exchange (ETDEWEB)

    1984-01-01

    Holding a ship or vessel in a fixed position over specific spots is essential in drilling subsea wells. Conventional anchors and holding systems have thus been transformed into permanent mooring points capable of withstanding enormous stresses. This book specifies the parameters directly governing behavior of these new anchors, studies the mechanisms involved in anchor/seabed interaction and interprets these in the context of soil mechanics, and draws practical conclusions in the form of methods for predicting holding capacity in different types of subsea soils. Contents are: history of anchors; high-capacity anchoring systems; kinetics of anchors; holding power of anchors; anchoring site survey; choice of an anchor; and anchoring tests.

  11. A Unifying Model for the Analysis of Phenotypic, Genetic and Geographic Data

    DEFF Research Database (Denmark)

    Guillot, Gilles; Rena, Sabrina; Ledevin, Ronan; Michaux, Johan; Claude, Julien

    2012-01-01

    advantage: (i) it incorporates information about the spatial distribution of the samples, with the aim to increase inference power and to relate more explicitly observed patterns to geography; and (ii) it allows one to analyze genetic and phenotypic data within a unied model and inference framework, thus......Recognition of evolutionary units (species, populations) requires integrating several kinds of data such as genetic or phenotypic markers or spatial information, in order to get a comprehensive view concerning the dierentiation of the units. We propose a statistical model with a double original...

  12. UPPER BOUND ANALYSIS OF HORIZONTALLY EMBEDDED ANCHORS BASED ON BLOCK SET MECHANISM%基于组合块体集的浅埋条形锚板上限分析

    Institute of Scientific and Technical Information of China (English)

    余生兵; 黄茂松

    2011-01-01

    基于极限分析法的基本原理以及集成与组合的思路,推导组合块体集的内能耗散和重力做功,运用组合的思想构造斜坡地形下浅埋水平条形锚板的运动许可速度场.首先分析地表水平条件下法向受力水平条形锚板抗拔承载力,并与文献中已有解和模型试验进行对比,验证块体集上限法的优越性.然后详细研究斜坡地形条件下土体重度、不排水抗剪强度、斜坡倾角等因素对条形锚板抗拔承载力和破坏面形状的影响.分析结果表明:重力叠加法并不适用于斜坡地形情况;随着斜坡倾角的增大,锚板的破坏面向坡角方向倾斜;锚板埋深比越大,斜坡倾角的影响也越显著.块体集上限分析方法构造简单,求解快捷,能够为工程设计提供依据.%Based on the bound theorems of limit analysis, admissible velocity field of horizontal strip anchor is constructed by using a combination of several rotational block sets. An application to upper bound analysis of vertically loaded strip anchors on horizontal ground surface is given first to illustrate the utility and effectiveness of the proposed method, and include detailed comparisons with results obtained from other approaches. Then the pull-out capacities of strip anchors in undrained clay with sloping ground surface are analyzed. Pull-out capacity and failure surface characteristics under different embedment ratios, undrained strength, inclined angles of slopes and weight of soil are studied. The results show that the superposition of gravity is not applicable to the case of sloping ground surface. The variation of slope angle has a significant impact on failure surface. The block set mechanism is based on a very simple concept which is integration and combination and can be a reference for the practical design.

  13. Oriented circular dichroism analysis of chiral surface-anchored metal-organic frameworks grown by liquid-phase epitaxy and upon loading with chiral guest compounds

    KAUST Repository

    Gu, Zhigang

    2014-06-17

    Oriented circular dichroism (OCD) is explored and successfully applied to investigate chiral surface-anchored metal-organic frameworks (SURMOFs) based on camphoric acid (D- and Lcam) with the composition [Cu2(Dcam) 2x(Lcam)2-2x(dabco)]n (dabco=1,4-diazabicyclo- [2.2.2]-octane). The three-dimensional chiral SURMOFs with high-quality orientation were grown on quartz glass plates by using a layer-by-layer liquid-phase epitaxy method. The growth orientation, as determined by X-ray diffraction (XRD), could be switched between the [001] and [110] direction by using either OH- or COOH-terminated substrates. These SURMOFs were characterized by using OCD, which confirmed the ratio as well as the orientation of the enantiomeric linker molecules. Theoretical computations demonstrate that the OCD band intensities of the enantiopure [Cu2(Dcam)2(dabco)] n grown in different orientations are a direct result of the anisotropic nature of the chiral SURMOFs. Finally, the enantiopure [Cu 2(Dcam)2(dabco)]n and [Cu2(Lcam) 2(dabco)]n SURMOFs were loaded with the two chiral forms of ethyl lactate [(+)-ethyl-D-lactate and (-)-ethyl-L-lactate)]. An enantioselective enrichment of >60 % was observed by OCD when the chiral host scaffold was loaded from the racemic mixture. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Comparative Analysis of Marker-Assisted and Phenotypic Selection for Yield Components in Cucumber

    Science.gov (United States)

    Theorectical studies suggest that marker-assisted selection (MAS) has case-specific advantages over phenotypic selection (PHE) for selection of quantitative traits. However, few studies have been conducted that empirically compare these selection methods in the context of a plant breeding program. ...

  15. Clinical and genetic analysis of 29 Brazilian patients with Huntington's disease-like phenotype

    Directory of Open Access Journals (Sweden)

    Guilherme Riccioppo Rodrigues

    2011-06-01

    Full Text Available Huntington's disease (HD is a neurodegenerative disorder characterized by chorea, behavioral disturbances and dementia, caused by a pathological expansion of the CAG trinucleotide in the HTT gene. Several patients have been recognized with the typical HD phenotype without the expected mutation. The objective of this study was to assess the occurrence of diseases such as Huntington's disease-like 2 (HDL2, spinocerebellar ataxia (SCA 1, SCA2, SCA3, SCA7, dentatorubral-pallidoluysian atrophy (DRPLA and chorea-acanthocytosis (ChAc among 29 Brazilian patients with a HD-like phenotype. In the group analyzed, we found 3 patients with HDL2 and 2 patients with ChAc. The diagnosis was not reached in 79.3% of the patients. HDL2 was the main cause of the HD-like phenotype in the group analyzed, and is attributable to the African ancestry of this population. However, the etiology of the disease remains undetermined in the majority of the HD negative patients with HD-like phenotype.

  16. Stochastic modeling and experimental analysis of phenotypic switching and survival of cancer cells under stress

    Science.gov (United States)

    Zamani Dahaj, Seyed Alireza; Kumar, Niraj; Sundaram, Bala; Celli, Jonathan; Kulkarni, Rahul

    The phenotypic heterogeneity of cancer cells is critical to their survival under stress. A significant contribution to heterogeneity of cancer calls derives from the epithelial-mesenchymal transition (EMT), a conserved cellular program that is crucial for embryonic development. Several studies have investigated the role of EMT in growth of early stage tumors into invasive malignancies. Also, EMT has been closely associated with the acquisition of chemoresistance properties in cancer cells. Motivated by these studies, we analyze multi-phenotype stochastic models of the evolution of cancers cell populations under stress. We derive analytical results for time-dependent probability distributions that provide insights into the competing rates underlying phenotypic switching (e.g. during EMT) and the corresponding survival of cancer cells. Experimentally, we evaluate these model-based predictions by imaging human pancreatic cancer cell lines grown with and without cytotoxic agents and measure growth kinetics, survival, morphological changes and (terminal evaluation of) biomarkers with associated epithelial and mesenchymal phenotypes. The results derived suggest approaches for distinguishing between adaptation and selection scenarios for survival in the presence of external stresses.

  17. Optimizing the phenotyping of rodent ASD models: enrichment analysis of mouse and human neurobiological phenotypes associated with high-risk autism genes identifies morphological, electrophysiological, neurological, and behavioral features

    Directory of Open Access Journals (Sweden)

    Buxbaum Joseph D

    2012-02-01

    in ASD genes result in defined groups of changes in mouse models and support a broad neurobiological approach to phenotyping rodent models for ASD, with a focus on biochemistry and molecular biology, brain and neuronal morphology, and electrophysiology, as well as both neurological and additional behavioral analyses. Analysis of human phenotypes associated with these genes reinforced these conclusions, supporting face validity for these approaches to phenotyping of ASD models. Such phenotyping is consistent with the successes in Fmr1 knockout mice, in which morphological changes recapitulated human findings and electrophysiological deficits resulted in molecular insights that have since led to clinical trials. We propose both broad domains and, based on expert review of more than 50 publications in each of the four neurobiological domains, specific tests to be applied to rodent models of ASD.

  18. Shifting Nominal Anchors: The Experience of Mexico

    OpenAIRE

    Leonardo Leiderman; Nissan Liviatan; Alfredo Thorne

    1995-01-01

    In the mid-1980’s Mexico successfully brought down its high rate of inflation by using the exchange rate as nominal anchor in combination with strict fiscal discipline, tight monetary policy, and incomes policy. This paper discusses the role of exchange rate policy as nominal anchor in Mexico and develops the inflation target as the monetary framework for anchoring prices. It also describes how Mexico is applying this frame work while shifting to a more flexible exchange regime and discusses ...

  19. Capital Asset Pricing Model Adjusted for Anchoring

    OpenAIRE

    Hammad, Siddiqi

    2015-01-01

    I show that adjusting CAPM for anchoring provides a unified explanation for the size, value, and momentum effects. Anchoring adjusted CAPM (ACAPM) predicts that stock splits are associated with positive abnormal returns and an increase in return volatility, whereas the reverse stock-splits are associated with negative abnormal returns and a fall in return volatility. Existing empirical evidence strongly supports these predictions. Anchoring has the effect of pushing up the equity premium, a ...

  20. Phenotypic malignant changes and untargeted lipidomic analysis of long-term exposed prostate cancer cells to endocrine disruptors

    Energy Technology Data Exchange (ETDEWEB)

    Bedia, Carmen, E-mail: carmen.bedia@idaea.csic.es; Dalmau, Núria, E-mail: nuria.dalmau@idaea.csic.es; Jaumot, Joaquim, E-mail: joaquim.jaumot@idaea.csic.es; Tauler, Romà, E-mail: roma.tauler@idaea.csic.es

    2015-07-15

    Endocrine disruptors (EDs) are a class of environmental toxic molecules able to interfere with the normal hormone metabolism. Numerous studies involve EDs exposure to initiation and development of cancers, including prostate cancer. In this work, three different EDs (aldrin, aroclor 1254 and chlorpyrifos (CPF)) were investigated as potential inducers of a malignant phenotype in DU145 prostate cancer cells after a chronic exposure. Epithelial to mesenchymal transition (EMT) induction, proliferation, migration, colony formation and release of metalloproteinase 2 (MMP-2) were analyzed in 50-day exposed cells to the selected EDs. As a result, aldrin and CPF exposure led to an EMT induction (loss of 16% and 14% of E-cadherin levels, respectively, compared to the unexposed cells). Aroclor and CPF presented an increased migration (134% and 126%, respectively), colony formation (204% and 144%, respectively) and MMP-2 release (137% in both cases) compared to the unexposed cells. An untargeted lipidomic analysis was performed to decipher the lipids involved in the observed transformations. As general results, aldrin exposure showed a global decrease in phospholipids and sphingolipids, and aroclor and CPF showed an increase of certain phospholipids, glycosphingolipids as well as a remarkable increase of some cardiolipin species. Furthermore, the three exposures resulted in an increase of some triglyceride species. In conclusion, some significant changes in lipids were identified and thus we postulate that some lipid compounds and lipid metabolic pathways could be involved in the acquisition of the malignant phenotype in exposed prostate cancer cells to the selected EDs. - Highlights: • Aldrin, aroclor and chlorpyrifos induced an aggressive phenotype in DU145 cells. • An untargeted lipidomic analysis has been performed on chronic exposed cells. • Lipidomic results showed changes in specific lipid species under chronic exposure. • These lipids may have a role in the

  1. Phenotypic malignant changes and untargeted lipidomic analysis of long-term exposed prostate cancer cells to endocrine disruptors

    International Nuclear Information System (INIS)

    Endocrine disruptors (EDs) are a class of environmental toxic molecules able to interfere with the normal hormone metabolism. Numerous studies involve EDs exposure to initiation and development of cancers, including prostate cancer. In this work, three different EDs (aldrin, aroclor 1254 and chlorpyrifos (CPF)) were investigated as potential inducers of a malignant phenotype in DU145 prostate cancer cells after a chronic exposure. Epithelial to mesenchymal transition (EMT) induction, proliferation, migration, colony formation and release of metalloproteinase 2 (MMP-2) were analyzed in 50-day exposed cells to the selected EDs. As a result, aldrin and CPF exposure led to an EMT induction (loss of 16% and 14% of E-cadherin levels, respectively, compared to the unexposed cells). Aroclor and CPF presented an increased migration (134% and 126%, respectively), colony formation (204% and 144%, respectively) and MMP-2 release (137% in both cases) compared to the unexposed cells. An untargeted lipidomic analysis was performed to decipher the lipids involved in the observed transformations. As general results, aldrin exposure showed a global decrease in phospholipids and sphingolipids, and aroclor and CPF showed an increase of certain phospholipids, glycosphingolipids as well as a remarkable increase of some cardiolipin species. Furthermore, the three exposures resulted in an increase of some triglyceride species. In conclusion, some significant changes in lipids were identified and thus we postulate that some lipid compounds and lipid metabolic pathways could be involved in the acquisition of the malignant phenotype in exposed prostate cancer cells to the selected EDs. - Highlights: • Aldrin, aroclor and chlorpyrifos induced an aggressive phenotype in DU145 cells. • An untargeted lipidomic analysis has been performed on chronic exposed cells. • Lipidomic results showed changes in specific lipid species under chronic exposure. • These lipids may have a role in the

  2. Identification of Vaccine-Altered Circulating B Cell Phenotypes Using Mass Cytometry and a Two-Step Clustering Analysis.

    Science.gov (United States)

    Pejoski, David; Tchitchek, Nicolas; Rodriguez Pozo, André; Elhmouzi-Younes, Jamila; Yousfi-Bogniaho, Rahima; Rogez-Kreuz, Christine; Clayette, Pascal; Dereuddre-Bosquet, Nathalie; Lévy, Yves; Cosma, Antonio; Le Grand, Roger; Beignon, Anne-Sophie

    2016-06-01

    Broadening our understanding of the abundance and phenotype of B cell subsets that are induced or perturbed by exogenous Ags will improve the vaccine evaluation process. Mass cytometry (CyTOF) is being used to increase the number of markers that can be investigated in single cells, and therefore characterize cell phenotype at an unprecedented level. We designed a panel of CyTOF Abs to compare the B cell response in cynomolgus macaques at baseline, and 8 and 28 d after the second homologous immunization with modified vaccinia virus Ankara. The spanning-tree progression analysis of density-normalized events (SPADE) algorithm was used to identify clusters of CD20(+) B cells. Our data revealed the phenotypic complexity and diversity of circulating B cells at steady-state and significant vaccine-induced changes in the proportions of some B cell clusters. All SPADE clusters, including those altered quantitatively by vaccination, were characterized phenotypically and compared using double hierarchical clustering. Vaccine-altered clusters composed of previously described subsets including CD27(hi)CD21(lo) activated memory and CD27(+)CD21(+) resting memory B cells, and subphenotypes with novel patterns of marker coexpression. The expansion, followed by the contraction, of a single memory B cell SPADE cluster was positively correlated with serum anti-vaccine Ab titers. Similar results were generated by a different algorithm, automatic classification of cellular expression by nonlinear stochastic embedding. In conclusion, we present an in-depth characterization of B cell subphenotypes and proportions, before and after vaccination, using a two-step clustering analysis of CyTOF data, which is suitable for longitudinal studies and B cell subsets and biomarkers discovery. PMID:27183591

  3. Anchoring contextual analysis in health policy and systems research: A narrative review of contextual factors influencing health committees in low and middle income countries.

    Science.gov (United States)

    George, Asha; Scott, Kerry; Garimella, Surekha; Mondal, Shinjini; Ved, Rajani; Sheikh, Kabir

    2015-05-01

    Health committees, councils or boards (HCs) mediate between communities and health services in many health systems. Despite their widespread prevalence, HC functions vary due to their diversity and complexity, not least because of their context specific nature. We undertook a narrative review to better understand the contextual features relevant to HCs, drawing from Scopus and the internet. We found 390 English language articles from journals and grey literature since 1996 on health committees, councils and boards. After screening with inclusion and exclusion criteria, we focused on 44 articles. Through an iterative process of exploring previous attempts at understanding context in health policy and systems research (HPSR) and the HC literature, we developed a conceptual framework that delineates these contextual factors into four overlapping spheres (community, health facilities, health administration, society) with cross-cutting issues (awareness, trust, benefits, resources, legal mandates, capacity-building, the role of political parties, non-governmental organizations, markets, media, social movements and inequalities). While many attempts at describing context in HPSR result in empty arenas, generic lists or amorphous detail, we suggest anchoring an understanding of context to a conceptual framework specific to the phenomena of interest. By doing so, our review distinguishes between contextual elements that are relatively well understood and those that are not. In addition, our review found that contextual elements are dynamic and porous in nature, influencing HCs but also being influenced by them due to the permeability of HCs. While reforms focus on tangible HC inputs and outputs (training, guidelines, number of meetings held), our review of contextual factors highlights the dynamic relationships and broader structural elements that facilitate and/or hinder the role of health committees in health systems. Such an understanding of context points to its

  4. Human breath analysis may support the existence of individual metabolic phenotypes.

    Directory of Open Access Journals (Sweden)

    Pablo Martinez-Lozano Sinues

    Full Text Available The metabolic phenotype varies widely due to external factors such as diet and gut microbiome composition, among others. Despite these temporal fluctuations, urine metabolite profiling studies have suggested that there are highly individual phenotypes that persist over extended periods of time. This hypothesis was tested by analyzing the exhaled breath of a group of subjects during nine days by mass spectrometry. Consistent with previous metabolomic studies based on urine, we conclude that individual signatures of breath composition exist. The confirmation of the existence of stable and specific breathprints may contribute to strengthen the inclusion of breath as a biofluid of choice in metabolomic studies. In addition, the fact that the method is rapid and totally non-invasive, yet individualized profiles can be tracked, makes it an appealing approach.

  5. Modelling phenotypic flexibility: an optimality analysis of gizzard size in Red Knots Calidris canutus

    OpenAIRE

    van Gils, Jan A; Piersma, Theunis; Dekinga, Anne; Battley, Phil F.

    2006-01-01

    Reversible phenotypic changes, such as those observed in nutritional organs of long-distance migrants, increasingly receive the attention of ornithologists. In this paper we review the cost-benefit studies that have been performed on the flexible gizzard of Red Knots Calidris cunutus. By varying the hardness of the diet on offer gizzard mass could experimentally be manipulated, which allowed quantification of the energetic costs and benefits as a function of gizzard size. These functions were...

  6. SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction

    OpenAIRE

    Abraham Gad; Kowalczyk Adam; Zobel Justin; Inouye Michael

    2012-01-01

    Abstract Background A central goal of genomics is to predict phenotypic variation from genetic variation. Fitting predictive models to genome-wide and whole genome single nucleotide polymorphism (SNP) profiles allows us to estimate the predictive power of the SNPs and potentially develop diagnostic models for disease. However, many current datasets cannot be analysed with standard tools due to their large size. Results We introduce SparSNP, a tool for fitting lasso linear models for massive S...

  7. Clinical and genetic analysis of 29 Brazilian patients with Huntington’s disease-like phenotype

    OpenAIRE

    Guilherme Riccioppo Rodrigues; Walker, Ruth H.; Benedikt Bader; Adrian Danek; Alexis Brice; Cécile Cazeneuve; Odile Russaouen; Iscia Lopes-Cendes; Wilson Marques Jr; Vitor Tumas

    2011-01-01

    Huntington’s disease (HD) is a neurodegenerative disorder characterized by chorea, behavioral disturbances and dementia, caused by a pathological expansion of the CAG trinucleotide in the HTT gene. Several patients have been recognized with the typical HD phenotype without the expected mutation. The objective of this study was to assess the occurrence of diseases such as Huntington’s disease-like 2 (HDL2), spinocerebellar ataxia (SCA) 1, SCA2, SCA3, SCA7, dentatorubral-pallidol...

  8. In vitro analysis of the invasive phenotype of SUM 149, an inflammatory breast cancer cell line

    Directory of Open Access Journals (Sweden)

    Dharmawardhane Suranganie F

    2005-04-01

    Full Text Available Abstract Background Inflammatory breast cancer (IBC is the most lethal form of locally invasive breast cancer known. However, very little information is available on the cellular mechanisms responsible for manifestation of the IBC phenotype. To understand the unique phenotype of IBC, we compared the motile and adhesive interactions of an IBC cell line, SUM 149, to the non-IBC cell line SUM 102. Results Our results demonstrate that both IBC and non-IBC cell lines exhibit similar adhesive properties to basal lamina, but SUM 149 showed a marked increase in adhesion to collagen I. In vitro haptotaxis assays demonstrate that SUM 149 was less invasive, while wound healing assays show a less in vitro migratory phenotype for SUM 149 cells relative to SUM 102 cells. We also demonstrate a role for Rho and E-cadherin in the unique invasive phenotype of IBC. Immunoblotting reveals higher E-cadherin and RhoA expression in the IBC cell line but similar RhoC expression. Rhodamine phalloidin staining demonstrates increased formation of actin stress fibers and larger focal adhesions in SUM 149 relative to the SUM 102 cell line. Conclusion The observed unique actin and cellular architecture as well as the invasive and adhesive responses to the extracellular matrix of SUM 149 IBC cells suggest that the preference of IBC cells for connective tissue, possibly a mediator important for the vasculogenic mimicry via tubulogenesis seen in IBC pathological specimens. Overexpression of E-cadherin and RhoA may contribute to passive dissemination of IBC by promoting cell-cell adhesion and actin cytoskeletal structures that maintain tissue integrity. Therefore, we believe that these findings indicate a passive metastatic mechanism by which IBC cells invade the circulatory system as tumor emboli rather than by active migratory mechanisms.

  9. Improving persistence in red clover: Insights from QTL analysis and comparative phenotypic evaluation

    DEFF Research Database (Denmark)

    Herrmann, Dorris; Boller, Beat; Studer, Bruno; Widmer, Franco; Kölliker, Roland

    2008-01-01

    Cultivars of red clover (Trifolium pratense L.) often suffer from low persistence, leading to insufficient legume proportions in pluriannual forage stands. Persistence is a complex trait often negatively correlated with other important traits and its phenotyping is laborious. Consequently....... Moreover, length of stem may present a candidate character for indirect selection of these two traits. The QTLs and the indirect selection criteria identified in this study may substantially assist future breeding efforts for the improvement of persistence in red clover...

  10. Factor analysis demonstrates a common schizoidal phenotype within autistic and schizotypal tendency: Implications for neuroscientific studies

    OpenAIRE

    Talitha Caitlyn Ford; David Philip Crewther

    2014-01-01

    Behavioral and cognitive dysfunction, particularly social and communication impairments, are shared between autism and schizophrenia spectrum disorders, while evidence for a diametric autism-positive schizophrenia symptom profile is inconsistent. We investigated the shared phenotype at a personality trait level, particularly its resemblance to schizoid personality disorder, as well as differential aspects of the autism–schizophrenia model. Items of the autism spectrum quotient (AQ) and schizo...

  11. The phenotype of 45,X/46,XY mosaicism: an analysis of 92 prenatally diagnosed cases.

    OpenAIRE

    Chang, H. J.; Clark, R D; Bachman, H

    1990-01-01

    We undertook an international survey of prenatally diagnosed 45,X/46,XY mosaicism to ascertain the phenotypic spectrum of this condition. Ninety-two cases were obtained by means of a questionnaire sent to over 730 cytogenetic laboratories. Seventy-six cases (75 males and 1 female) had physical examinations after delivery or termination of pregnancy. Among these, there were four significant genital anomalies: three hypospadias and one female with clitoromegaly. Gonadal histology was abnormal i...

  12. Identifiable Phenotyping using Constrained Non-Negative Matrix Factorization

    OpenAIRE

    Joshi, Shalmali; Gunasekar, Suriya; Sontag, David; Ghosh, Joydeep

    2016-01-01

    This work proposes a new algorithm for automated and simultaneous phenotyping of multiple co-occurring medical conditions, also referred as comorbidities, using clinical notes from the electronic health records (EHRs). A basic latent factor estimation technique of non-negative matrix factorization (NMF) is augmented with domain specific constraints to obtain sparse latent factors that are anchored to a fixed set of chronic conditions. The proposed anchoring mechanism ensures a one-to-one iden...

  13. Morphological phenotypic dispersion of garlic cultivars by cluster analysis and multidimensional scaling

    Directory of Open Access Journals (Sweden)

    Anderson Rodrigo da Silva

    2014-02-01

    Full Text Available Multivariate techniques have become a useful tool for studying the phenotypic diversity of Germplasm Bank accessions, since they make it possible to combine a variety of different information from these accessions. This study aimed to characterize the phenotypic dispersion of garlic (Allium sativum L. using two multivariate techniques with different objective functions. Twenty accessions were morphologically characterized for bulb diameter, length, and weight; number of cloves per bulb; number of leaves per plant; and leaf area. Techniques based on generalized quadratic distance of Mahalanobis, UPGMA (Unweighted Pair Group Method with Arithmetic Mean clustering, and nMDS (nonmetrric MultiDimensional Scaling were applied and the relative importance of variables quantified. The two multivariate techniques were capable of identifying cultivars with different characteristics, mainly regarding their classification in subgroups of common garlic or noble garlic, according to the number of cloves per bulb. The representation of the phenotypic distance of cultivars by multidimensional scaling was slightly more effective than that with UPGMA clustering.

  14. PFGE and antibiotic susceptibility phenotype analysis of Pseudomonas aeruginosa strain chronically infecting Cystic Fibrosis patients

    Directory of Open Access Journals (Sweden)

    Giovanna Pulcrano

    2008-09-01

    Full Text Available Pseudomonas aeruginosa is the leading cause of chronic lung infection and following pulmonary worsening of cystic fibrosis patients. To verify whether bacterial modifications regarding motility, mucoidy, and serum susceptibility proceeded from an adaptation to chronic infection or a replacement with a new strain, sequential P. aeruginosa isolates of known phenotype collected from 5 cystic fibrosis patients were typed by pulsed-field gel electophoresis (PFGE. Antimicrobial susceptibility testing of all isolates was performed by the disc diffusion method. PFGE typing demonstrated that strains dissimilar in colony morphotype and of different antibiotic susceptibility patterns could be of the same genotype. Some patients were colonized with a rather constant P. aeruginosa flora, with strains of different phenotypes but of one genotype. Instead, some patients may be colonized by more than one genotype. Secretion of mucoid exopolysaccharide and acquisition of a new antibiotic susceptibility phenotype in these strain appear to evolve during chronic colonization in cystic fibrosis patients from specific adaptation to infection rather than from acquisition of new bacterial strains.

  15. A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Olin K Silander

    2012-01-01

    Full Text Available Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as "phenotypic noise." In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alone.

  16. Localization in Wireless Sensor Networks and Anchor Placement

    Directory of Open Access Journals (Sweden)

    Benjamin Tatham

    2012-06-01

    Full Text Available Applications of wireless sensor network (WSN often expect knowledge of the precise location of the nodes. Many different localization protocols have been proposed that allow nodes to derive their location rather than equipping them with dedicated localization hardware such as GPS receivers, which increases node costs. We provide a brief survey of the major approaches to software-based node localization in WSN. One class of localization protocols with good localization performance patches together relative-coordinate, local maps into a global-coordinate map. These protocols require some nodes that know their absolute coordinates, called anchor nodes. While many factors influence the node position errors, in this class of protocols, using Procrustes Analysis, the placement of the anchor nodes can significantly impact the error. Through simulation, using the Curvilinear Component Analysis (CCA-MAP protocol as a representative protocol in this category, we show the impact of anchor node placement and propose a set of guidelines to ensure the best possible outcome, while using the smallest number of anchor nodes possible.

  17. Method of fabrication of anchored nanostructure materials

    Science.gov (United States)

    Seals, Roland D; Menchhofer, Paul A; Howe, Jane Y; Wang, Wei

    2013-11-26

    Methods for fabricating anchored nanostructure materials are described. The methods include heating a nano-catalyst under a protective atmosphere to a temperature ranging from about 450.degree. C. to about 1500.degree. C. and contacting the heated nano-catalysts with an organic vapor to affix carbon nanostructures to the nano-catalysts and form the anchored nanostructure material.

  18. Suction anchors for floating production systems

    Energy Technology Data Exchange (ETDEWEB)

    Tjelta, T.I.; Rusas, P. [Statoil a.s. (Norway); Edvardsen, G. [HEX a.s. (Norway)

    1996-12-31

    Since the suction anchor is a recent development in its current use, this work provides a brief historical background. It is shown that the suction anchor throughout evolution today is a competitive foundation solution for many applications. Examples from these categories are included in this paper. Also several installation methods are discussed. 3 refs., 7 figs., 2 tabs.

  19. Carnitine palmitoyltransferase II (CPT II) deficiency: genotype-phenotype analysis of 50 patients.

    Science.gov (United States)

    Joshi, Pushpa Raj; Deschauer, Marcus; Zierz, Stephan

    2014-03-15

    Clinical, biochemical and molecular genetic data in a cohort of 50 patients with muscle CPT II deficiency are reported. Attacks of myoglobinuria occurred in 86% of patients. In 94% of patients the triggering factor was exercise. Although the myopathic form is often called the adult from, in 60% of patients, the age of onset was in childhood (1-12 years). All the patients in whom biochemical activity was measured had normal enzyme activity of total CPT I+II but the activity was significantly inhibited by malonyl-CoA and Triton. The p.S113L mutation was detected in 38/40 index patients (95%) in at least one allele. Sixty percent of index patients were homozygous for this mutation. Thirteen other mutations, all in compound heterozygote form, were also identified. There was no significant difference in ages of onset, clinical and biochemical phenotype of patients with p.S113L mutation in homozygous or compound heterozygous form. The exception was a tendency of slightly higher residual enzyme activity upon malonyl-CoA inhibition in compound heterozygotes. Phenotype was also not significantly different in patients with missense mutations on both alleles and patients with truncating mutation on one allele and missense mutation on the other allele. However, the only exception was that, attacks were triggered by fasting in almost all the patients with truncating mutations. In contrast, fasting triggered the attacks only in one third of patients with missense mutations on both alleles. The data indicate that within the muscle form of CPT II deficiency, the various genotypes have only marginal influence on the clinical and biochemical phenotype. PMID:24398345

  20. Canine hip dysplasia: phenotypic scoring and the role of estimated breeding value analysis.

    Science.gov (United States)

    Soo, M; Worth, Aj

    2015-03-01

    Canine hip dysplasia (CHD) is a developmental orthopaedic disease of the coxofemoral joints with a multifactorial mode of inheritance. Multiple gene effects are influenced by environmental factors; therefore, it is unlikely that a simple genetic screening test with which to identify susceptible individuals will be developed in the near future. In the absence of feasible methods for objectively quantifying clinical CHD, radiographic techniques have been developed and widely used to identify dogs for breeding which are less affected by the disease. A hip-extended ventrodorsal view of the pelvis has been traditionally used to identify dogs with subluxation and/or osteoarthritis of the coxofemoral joints. More recently, there has been emphasis on the role of coxofemoral joint laxity as a determinant of CHD and methods have been developed to measure passive hip laxity. Though well-established worldwide, the effectiveness of traditional phenotypic scoring schemes in reducing the prevalence of CHD has been variable. The most successful implementation of traditional CHD scoring has occurred in countries or breeding colonies with mandatory scoring and open registries with access to pedigree records. Several commentators have recommended that for quantitative traits like CHD, selection of breeding stock should be based on estimated breeding values (EBV) rather than individual hip score/grade. The EBV is a reflection of the genetic superiority of an animal compared to its counterparts and is calculated from the phenotype of an individual and its relatives and their pedigree relationship. Selecting breeding stock on the basis of a dog's genetic merit, ideally based on a highly predictive phenotype, will confer the breeder with greater selection power, accelerate genetic improvement towards better hip conformation and thus more likely decrease the prevalence of CHD. PMID:25072401

  1. Are clear cell carcinomas of the ovary and endometrium phenotypically identical? A proteomic analysis.

    Science.gov (United States)

    Fata, Cynthia R; Seeley, Erin H; Desouki, Mohamed M; Du, Liping; Gwin, Katja; Hanley, Krisztina Z; Hecht, Jonathan L; Jarboe, Elke A; Liang, Sharon X; Parkash, Vinita; Quick, Charles M; Zheng, Wenxin; Shyr, Yu; Caprioli, Richard M; Fadare, Oluwole

    2015-10-01

    Phenotypic differences between otherwise similar tumors arising from different gynecologic locations may be highly significant in understanding the underlying driver molecular events at each site and may potentially offer insights into differential responses to treatment. In this study, the authors sought to identify and quantify phenotypic differences between ovarian clear cell carcinoma (OCCC) and endometrial clear cell carcinoma (ECCC) using a proteomic approach. Tissue microarrays were constructed from tumor samples of 108 patients (54 ECCCs and 54 OCCCs). Formalin-fixed samples on microarray slides were analyzed by matrix-assisted laser desorption/ionization mass spectrometry, and 730 spectral peaks were generated from the combined data set. A linear mixed-effect model with random intercept was used to generate 93 (12.7%) peaks that were significantly different between OCCCs and ECCCs at the fold cutoffs of 1.5 and 0.667 and an adjusted P value cutoff of 1.0 × 10(-10). Liquid chromatography-tandem mass spectrometry was performed on selected cores from each group, and peptides identified therefrom were compared with lists of statistically significant peaks from the aforementioned linear mixed-effects model to find matches within 0.2 Da. A total of 53 candidate proteins were thus identified as being differentially expressed in OCCCs and ECCCs, 45 (85%) of which were expressed at higher levels in ECCCs than OCCCs. These proteins were functionally diverse and did not highlight a clearly dominant cellular theme or molecular pathway. Although ECCCs and OCCCs are very similar, some phenotypic differences are demonstrable. Additional studies of these differentially expressed proteins may ultimately clarify the significance of these differences. PMID:26243671

  2. Systematic Phenotype Analysis of Arabidopsis Ds-tagged Mutants to Unravel Gene Functions in Abiotic Stress Response as well as Growth and Development

    International Nuclear Information System (INIS)

    By the availability of various mutant resources in Arabidopsis, it is now possible to investigate mutant lines for almost every gene. Arabidopsis is then, not only a model plant for plant research, but also a model species in which it is possible to carry out 'saturation mutagenesis' for all genes, and to totally analyze each gene and mutant of one organism. One of the future goals of the 'phenome' project is to collect information about the knockout-type mutant phenotypes for each Arabidopsis gene. We have generated thousands of Dissociation (Ds) transposon-tagged lines, which have a single insertion because of an advantage of the Activator/Dissociation (Ac/Ds) system, and deposited it to the RIKEN BioResource Center. In this resource, we selected 4,000 transposon-tagged lines with a transposon insertion in gene-coding regions, and systematically observed the visible phenotype of each line as a first step of phenome analysis. In total, about 200 clear visible phenotypes were classified into 43 categories of morphological phenotypes. Phenotypic images have been entered into a searchable database. Parallel to this, we have been selecting homozygous transposon-insertional plants, which would be useful resources to detect other phenotypes besides the visible ones. We are setting three categories of measurement to search various traits for total phenome analysis, such as physical, chemical or biological methods. Recently, we started to investigate biologically-measured phenotypes, which are stress-responsive or conditional phenotypes, using homozygous mutant resources. We are also collecting any mutant phenotype information from published reports in journal research activity to make a comprehensive phenotype database of Arabidopsis genes and mutants. (author)

  3. Auditory hedonic phenotypes in dementia: A behavioural and neuroanatomical analysis

    Science.gov (United States)

    Fletcher, Phillip D.; Downey, Laura E.; Golden, Hannah L.; Clark, Camilla N.; Slattery, Catherine F.; Paterson, Ross W.; Schott, Jonathan M.; Rohrer, Jonathan D.; Rossor, Martin N.; Warren, Jason D.

    2015-01-01

    Patients with dementia may exhibit abnormally altered liking for environmental sounds and music but such altered auditory hedonic responses have not been studied systematically. Here we addressed this issue in a cohort of 73 patients representing major canonical dementia syndromes (behavioural variant frontotemporal dementia (bvFTD), semantic dementia (SD), progressive nonfluent aphasia (PNFA) amnestic Alzheimer's disease (AD)) using a semi-structured caregiver behavioural questionnaire and voxel-based morphometry (VBM) of patients' brain MR images. Behavioural responses signalling abnormal aversion to environmental sounds, aversion to music or heightened pleasure in music (‘musicophilia’) occurred in around half of the cohort but showed clear syndromic and genetic segregation, occurring in most patients with bvFTD but infrequently in PNFA and more commonly in association with MAPT than C9orf72 mutations. Aversion to sounds was the exclusive auditory phenotype in AD whereas more complex phenotypes including musicophilia were common in bvFTD and SD. Auditory hedonic alterations correlated with grey matter loss in a common, distributed, right-lateralised network including antero-mesial temporal lobe, insula, anterior cingulate and nucleus accumbens. Our findings suggest that abnormalities of auditory hedonic processing are a significant issue in common dementias. Sounds may constitute a novel probe of brain mechanisms for emotional salience coding that are targeted by neurodegenerative disease. PMID:25929717

  4. Evaluation of different lignocellulosic biomass pretreatments by phenotypic microarray-based metabolic analysis of fermenting yeast

    Directory of Open Access Journals (Sweden)

    Stuart Wilkinson

    2016-03-01

    Full Text Available Advanced generation biofuel production from lignocellulosic material (LCM was investigated.  A range of different thermo-chemical pre-treatments were evaluated with different LCM. The pre-treatments included; alkaline (5% NaOH at 50°C, acid (1% H2SO4 at 121°C and autohydrolytical methods (200°C aqueous based hydrothermal and were evaluated using samples of miscanthus, wheat-straw and willow. The liberation of sugars, presence of inhibitory compounds, and the degree of enhancement of enzymatic saccharification was accessed. The suitability of the pre-treatment generated hydrolysates (as bioethanol feedstocks for Saccharomyces cerevisiae was also accessed using a phenotypic microarray that measured yeast metabolic output. The use of the alkaline pre-treatment liberated more glucose and arabinose into both the pre-treatment generated hydrolysate and also the hydrolysate produced after enzymatic hydrolysis (when compared with other pre-treatments. However, hydrolysates derived from use of alkaline pre-treatments were shown to be unsuitable as a fermentation medium due to issues with colloidal stability (high viscosity.  Use of acid or autohydrolytical pre-treatments liberated high concentrations of monosaccharides regardless of the LCM used and the hydrolysates had good fermentation performance with measurable yeast metabolic output. Acid pre-treated wheat straw hydrolysates were then used as a model system for larger scale fermentations to confirm both the results of the phenotypic microarray and its validity as an effective high-throughput screening tool.

  5. Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress

    KAUST Repository

    Pires, Inês S.

    2015-07-22

    Increase in soil salinity levels is becoming a major cause of crop yield losses worldwide. Rice (Oryza sativa) is the most salt-sensitive cereal crop, and many studies have focused on rice salinity tolerance, but a global understanding of this crop\\'s response to salinity is still lacking. We systematically analyzed phenotypic data previously collected for 56 rice genotypes to assess the extent to which rice uses three known salinity tolerance mechanisms: shoot-ion independent tolerance (or osmotic tolerance), ion exclusion, and tissue tolerance. In general, our analyses of different phenotypic traits agree with results of previous rice salinity tolerance studies. However, we also established that the three salinity tolerance mechanisms mentioned earlier appear among rice genotypes and that none of them is predominant. Against the pervasive view in the literature that the K+/Na+ ratio is the most important trait in salinity tolerance, we found that the K+ concentration was not significantly affected by salt stress in rice, which puts in question the importance of K+/Na+ when analyzing rice salt stress response. Not only do our results contribute to improve our global understanding of salt stress response in an important crop, but we also use our results together with an extensive literature research to highlight some issues commonly observed in salinity stress tolerance studies and to propose solutions for future experiments.

  6. Integrated method for adaptability and phenotypic stability analysis = Método integrado para análise de adaptabilidade e estabilidade fenotipica

    OpenAIRE

    Edmar Soares Vasconcelos; Múcio Silva Reis; Cosme Damião Cruz; Tuneo Sediyama; Carlos Alberto Scapim

    2011-01-01

    The objectives of this study were a description of the Centroid Method, which is used to investigate the phenotypic adaptability of genotypes and the inclusion of new ideotypes therein, creating the Integrated Method for adaptability and phenotypic stability analysis, as well as a comparison of the two methods in a study example. As an applied example of the new proposal, grain yield data of 14 soybean genotypes from experiments at four locations in the state of Minas Gerais were used. In a c...

  7. Anchored nanostructure materials and method of fabrication

    Science.gov (United States)

    Seals, Roland D; Menchhofer, Paul A; Howe, Jane Y; Wang, Wei

    2012-11-27

    Anchored nanostructure materials and methods for their fabrication are described. The anchored nanostructure materials may utilize nano-catalysts that include powder-based or solid-based support materials. The support material may comprise metal, such as NiAl, ceramic, a cermet, or silicon or other metalloid. Typically, nanoparticles are disposed adjacent a surface of the support material. Nanostructures may be formed as anchored to nanoparticles that are adjacent the surface of the support material by heating the nano-catalysts and then exposing the nano-catalysts to an organic vapor. The nanostructures are typically single wall or multi-wall carbon nanotubes.

  8. 基于框架预应力锚杆加固技术的重力式挡土墙的稳定性分析%Stability analysis of gravity retaining wall reinforced with framed prestressed anchors

    Institute of Scientific and Technical Information of China (English)

    朱彦鹏; 王勇; 周勇

    2012-01-01

    Based on the instability phenomenon of gravity retaining wall, the framed anchor with prestress was used to reinforce the retaining wall. On the basis of limit equilibrium theory and Coulomb earth pressure theory, the stability of retaining walls was analyzed and the solution formula of safety coefficient of stability of anti-slip and anti-overturning was derived. It was shown by illustrative computation and cont-rastive analysis, the result showed that the safety coefficient of stability of the gravity retaining wall with this kind of reinforcement techniques was significantly improved. The safety coefficient of stability would be increased by about 50% when the prestress was increased by 50 kN. However, taking the economic and security aspects into account, 100 kN prestress applied to the anchors would be the most optimaL%基于重力式挡土墙不稳定的现象,运用框架预应力锚杆加固技术对重力式挡土墙进行加固.以极限平衡理论及库仑土压力理论为基础,对挡土墙进行稳定性分析,推导出挡土墙的抗滑移稳定性和抗倾覆稳定性安全系数的求解计算公式.通过算例计算及对比分析,结果显示引入此加固技术的重力式挡墙的稳定性安全系数明显提高,在锚杆预应力每增加50 kN时,稳定性安全系数提高的幅度达到50%左右;从经济性和安全性两方面综合考虑,对锚杆施加100kN的预应力是最佳的.

  9. 基于可靠度分析的锚杆抗拔安全系数取值标准研究%Criteria for determining factor of safety of anchor against pull-out by using reliability analysis

    Institute of Scientific and Technical Information of China (English)

    王玉杰; 徐佳成; 汪小刚; 曾庆义

    2012-01-01

    现行规范中关于锚杆抗拔安全设计标准,通常是从锚杆杆体的抗拉强度、注浆体与杆体的黏结强度以及注浆体与周围岩土体的黏结强度这3方面来定义抗拔安全系数,并建议采用统一的取值标准。实际上由于力学机理、材料性质等方面的不同,这3种定义下的安全系数取值标准应有所不同。基于这一背景,应用可靠度分析理论,探讨锚杆抗拔在同一可靠度(失效概率)条件下,这3种定义的安全系数的差别,并为相关规程的修订工作中的锚杆抗拔安全系数取值标准的确定提供科学依据。%In the existing specifications and codes, the factor of safety of anchor against pull-out is generally defined by considering tensile strength of steel bar/strand, bond strength of grout and the steel bar/strand, and bond strength of grout and surrounding rock/soil. It results in three different types of factors of safety, which are being applied in practice. The current China's specifications and codes suggest the same allowable value for the above three different types of factors of safety. Actually, there is quite difference among them due to different pull-out failure mechanisms of tendon. In view of this limitation, the difference among them is studied and discussed under the same reliability (or failure probability) by using the reliability analysis, and the criteria for determining the factor of safety of anchor against pull-out are proposed.

  10. New Insights into Genotype-phenotype Correlations in Chinese Facioscapulohumeral Muscular Dystrophy: A Retrospective Analysis of 178 Patients

    Directory of Open Access Journals (Sweden)

    Feng Lin

    2015-01-01

    Conclusions: Although the number of D4Z4 repeats is known as one of the critical influences on genotype-phenotype correlation, a majority of phenotypic spectrum was still incompatible with their heterozygous contraction of the D4Z4 repeat, especial in female cases. Our results suggest that there are multi-factors synergistically modulating the phenotypic expression.

  11. Comprehensive analysis of gene mutation and phenotype of tuberous sclerosis complex in China

    Directory of Open Access Journals (Sweden)

    Guo-qiang HUANG

    2015-04-01

    Full Text Available Objective To summarize the clinical features of tuberous sclerosis complex (TSC, the distribution and description of TSC gene, and to probe into the correlation of genotype with phenotype.  Methods According to the 1998 International Tuberous Sclerosis Complex Diagnostic Criteria, a total of 163 TSC patients with pathogenic mutation in TSC gene (3 cases were detected in our hospital, and the other 160 cases were collected from other institutions in China were enrolled, and their gene detection results and clinical data were analyzed.  Results Among 163 cases, TSC1 mutation (31 cases accounted for 19.02% [32.26% (10/31 in exon 15, 16.13% (5/31 in exon 21, 12.90% (4/31 in exon 18], and TSC2 mutation (132 cases accounted for 80.98% [9.85% (13/132 in exon 37, 7.58% (10/132 in exon 40, 6.82%(9/132 in exon 33]. The proportion of base replacement in TSC1 was 41.94% (13/31, and 52.27% (69/132 in TSC2. Male patients exhibited significantly more subependymal nodules or calcifications than thefemale patients (χ2 = 8.016, P = 0.005. Sporadic patients exhibited significantly more cortical tubers than familial patients (χ2 = 6.273, P = 0.012. Patients with TSC2 mutations had significantly higher frequencies of hypomelanotic macules than patients with TSC1 mutations (χ2 = 6.756, P = 0.009. Patients with missense mutations were more likely to have facial angiofibromas compared with patients with other mutations (χ2 = 4.438, P = 0.035.  Conclusions Exon 15, 21 and 18 of TSC1 and exon 37, 40 and 33 of TSC2 accounted for higher percentage of mutations. Correlating genotypes with phenotypes should facilitate the individualized treatment and prognostic assessment of tuberous sclerosis complex. DOI: 10.3969/j.issn.1672-6731.2015.04.013

  12. Analysis of the interaction of extracellular matrix and phenotype of bladder cancer cells

    International Nuclear Information System (INIS)

    The extracellular matrix has a major effect upon the malignant properties of bladder cancer cells both in vitro in 3-dimensional culture and in vivo. Comparing gene expression of several bladder cancer cells lines grown under permissive and suppressive conditions in 3-dimensional growth on cancer-derived and normal-derived basement membrane gels respectively and on plastic in conventional tissue culture provides a model system for investigating the interaction of malignancy and extracellular matrix. Understanding how the extracellular matrix affects the phenotype of bladder cancer cells may provide important clues to identify new markers or targets for therapy. Five bladder cancer cell lines and one immortalized, but non-tumorigenic, urothelial line were grown on Matrigel, a cancer-derived ECM, on SISgel, a normal-derived ECM, and on plastic, where the only ECM is derived from the cells themselves. The transcriptomes were analyzed on an array of 1186 well-annotated cancer derived cDNAs containing most of the major pathways for malignancy. Hypervariable genes expressing more variability across cell lines than a set expressing technical variability were analyzed further. Expression values were clustered, and to identify genes most likely to represent biological factors, statistically over-represented ontologies and transcriptional regulatory elements were identified. Approximately 400 of the 1186 total genes were expressed 2 SD above background. Approximately 100 genes were hypervariable in cells grown on each ECM, but the pattern was different in each case. A core of 20 were identified as hypervariable under all 3 growth conditions, and 33 were hypervariable on both SISgel and Matrigel, but not on plastic. Clustering of the hypervariable genes showed very different patterns for the same 6 cell types on the different ECM. Even when loss of cell cycle regulation was identified, different genes were involved, depending on the ECM. Under the most permissive conditions

  13. Analysis of image-based phenotypic parameters for high throughput gene perturbation assays.

    Science.gov (United States)

    Song, Mee; Jeong, Euna; Lee, Tae-Kyu; Tsoy, Yury; Kwon, Yong-Jun; Yoon, Sukjoon

    2015-10-01

    Although image-based phenotypic assays are considered a powerful tool for siRNA library screening, the reproducibility and biological implications of various image-based assays are not well-characterized in a systematic manner. Here, we compared the resolution of high throughput assays of image-based cell count and typical cell viability measures for cancer samples. It was found that the optimal plating density of cells was important to obtain maximal resolution in both types of assays. In general, cell counting provided better resolution than the cell viability measure in diverse batches of siRNAs. In addition to cell count, diverse image-based measures were simultaneously collected from a single screening and showed good reproducibility in repetitions. They were classified into a few functional categories according to biological process, based on the differential patterns of hit (i.e., siRNAs) prioritization from the same screening data. The presented systematic analyses of image-based parameters provide new insight to a multitude of applications and better biological interpretation of high content cell-based assays. PMID:26256799

  14. Meta-analysis of melanin-concentrating hormone signaling-deficient mice on behavioral and metabolic phenotypes.

    Directory of Open Access Journals (Sweden)

    Kenkichi Takase

    Full Text Available The demand for meta-analyses in basic biomedical research has been increasing because the phenotyping of genetically modified mice does not always produce consistent results. Melanin-concentrating hormone (MCH has been reported to be involved in a variety of behaviors that include feeding, body-weight regulation, anxiety, sleep, and reward behavior. However, the reported behavioral and metabolic characteristics of MCH signaling-deficient mice, such as MCH-deficient mice and MCH receptor 1 (MCHR1-deficient mice, are not consistent with each other. In the present study, we performed a meta-analysis of the published data related to MCH-deficient and MCHR1-deficient mice to obtain robust conclusions about the role of MCH signaling. Overall, the meta-analysis revealed that the deletion of MCH signaling enhanced wakefulness, locomotor activity, aggression, and male sexual behavior and that MCH signaling deficiency suppressed non-REM sleep, anxiety, responses to novelty, startle responses, and conditioned place preferences. In contrast to the acute orexigenic effect of MCH, MCH signaling deficiency significantly increased food intake. Overall, the meta-analysis also revealed that the deletion of MCH signaling suppressed the body weight, fat mass, and plasma leptin, while MCH signaling deficiency increased the body temperature, oxygen consumption, heart rate, and mean arterial pressure. The lean phenotype of the MCH signaling-deficient mice was also confirmed in separate meta-analyses that were specific to sex and background strain (i.e., C57BL/6 and 129Sv. MCH signaling deficiency caused a weak anxiolytic effect as assessed with the elevated plus maze and the open field test but also caused a weak anxiogenic effect as assessed with the emergence test. MCH signaling-deficient mice also exhibited increased plasma corticosterone under non-stressed conditions, which suggests enhanced activity of the hypothalamic-pituitary-adrenal axis. To the best of our

  15. Mooring Anchors for Marine Renewable Energy Foundations

    OpenAIRE

    Stevens, Robert F.; Rahim, Amir

    2014-01-01

    With the increasing use of offshore wind turbines, it has become necessary to explore deep-water sites for locating wind farms. Floating turbines are an ideal choice for these locations. Such turbines are anchored with mooring chains to the sea floor using suction anchors, driven piles or gravity foundations. This paper presents design methods for these types of foundations. Moored gravity foundations have been used for the much larger floating oil and gas installations. These concrete founda...

  16. Anchoring Adjusted Capital Asset Pricing Model

    OpenAIRE

    Hammad, Siddiqi

    2015-01-01

    An anchoring adjusted Capital Asset Pricing Model (ACAPM) is developed in which the payoff volatilities of well-established stocks are used as starting points that are adjusted to form volatility judgments about other stocks. Anchoring heuristic implies that such adjustments are typically insufficient. ACAPM converges to CAPM with correct adjustment, so CAPM is a special case of ACAPM. The model provides a unified explanation for the size, value, and momentum effects in the stock market. A ke...

  17. FRP-to-concrete joint assemblies anchored with multiple FRP anchors: experimental investigation

    OpenAIRE

    Zhang, H.; Smith, ST

    2010-01-01

    Higher strains can be developed in fibre-reinforced polymer (FRP) composites which are bonded to the surfaces of concrete members if the FRP is anchored. Anchors made from FRP (also known as FRP spike anchors but herein referred to as FRP anchors) are a promising type of anchorage as they can be applied to a variety of different shaped structural elements and they have been shown to be effective in en-hancing the strain capacity of externally bonded FRP. Limited research, however, has been co...

  18. Flapping states of an el astically anchored wing in a uniform flow

    OpenAIRE

    Orchini, A.; Mazzino, A; Guerrero, J.; Festa, R.; Boragno, C.

    2012-01-01

    Linear stability analysis of an elastically anchored wing in a uniform flow is investigated both analytically and numerically. The analytical formulation explicitly takes into account the effect of the wake on the wing by means of Theodorsen's theory. Three different parameters non-trivially rule the observed dynamics: mass density ratio between wing and fluid, spring elastic constant and distance between the wing center of mass and the spring anchor point on the wing. We found relationships ...

  19. Ocular Phenotype Analysis of a Family With Biallelic Mutations in the BEST1 Gene

    DEFF Research Database (Denmark)

    Sharon, Dror; Al-Hamdani, Sermed; Engelsberg, Karl;

    2014-01-01

    PURPOSE: To investigate the genetic cause and perform a comprehensive clinical analysis of a Danish family with autosomal recessive bestrophinopathy; to investigate whether Bestrophin may be expressed in normal human retina. DESIGN: Retrospective clinical and molecular genetic analysis and immuno...... function, autosomal recessive bestrophinopathy may be a suitable first candidate, among the BEST1-related ocular conditions, for gene replacement therapy....

  20. Anchoring FRP Composite Armor in Flexible Offshore Riser Systems

    DEFF Research Database (Denmark)

    Costache, Andrei

    Unbonded flexible pipes find extensive use in the offshore oil industry. Although more expensive than rigid pipe, the total cost of flexible pipe installations are often less. This is because flexible pipes are easier to store and deploy, coupled with superior fatigue performance. Among other...... composite materials. One of the problems related to the substitution of tensile steel members is that anchoring in the metallic end fittings of the pipe is very challenging.The purpose of this thesis is to ensure the transfer of tensile loads between a unidirectional fiber reinforced polymer and a metallic...... the grip, and to measure the contact stresses distribution and evolution during pullout.The results of the experimental and numerical analysis show that it is possible to reliably anchor composite materials using a metallic grip. The models developed during the project show how to improve the...

  1. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

    Science.gov (United States)

    Finak, Greg; Langweiler, Marc; Jaimes, Maria; Malek, Mehrnoush; Taghiyar, Jafar; Korin, Yael; Raddassi, Khadir; Devine, Lesley; Obermoser, Gerlinde; Pekalski, Marcin L.; Pontikos, Nikolas; Diaz, Alain; Heck, Susanne; Villanova, Federica; Terrazzini, Nadia; Kern, Florian; Qian, Yu; Stanton, Rick; Wang, Kui; Brandes, Aaron; Ramey, John; Aghaeepour, Nima; Mosmann, Tim; Scheuermann, Richard H.; Reed, Elaine; Palucka, Karolina; Pascual, Virginia; Blomberg, Bonnie B.; Nestle, Frank; Nussenblatt, Robert B.; Brinkman, Ryan Remy; Gottardo, Raphael; Maecker, Holden; McCoy, J Philip

    2016-01-01

    Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, and is essential for successful cross-study and cross-center comparison of data. Experts developed five standardized, eight-color panels for identification of major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents in 96-well plates. We present the results of a coordinated analysis of samples across nine laboratories using these panels with standardized operating procedures (SOPs). Manual gating was performed by each site and by a central site. Automated gating algorithms were developed and tested by the FlowCAP consortium. Centralized manual gating can reduce cross-center variability, and we sought to determine whether automated methods could streamline and standardize the analysis. Within-site variability was low in all experiments, but cross-site variability was lower when central analysis was performed in comparison with site-specific analysis. It was also lower for clearly defined cell subsets than those based on dim markers and for rare populations. Automated gating was able to match the performance of central manual analysis for all tested panels, exhibiting little to no bias and comparable variability. Standardized staining, data collection, and automated gating can increase power, reduce variability, and streamline analysis for immunophenotyping. PMID:26861911

  2. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium.

    Science.gov (United States)

    Finak, Greg; Langweiler, Marc; Jaimes, Maria; Malek, Mehrnoush; Taghiyar, Jafar; Korin, Yael; Raddassi, Khadir; Devine, Lesley; Obermoser, Gerlinde; Pekalski, Marcin L; Pontikos, Nikolas; Diaz, Alain; Heck, Susanne; Villanova, Federica; Terrazzini, Nadia; Kern, Florian; Qian, Yu; Stanton, Rick; Wang, Kui; Brandes, Aaron; Ramey, John; Aghaeepour, Nima; Mosmann, Tim; Scheuermann, Richard H; Reed, Elaine; Palucka, Karolina; Pascual, Virginia; Blomberg, Bonnie B; Nestle, Frank; Nussenblatt, Robert B; Brinkman, Ryan Remy; Gottardo, Raphael; Maecker, Holden; McCoy, J Philip

    2016-01-01

    Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, and is essential for successful cross-study and cross-center comparison of data. Experts developed five standardized, eight-color panels for identification of major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents in 96-well plates. We present the results of a coordinated analysis of samples across nine laboratories using these panels with standardized operating procedures (SOPs). Manual gating was performed by each site and by a central site. Automated gating algorithms were developed and tested by the FlowCAP consortium. Centralized manual gating can reduce cross-center variability, and we sought to determine whether automated methods could streamline and standardize the analysis. Within-site variability was low in all experiments, but cross-site variability was lower when central analysis was performed in comparison with site-specific analysis. It was also lower for clearly defined cell subsets than those based on dim markers and for rare populations. Automated gating was able to match the performance of central manual analysis for all tested panels, exhibiting little to no bias and comparable variability. Standardized staining, data collection, and automated gating can increase power, reduce variability, and streamline analysis for immunophenotyping. PMID:26861911

  3. Different genomic relationship matrices for single-step analysis using phenotypic, pedigree and genomic information

    Directory of Open Access Journals (Sweden)

    Aguilar Ignacio

    2011-01-01

    Full Text Available Abstract Background The incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously. In such a single-step procedure, genomic and pedigree-based relationships have to be compatible. As there are many options to create genomic relationships, there is a question of which is optimal and what the effects of deviations from optimality are. Methods Data of litter size (total number born per litter for 338,346 sows were analyzed. Illumina PorcineSNP60 BeadChip genotypes were available for 1,989. Analyses were carried out with the complete data set and with a subset of genotyped animals and three generations pedigree (5,090 animals. A single-trait animal model was used to estimate variance components and breeding values. Genomic relationship matrices were constructed using allele frequencies equal to 0.5 (G05, equal to the average minor allele frequency (GMF, or equal to observed frequencies (GOF. A genomic matrix considering random ascertainment of allele frequencies was also used (GOF*. A normalized matrix (GN was obtained to have average diagonal coefficients equal to 1. The genomic matrices were combined with the numerator relationship matrix creating H matrices. Results In G05 and GMF, both diagonal and off-diagonal elements were on average greater than the pedigree-based coefficients. In GOF and GOF*, the average diagonal elements were smaller than pedigree-based coefficients. The mean of off-diagonal coefficients was zero in GOF and GOF*. Choices of G with average diagonal coefficients different from 1 led to greater estimates of additive variance in the smaller data set. The correlation between EBV and genomic EBV (n = 1,989 were: 0.79 using G05, 0.79 using GMF, 0.78 using GOF, 0.79 using GOF*, and 0.78 using GN. Accuracies calculated by inversion increased with all genomic matrices. The accuracies of genomic-assisted EBV

  4. Anchors as Semantic Primes in Value Construction: An EEG Study of the Anchoring Effect.

    Directory of Open Access Journals (Sweden)

    Qingguo Ma

    Full Text Available Previous research regarding anchoring effects has demonstrated that human judgments are often assimilated to irrelevant information. Studies have demonstrated that anchors influence the economic valuation of various products and experiences; however, the cognitive explanations of this effect remain controversial, and its neural mechanisms have rarely been explored. In the current study, we conducted an electroencephalography (EEG experiment to investigate the anchoring effect on willingness to accept (WTA for an aversive hedonic experience and the role of anchors in this judgment heuristic. The behavioral results demonstrated that random numbers affect participants' WTA for listening to pieces of noise. The participants asked for higher pay after comparing their WTA with higher numbers. The EEG results indicated that anchors also influenced the neural underpinnings of the valuation process. Specifically, when a higher anchor number was drawn, larger P2 and late positive potential amplitudes were elicited, reflecting the anticipation of more intensive pain from the subsequent noise. Moreover, higher anchors induced a stronger theta band power increase compared with lower anchors when subjects listened to the noises, indicating that the participants felt more unpleasant during the actual experience of the noise. The levels of unpleasantness during both anticipation and experience were consistent with the semantic information implied by the anchors. Therefore, these data suggest that a semantic priming process underlies the anchoring effect in WTA. This study provides proof for the robustness of the anchoring effect and neural evidence of the semantic priming model. Our findings indicate that activated contextual information, even seemingly irrelevant, can be embedded in the construction of economic value in the brain.

  5. Causes analysis and treatment for rock-anchored cracks in underground workshop%地下厂房岩锚梁裂缝成因分析及处理

    Institute of Scientific and Technical Information of China (English)

    龚少红; 邓瞻; 张恩宝

    2011-01-01

    In light of rock-anchored cracks occurring in underground workshop excavation of Guandi hydropower station, integrating with in-situ geological conditions and monitoring data, the paper analyzes and studies rock-anchored cracking causes, puts forward chemical grouting processing measures, and makes specific illustration, with a view to guarantee the stability and security of rock-anchored beam.%针对官地水电站厂房下卧开挖过程中出现的岩锚梁裂缝,结合现场地质条件、监测数据,对岩锚梁裂缝的成因进行详细的分析研究后提出了对其裂缝进行化学灌浆处理措施,并作了具体阐述,以保证岩锚梁的稳定性和安全性。

  6. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

    OpenAIRE

    Greg Finak; Marc Langweiler; Maria Jaimes; Mehrnoush Malek; Jafar Taghiyar; Yael Korin; Khadir Raddassi; Lesley Devine; Gerlinde Obermoser; Pekalski, Marcin L.; Nikolas Pontikos; Alain Diaz; Susanne Heck; Federica Villanova; Nadia Terrazzini

    2016-01-01

    Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, and is essential for successful cross-study and cross-center comparison of data. Experts developed five standardized, eight-color panels for identification of major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents in 96-well plates. We present the results of a coordinated analysis of samples across nine laborato...

  7. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes

    Directory of Open Access Journals (Sweden)

    Eils Roland

    2005-11-01

    Full Text Available Abstract Background The extensive use of DNA microarray technology in the characterization of the cell transcriptome is leading to an ever increasing amount of microarray data from cancer studies. Although similar questions for the same type of cancer are addressed in these different studies, a comparative analysis of their results is hampered by the use of heterogeneous microarray platforms and analysis methods. Results In contrast to a meta-analysis approach where results of different studies are combined on an interpretative level, we investigate here how to directly integrate raw microarray data from different studies for the purpose of supervised classification analysis. We use median rank scores and quantile discretization to derive numerically comparable measures of gene expression from different platforms. These transformed data are then used for training of classifiers based on support vector machines. We apply this approach to six publicly available cancer microarray gene expression data sets, which consist of three pairs of studies, each examining the same type of cancer, i.e. breast cancer, prostate cancer or acute myeloid leukemia. For each pair, one study was performed by means of cDNA microarrays and the other by means of oligonucleotide microarrays. In each pair, high classification accuracies (> 85% were achieved with training and testing on data instances randomly chosen from both data sets in a cross-validation analysis. To exemplify the potential of this cross-platform classification analysis, we use two leukemia microarray data sets to show that important genes with regard to the biology of leukemia are selected in an integrated analysis, which are missed in either single-set analysis. Conclusion Cross-platform classification of multiple cancer microarray data sets yields discriminative gene expression signatures that are found and validated on a large number of microarray samples, generated by different laboratories and

  8. Retrospective analysis of cohort database: Phenotypic variability in a large dataset of patients confirmed to have homozygous familial hypercholesterolemia.

    Science.gov (United States)

    Raal, Frederick J; Sjouke, Barbara; Hovingh, G Kees; Isaac, Barton F

    2016-06-01

    These data describe the phenotypic variability in a large cohort of patients confirmed to have homozygous familial hypercholesterolemia. Herein, we describe the observed relationship of treated low-density lipoprotein cholesterol with age. We also overlay the low-density lipoprotein receptor gene (LDLR) functional status with these phenotypic data. A full description of these data is available in our recent study published in Atherosclerosis, "Phenotype Diversity Among Patients With Homozygous Familial Hypercholesterolemia: A Cohort Study" (Raal et al., 2016) [1]. PMID:27182539

  9. Retrospective analysis of cohort database: Phenotypic variability in a large dataset of patients confirmed to have homozygous familial hypercholesterolemia

    OpenAIRE

    Raal, Frederick J.; Sjouke, Barbara; Hovingh, G. Kees; Isaac, Barton F.

    2016-01-01

    These data describe the phenotypic variability in a large cohort of patients confirmed to have homozygous familial hypercholesterolemia. Herein, we describe the observed relationship of treated low-density lipoprotein cholesterol with age. We also overlay the low-density lipoprotein receptor gene (LDLR) functional status with these phenotypic data. A full description of these data is available in our recent study published in Atherosclerosis, “Phenotype Diversity Among Patients With Homozygou...

  10. The role of voltage-gated calcium channels in neurotransmitter phenotype specification: Coexpression and functional analysis in Xenopus laevis

    OpenAIRE

    Lewis, Brittany B.; Miller, Lauren E.; Herbst, Wendy A; Saha, Margaret S.

    2014-01-01

    Calcium activity has been implicated in many neurodevelopmental events, including the specification of neurotransmitter phenotypes. Higher levels of calcium activity lead to an increased number of inhibitory neural phenotypes, whereas lower levels of calcium activity lead to excitatory neural phenotypes. Voltage-gated calcium channels (VGCCs) allow for rapid calcium entry and are expressed during early neural stages, making them likely regulators of activity-dependent neurotransmitter phenoty...

  11. Array-CGH characterization and genotype-phenotype analysis in a patient with a ring chromosome 6

    OpenAIRE

    Ciocca, Laura; Surace, Cecilia; Digilio, Maria Cristina; Roberti, Maria Cristina; Sirleto, Pietro; Lombardo, Antonietta; Russo, Serena; Brizi, Valerio; Grotta, Simona; Cini, Claudio; Angioni, Adriano

    2013-01-01

    Background Ring chromosome 6 is a rare constitutional abnormality that generally occurs de novo. The related phenotype may be highly variable ranging from an almost normal phenotype to severe malformations and mental retardation. These features are mainly present when genetic material at the end of the chromosome is lost. The severity of the phenotype seems to be related to the size of the deletion. About 25 cases have been described to date, but the vast majority reports only conventional cy...

  12. A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions.

    Science.gov (United States)

    Makendi, Carine; Page, Andrew J; Wren, Brendan W; Le Thi Phuong, Tu; Clare, Simon; Hale, Christine; Goulding, David; Klemm, Elizabeth J; Pickard, Derek; Okoro, Chinyere; Hunt, Martin; Thompson, Corinne N; Phu Huong Lan, Nguyen; Tran Do Hoang, Nhu; Thwaites, Guy E; Le Hello, Simon; Brisabois, Anne; Weill, François-Xavier; Baker, Stephen; Dougan, Gordon

    2016-02-01

    Salmonella enterica serovar Weltevreden (S. Weltevreden) is an emerging cause of diarrheal and invasive disease in humans residing in tropical regions. Despite the regional and international emergence of this Salmonella serovar, relatively little is known about its genetic diversity, genomics or virulence potential in model systems. Here we used whole genome sequencing and bioinformatics analyses to define the phylogenetic structure of a diverse global selection of S. Weltevreden. Phylogenetic analysis of more than 100 isolates demonstrated that the population of S. Weltevreden can be segregated into two main phylogenetic clusters, one associated predominantly with continental Southeast Asia and the other more internationally dispersed. Subcluster analysis suggested the local evolution of S. Weltevreden within specific geographical regions. Four of the isolates were sequenced using long read sequencing to produce high quality reference genomes. Phenotypic analysis in Hep-2 cells and in a murine infection model indicated that S. Weltevreden were significantly attenuated in these models compared to the classical S. Typhimurium reference strain SL1344. Our work outlines novel insights into this important emerging pathogen and provides a baseline understanding for future research studies. PMID:26867150

  13. A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions.

    Directory of Open Access Journals (Sweden)

    Carine Makendi

    2016-02-01

    Full Text Available Salmonella enterica serovar Weltevreden (S. Weltevreden is an emerging cause of diarrheal and invasive disease in humans residing in tropical regions. Despite the regional and international emergence of this Salmonella serovar, relatively little is known about its genetic diversity, genomics or virulence potential in model systems. Here we used whole genome sequencing and bioinformatics analyses to define the phylogenetic structure of a diverse global selection of S. Weltevreden. Phylogenetic analysis of more than 100 isolates demonstrated that the population of S. Weltevreden can be segregated into two main phylogenetic clusters, one associated predominantly with continental Southeast Asia and the other more internationally dispersed. Subcluster analysis suggested the local evolution of S. Weltevreden within specific geographical regions. Four of the isolates were sequenced using long read sequencing to produce high quality reference genomes. Phenotypic analysis in Hep-2 cells and in a murine infection model indicated that S. Weltevreden were significantly attenuated in these models compared to the classical S. Typhimurium reference strain SL1344. Our work outlines novel insights into this important emerging pathogen and provides a baseline understanding for future research studies.

  14. Comparative analysis of phenotypes features in two common genetic variants of limb-girdle muscular dystrophy

    OpenAIRE

    I. V. Sharkova; E. L. Dadali; I. V. Ugarov; O. P. Ryzhkova; A. V. Polyakov

    2015-01-01

    The algorithm of differential diagnosis of the two most common genetic variants the limb-girdle muscular dystrophy (LGMD2A and DMD), developed on the basis of a comprehensive survey of 85 patients with a diagnosis specification using techniques of DNA analysis. It is shown that the accurate diagnosis of LGMD genetic types should be based on the results of the clinical and genealogical, biochemical and molecular genetic analysis. The proposed algorithm will significantly reduces the economic a...

  15. Comparative analysis of phenotypes features in two common genetic variants of limb-girdle muscular dystrophy

    Directory of Open Access Journals (Sweden)

    I. V. Sharkova

    2015-01-01

    Full Text Available The algorithm of differential diagnosis of the two most common genetic variants the limb-girdle muscular dystrophy (LGMD2A and DMD, developed on the basis of a comprehensive survey of 85 patients with a diagnosis specification using techniques of DNA analysis. It is shown that the accurate diagnosis of LGMD genetic types should be based on the results of the clinical and genealogical, biochemical and molecular genetic analysis. The proposed algorithm will significantly reduces the economic and time costs with expensive DNA testing.

  16. Comparative analysis of features phenotype limb-girdle muscular dystrophy 2А and 2I types

    Directory of Open Access Journals (Sweden)

    I. V. Sharkova

    2013-01-01

    Full Text Available A comparative analysis of the frequency of occurrence of 36 clinical symptoms in the three groups of patients with LGMD 2A and LGMD 2Itypes and LGMD those patients who have mutations in CAPN3 and FKRP was detected. The absence of a particular symptom, allowing for thedifferentiation of these genetic variants on clinical level. An algorithm for molecular genetic investigation of patients according to age at onset and some clinical symptoms. The proposed algorithm can significantly reduce the economic and time costs during expensive standing DNA analysis.

  17. Investigations of Potential Phenotypes of Foot Osteoarthritis: Cross‐Sectional Analysis From the Clinical Assessment Study of the Foot

    Science.gov (United States)

    Marshall, Michelle; Thomas, Martin J.; Menz, Hylton B.; Myers, Helen L.; Thomas, Elaine; Downes, Thomas; Peat, George; Roddy, Edward

    2016-01-01

    Objective To investigate the existence of distinct foot osteoarthritis (OA) phenotypes based on pattern of joint involvement and comparative symptom and risk profiles. Methods Participants ages ≥50 years reporting foot pain in the previous year were drawn from a population‐based cohort. Radiographs were scored for OA in the first metatarsophalangeal (MTP) joint, first and second cuneometatarsal, navicular first cuneiform, and talonavicular joints according to a published atlas. Chi‐square tests established clustering, and odds ratios (ORs) examined symmetry and pairwise associations of radiographic OA in the feet. Distinct underlying classes of foot OA were investigated by latent class analysis (LCA) and their association with symptoms and risk factors was assessed. Results In 533 participants (mean age 64.9 years, 55.9% female) radiographic OA clustered across both feet (P < 0.001) and was highly symmetrical (adjusted OR 3.0, 95% confidence interval 2.1, 4.2). LCA identified 3 distinct classes of foot OA: no or minimal foot OA (64%), isolated first MTP joint OA (22%), and polyarticular foot OA (15%). After adjustment for age and sex, polyarticular foot OA was associated with nodal OA, increased body mass index, and more pain and functional limitation compared to the other classes. Conclusion Patterning of radiographic foot OA has provided insight into the existence of 2 forms of foot OA: isolated first MTP joint OA and polyarticular foot OA. The symptom and risk factor profiles in individuals with polyarticular foot OA indicate a possible distinctive phenotype of foot OA, but further research is needed to explore the characteristics of isolated first MTP joint and polyarticular foot OA. PMID:26238801

  18. Monitoring ground anchor using non-destructive ground anchor integrity test (NDT-GRANIT)

    International Nuclear Information System (INIS)

    Monitoring at ground anchor commonly uses a pull out test method, therefor we developing a non-destructive ground anchor integrity testing (NDT-GRANIT). NDT-GRANIT using the principle of seismic waves that have been modified into form of sweep signal, the signal will be demodulated, filtered, and Fourier transformation (inverse discrete Fourier transform) so the data can be interpreted reflected wave from the ground anchor. The method was applied to determine whether the ground anchor still gripped in the subsurface by looking the attenuation of the wave generated sources. From the result we can see that ground anchor does not grip. To validate the results of the comparison method of measurement used pile integrity test

  19. Waardenburg syndrome type I: Dental phenotypes and genetic analysis of an extended family

    OpenAIRE

    Sólia-Nasser, Luciano; de Aquino, Sibele-Nascimento; Paranaíba, Lívia-Maris-R.; Gomes, Andreia; dos-Santos-Neto, Pedro; Coletta, Ricardo-D.; Cardoso, Aline-Francoise; Frota, Ana-Cláudia; Martelli-Júnior, Hercílio

    2016-01-01

    Background The aim of this study was to describe the pattern of inheritance and the clinical features in a large family with Waardenburg syndrome type I (WS1), detailing the dental abnormalities and screening for PAX3 mutations. Material and Methods To characterize the pattern of inheritance and clinical features, 29 family members were evaluated by dermatologic, ophthalmologic, otorhinolaryngologic and orofacial examination. Molecular analysis of the PAX3 gene was performed. Results The pedi...

  20. Molecular analysis of the 18q- syndrome--and correlation with phenotype.

    OpenAIRE

    Kline, A D; White, M E; Wapner, R; Rojas, K; Biesecker, L G; Kamholz, J; Zackai, E. H.; Muenke, M; Scott, C I; Overhauser, J

    1993-01-01

    Seven individuals with deletions of the distal long arm of chromosome 18 were evaluated at the clinical, cytogenetic, and molecular levels. The patients had varying degrees of typical clinical findings associated with the 18q- syndrome. Cytogenetic analysis revealed deletions from 18q21.3 or 18q22.2 to qter. Somatic cell hybrids derived from the patients were molecularly characterized using ordered groups of probes isolated from a chromosome 18-specific library. In general, the size of the de...

  1. Phenotypic and genome-wide analysis of an antibiotic-resistant small colony variant (SCV of Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Qing Wei

    Full Text Available BACKGROUND: Small colony variants (SCVs are slow-growing bacteria, which often show increased resistance to antibiotics and cause latent or recurrent infections. It is therefore important to understand the mechanisms at the basis of this phenotypic switch. METHODOLOGY/PRINCIPAL FINDINGS: One SCV (termed PAO-SCV was isolated, showing high resistance to gentamicin and to the cephalosporine cefotaxime. PAO-SCV was prone to reversion as evidenced by emergence of large colonies with a frequency of 10(-5 on media without antibiotics while it was stably maintained in presence of gentamicin. PAO-SCV showed a delayed growth, defective motility, and strongly reduced levels of the quorum sensing Pseudomonas quinolone signal (PQS. Whole genome expression analysis further suggested a multi-layered antibiotic resistance mechanism, including simultaneous over-expression of two drug efflux pumps (MexAB-OprM, MexXY-OprM, the LPS modification operon arnBCADTEF, and the PhoP-PhoQ two-component system. Conversely, the genes for the synthesis of PQS were strongly down-regulated in PAO-SCV. Finally, genomic analysis revealed the presence of mutations in phoP and phoQ genes as well as in the mexZ gene encoding a repressor of the mexXY and mexAB-oprM genes. Only one mutation occurred only in REV, at nucleotide 1020 of the tufA gene, a paralog of tufB, both encoding the elongation factor Tu, causing a change of the rarely used aspartic acid codon GAU to the more common GAC, possibly causing an increase of tufA mRNA translation. High expression of phoP and phoQ was confirmed for the SCV variant while the revertant showed expression levels reduced to wild-type levels. CONCLUSIONS: By combining data coming from phenotypic, gene expression and proteome analysis, we could demonstrate that resistance to aminoglycosides in one SCV mutant is multifactorial including overexpression of efflux mechanisms, LPS modification and is accompanied by a drastic down-regulation of the

  2. Phenotype and genotype analysis of a Chinese family with prelingual X-linked hereditary hearing impairment

    Institute of Scientific and Technical Information of China (English)

    HAN Bing; CHENG Jing; YANG Shu-zhi; CAO Ju-yang; SHEN Wei-dong; JI Fei; KANG Dong-yang; ZHANG Xin; DAI Pu; YUAN Hui-jun

    2009-01-01

    Background X-linked hearing impairment is clinically and genetically a heterogeneous disease.Although many disorders manifest with hearing loss,a limited number of sex-linked loci and only one gene (POU3F4) have been shown to be implicated in X-linked non-syndromic hearing impairment.In the present study,we have performed a clinical and genetic analysis of a Chinese family with X-linked non-syndromic hearing loss,with emphasis on audiological findings and genomic mapping.Methods The clinical features of Family JX01 were evaluated by physical and audiometric examination in eighteen family members.Mutation screening of POU3F4 was identified by polymerase chain reaction (PCR) amplification and sequencing.Molecular evaluation consisted of X-chromosome wide genotyping by microsatellite makers (STR),followed by analyzing using MLINK computer program.Results Five affected males demonstrated bilateral,symmetrical sensorineural and profound hearing loss.The hearing impairment started prelingual.The female carriers did not have any complain of hearing loss,however,two of them were tested with milder loss with high frequency.No causative mutations in POU3F4 gene were detected by DNA sequencing.Linkage analysis indicated that the responsible gene was linked to locus DXS1227 (maximum lod score=2.04 at θ=0).Conclusions The affected males in Family JX01 have profound prelingual sensorineural hearing impairment,In addition,two female carriers showed mild to moderate hearing losses.However,none of females complained of any hearing loss.Analysis of hereditary deafness in this family mapped most compatibly to the Xq27.2.

  3. The use of phenotypic correlations and factor analysis in determining characters for grain yield selection in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Toker, Cengiz; Ilhan Cagirgan, M

    2004-01-01

    To our knowledge, this is the first report on the use of factor analysis in determining characters for yield selection in chickpea (Cicer arietinum L.). The present investigation was undertaken to evaluate yield criteria in chickpea using phenotypic correlations and factor analysis. Factor 1 composed of biological yield, reaction to ascochyta blight (Ascochyta rabiei (Pass.) Labr.), plant height, grain yield and harvest index. Factor 2 consisted of branches and pods per plant. Factor 3 encompassed of only the grain weight. The total factors explained 92.9% of the total variance caused in the characters. The grain yield was positively and statistically significant correlated with biological yield, harvest index, plant height, branches and pods per plant, while it was negatively and statistically significant related with reaction to ascochyta blight and grain weight. Biological yield, harvest index, plant height and reaction to ascochyta blight instead of many selection criteria should previously be evaluated in selection to increase the grain yield in chickpea breeding programs. Pods per plant should be handed together with and branches per plant. Apart from the other selection criteria, the grain weight should solely be evaluated to select large grained genotypes. PMID:15198713

  4. Analysis of Tox5 gene expression in Gibberella pulicaris strains with different trichothecene production phenotypes.

    OpenAIRE

    Hohn, T M; Desjardins, A. E.; McCormick, S P

    1993-01-01

    The Tox5 gene encodes trichodiene synthase, the first unique enzyme in the trichothecene biosynthetic pathway. In Gibberella pulicaris R-6380, the level of Tox5 mRNA was found to increase 47-fold in early stationary phase. Sequence analysis of the Tox5 promoter regions from geographically distinct strains of G. pulicaris revealed the existence of two Tox5 alleles (Tox5-1 and Tox5-2). All G. pulicaris strains that produce high levels of trichothecenes in liquid culture carry a 42-nucleotide (n...

  5. Time-varying reliability analysis of anchor system of rock slopes with double slide blocks%双滑块边坡锚固系统时变可靠性分析

    Institute of Scientific and Technical Information of China (English)

    陈昌富; 成晓炜

    2012-01-01

    考虑锚杆锚固段从岩体中拔出、拉杆拉断、拉杆从注浆体中拔出等失效模式,利用系统可靠性原理和极限平衡分析方法,并基于Monte-Carlo抽样原理提出双滑块岩质边坡锚固系统破坏概率的直接求解方法.同时考虑锚杆钢筋的腐蚀与软弱滑动面抗剪强度c、φ的时变性,建立了考虑锚杆多失效模式双滑块岩质边坡锚固系统的时变可靠性模型.算例计算结果表明:软弱滑动面上的强度参数c、φ的时变性和注浆体与围岩之间的抗力时变性对锚固系统的破坏概率的影响较大,而锚杆的腐蚀对锚固系统破坏概率的影响不明显.%Considering the multiple failure modes of anchor system such as pulling out of grouting mass from surrounding rock, the tensile failure of the pull rod and the shearing failure of interface between pull rod and grouting mass, etc., applying systematical reliability principle and limit equilibrium method, a direct solution of failure probability of anchor system of rock slope with double slide blocks is proposed based on Monte Carlo sample principle. Meanwhile, taking the time variation of shear strength indices of soft sliding surface c and φand the erosion of anchor bars into account, a time-variation reliability model of anchor system of rock slope with double slide blocks in consideration of multiple failure modes of anchor is established. The calculation results of examples show that the time-variations of shear strength indices of soft sliding surface c,φand the resistance between grouting body and surrounding rock have great impact on failure probability of anchor system, while erosion of anchor bars has less impact on it.

  6. Phenotypic Variability and Diversity Analysis of Bean Traits of Some Cocoa Hybrids in Nigeria

    Directory of Open Access Journals (Sweden)

    A.V. Oyedokun

    2011-03-01

    Full Text Available It is essential to understand the economic potential and superiority among cocoa hybrids. Therefore, the present study aims at detecting variability among cocoa hybrids for bean index in Nigeria. Dried bean of fourteen genotypes of cocoa were evaluated for their bean values. Analysis of variance (ANOVA was used to understand the variability among the fourteen genotypes and Principal Component Analysis (PCA was employed to identify distinguishing traits and the grouping of the genotypes based on similarities. The fourteen cocoa genotypes were significantly (p≤0.05 different from each other with respect to weight of one bean, bean length, width, thickness, 100 bean weight, bean length to width, length to thickness and width to thickness ratio. All the studied morphometric characters exhibited high (>70% broad sense heritability. G8, the hybrid between T53/5 and N38 was the most superior genotype for bean weight and some other bean characteristics. The mass of seventy-four dried cocoa bean of G8 approximated 100 g. The first three Principal Component axes explained 91% of the total variation and the PCA grouped the fourteen genotypes into four distinct clusters. Genotypes could be selected for specific traits and improvement of traits seemed to be genetically reliable.

  7. Waardenburg syndrome type I: Dental phenotypes and genetic analysis of an extended family

    Science.gov (United States)

    de Aquino, Sibele-Nascimento; Paranaíba, Lívia-Maris-R.; Gomes, Andreia; dos-Santos-Neto, Pedro; Coletta, Ricardo-D.; Cardoso, Aline-Francoise; Frota, Ana-Cláudia; Martelli-Júnior, Hercílio

    2016-01-01

    Background The aim of this study was to describe the pattern of inheritance and the clinical features in a large family with Waardenburg syndrome type I (WS1), detailing the dental abnormalities and screening for PAX3 mutations. Material and Methods To characterize the pattern of inheritance and clinical features, 29 family members were evaluated by dermatologic, ophthalmologic, otorhinolaryngologic and orofacial examination. Molecular analysis of the PAX3 gene was performed. Results The pedigree of the family,including the last four generations, was constructed and revealed non-consanguineous marriages. Out of 29 descendants, 16 family members showed features of WS1, with 9 members showing two major criteria indicative of WS1. Five patients showed white forelock and iris hypopigmentation, and four showed dystopia canthorum and iris hypopigmentation. Two patients had hearing loss. Dental abnormalities were identified in three family members, including dental agenesis, conical teeth and taurodontism. Sequencing analysis failed to identify mutations in the PAX3 gene. Conclusions These results confirm that WS1 was transmitted in this family in an autosomal dominant pattern with variable expressivity and high penetrance. The presence of dental manifestations, especially tooth agenesis and conical teeth which resulted in considerable aesthetic impact on affected individuals was a major clinical feature. Clinical relevance: This article reveals the presence of well-defined dental changes associated with WS1 and tries to establish a possible association between these two entities showing a new spectrum of WS1. Key words:Waardenburg syndrome, hearing loss, oral manifestations, mutation. PMID:27031059

  8. Evaluation of phenotypic diversity of apple (Malus sp. germplasm through the principle component analysis

    Directory of Open Access Journals (Sweden)

    Mratinić Evica

    2011-01-01

    Full Text Available A wide range of apple cultivars representing Malus sp. germplasm were collected from southern part of Serbia, where this specie has been in cultivation for a long time. Data for twelve traits were collected for 18 cultivars for three consecutive years. Cultivars differed in phenology, fruit weight, yield and chemical composition were evaluated. Correlations were identified among phenological and compositional traits. Principal component analysis (PCA was performed to study correlation among variables in set of apple cultivars evaluated and to interpret relationships among genotypes as a tool for germplasm characterization. Dulabija, intended for table consumption, and Stambolka, suitable for the processing, were identified as promising. Because of the large diversity identified, data should be collected for additional local apple cultivars.

  9. Relationship between commercially available DNA analysis and phenotypic observations on beef quality and tenderness.

    Science.gov (United States)

    Magolski, J D; Buchanan, D S; Maddock-Carlin, K R; Anderson, V L; Newman, D J; Berg, E P

    2013-11-01

    Warner-Bratzler shear force values from 560 mixed breed heifers and steers were used to determine estimates of genetic selection. Cattle were marketed from 2008 to 2011, and included five feedlot based research projects at the North Dakota State University-Carrington Research Extension Center. Samples were collected for IGENITY® analysis providing information that included selection indices and estimated breeding values for carcass traits. DNA-based test results were compared with actual carcass measurements. Marbling accounted for over 10% of the variation in WBSF while hot carcass weight was the second most influential carcass trait accounting for 4% (Pgrade, and fat thickness were low (R(2)=0.14, 0.02, 0.03, 0.03, and 0.02, respectively). Therefore selecting cattle for a higher degree of marbling and feeding a diet that meets or exceeds recommended nutrients for growth are the most important factors influencing beef tenderness and acceptability. PMID:23793083

  10. DESCRIPTIVE AND DISCRIMINATORY SIGNIFICANCE OF POD PHENOTYPIC TRAITS FOR DIVERSITY ANALYSIS OF COCOA GENOTYPES

    Directory of Open Access Journals (Sweden)

    Daniel B. Adewale

    2013-12-01

    Full Text Available Intra-specific genetic diversity analysis precedes crop breeding proposal for species improvement. Sixteen and twenty-four parental and hybrid cocoa genotypes were respectively laid out in a randomized complete block design of six replications at Ibadan, Nigeria. A sampling unit of fifteen uniformly ripe pods was collected for assessment from each plot. Six quantitative data from the pods were subjected to statistical analysis. Highly significant (P < 0.0001 variability existed among the 40 genotypes. Range of performance of the genotypes were: pod weight (0.43 – 0.86kg, pod length (15.9 – 27.96cm, pod girth (21.51 – 34.07cm, pod thickness (1.26 – 5.71cm, number of beans per pod (20 - 51 and bean weight per pod (0.017 - 0.41kg. Positive and significant (P < 0.001 correlation existed between pod weight and length, pod girth and bean number/pod. The mean Gower genetic distance among the 40 genotypes was 0.228; the least (0.023 existed between G25 and G30 while the highest (0.529 was between G17 and G35. The first three principal component axes explained 73% of the total variation. Three distinct groups emerged from the Ward clustering technique. Significant (P<0.05 intra and inter cluster variability existed in the study. High genetic diversity lies within the studied population. Pod traits were important descriptors for cocoa genotypes classification.

  11. Uplift of Symmetrical Anchor Plates by Using Grid-Fixed Reinforced Reinforcement in Cohesionless Soil

    Institute of Scientific and Technical Information of China (English)

    Hamed Niroumand; Khairul Anuar Kassim

    2014-01-01

    Uplift response of symmetrical anchor plates with and without grid fixed reinforced (GFR) reinforcement was evaluated in model tests and numerical simulations by Plaxis. Many variations of reinforcement layers were used to reinforce the sandy soil over symmetrical anchor plates. In the current research, different factors such as relative density of sand, embedment ratios, and various GFR parameters including size, number of layers, and the proximity of the layer to the symmetrical anchor plate were investigated in a scale model. The failure mechanism and the associated rupture surface were observed and evaluated. GFR, a tied up system made of fiber reinforcement polymer (FRP) strips and end balls, was connected to the geosynthetic material and anchored into the soil. Test results showed that using GFR reinforcement significantly improved the uplift capacity of anchor plates. It was found that the inclusion of one layer of GFR, which rested directly on the top of the anchor plate, was more effective in enhancing the anchor capacity itself than other methods. It was found that by including GFR the uplift response was improved by 29%. Multi layers of GFR proved more effective in enhancing the uplift capacity than a single GFR reinforcement. This is due to the additional anchorage provided by the GFR at each level of reinforcement. In general, the results show that the uplift capacity of symmetrical anchor plates in loose and dense sand can be significantly increased by the inclusion of GFR. It was also observed that the inclusion of GFR reduced the requirement for a large L/D ratio to achieve the required uplift capacity. The laboratory and numerical analysis results are found to be in agreement in terms of breakout factor and failure mechanism pattern.

  12. Application Research on Nondestructive Testing Technology for Quality of Anchor Based on Elastic Wave Reflection Method

    Science.gov (United States)

    Xiao, G.; Zhou, L.

    2014-12-01

    Anchor technology has been widely used to reinforce slopes, underground caverns, deep excavations and the foundation of dams. It has attracted more and more attention of research worldwide on how to find a comfortable method to test the quality of anchoring systems. According to the characteristics of anchor systems, we set up the kinetic equations and mathematical models, then solved the models using ANSYS / LS-DYNA program. We found that the simulated mathematical models perfectly match the experimental data. By changing one of the parameters or the input conditions in the model, we were able to understand the characteristic response of excitation energy, excitation length, structural defects, rock quality, and different data acquisition methods. For short anchor systems (grouting density. The obtained values were consistent with the actual experimental data. We also demonstrated that the kinetic energy of the collected waves from the bottom of the anchor had very close relationship with the grouting density and the position of the structural defects. For long anchors (> 60 m), mostly cable anchors, since little research could be followed, we started our research from designing the instrument, writing the program for data acquisition and analysis. We designed and developed novel sensors and preamplifiers. We used vertical stack technology to effectively enhance the weak signals from the deeper interfaces. In data processing, in addition to the traditional filter method, we also explored the current technology of signal processing such as true amplitude recovery and deconvolution, which enabled us to obtain improved signal to noise ratio and sensing precision. Through the above mentioned systematical studies, we developed a reliable nondestructive test method for both short and long anchors based on elastic wave reflection. This research is funded by National Natural Science Foundation of China (Grant No. 41202223)

  13. Analysis of large phenotypic variability of EEC and SHFM4 syndromes caused by K193E mutation of the TP63 gene.

    Directory of Open Access Journals (Sweden)

    Jianhua Wei

    Full Text Available EEC (ectrodactyly, ectodermal dysplasia, clefting; OMIM 604292 is an autosomal dominant developmental disorder resulting mainly from pathogenic mutations of the DNA-binding domain (DBD of the TP63 gene. In this study, we showed that K193E mutation in nine affected individuals of a four-generation kindred with a large degree of phenotypic variability causes four different syndromes or TP63-related disorders: EEC, Ectrodactyly-ectodermal dysplasia (EE, isolated ectodermal dysplasia, and isolated Split Hand/Foot Malformation type 4 (SHFM4. Genotype-phenotype and DBD structural modeling analysis showed that the K193-located loop L2-A is associated with R280 through hydrogen bonding interactions, while R280 mutations also often cause large phenotypic variability of EEC and SHFM4. Thus, we speculate that K193 and several other DBD mutation-associated syndromes may share similar pathogenic mechanisms, particularly in the case of the same mutation with different phenotypes. Our study and others also suggest that the phenotypic variability of EEC is attributed, at least partially, to genetic and/or epigenetic modifiers.

  14. Phenotypic analysis of bone marrow lymphocytes from children with acute thrombocytopenic purpura.

    Science.gov (United States)

    Guiziry, Dalai E L; El, Gendy Wessam; Farahat, Nahla; Hassab, Hoda

    2005-01-01

    Hematogones are benign immature B cells that commonly populate the bone marrow of children. Their presence has been noted to interfere with the flow-cytometric analysis of acute lymphoblastic leukemia (ALL), because their immunophenotype is similar to B-precursor cell lymphoblasts. Immune-mediated thrombocytopenia is a clinical condition characterized by increased platelet destruction due to sensitization of platelets by autoantibodies. The aim of this study was to determine the incidence and clinical impact of bone marrow hematogones in cases of acute immune thrombocytopenic purpura (ITP) among children. This was done by immunophenotyping of bone marrow lymphocytes of ITP cases and controls and follow up of cases. This study was done on 25 cases of ITP, 12 females and 13 males, their age ranged from 2 to 13 years. A control group was included in the study, 15 cases of apparently healthy children with matching age and sex taken from among bone marrow donors. Cases and controls were subjected to bone marrow lymphocyte immunophenotyping with flow-cytometry to verify the presence of hematogones. A statistically significant increase in the percentage of hematogones was demonstrated in their bone marrows. An increased percentage of CD10+ lymphocytes was demonstrated; with a mean of 18+/-15.2%, CD19+ with a mean of 27+/-16.3% and CD34+ with a mean of 3.7+/-3.2%. No correlation was found between the percentage of hematogones and peripheral platelet count or bone marrow lymphocytic count. In conclusion, there is an increase in the bone marrow hematogones in ITP cases in comparison to normal controls. This could be the sequence of an immunological response to the cause which determined the disease, or the regeneration of the stem cell compartment following transient damage. PMID:16734134

  15. Digit ratios by computer-assisted analysis confirm lack of anatomical evidence of prenatal androgen exposure in clinical phenotypes of polycystic ovary syndrome

    Directory of Open Access Journals (Sweden)

    Lehotay Denis C

    2010-12-01

    Full Text Available Abstract Background We recently showed that women with four clinical phenotypes of polycystic ovary syndrome (PCOS do not demonstrate anatomical evidence of elevated prenatal androgen exposure as judged by a lower ratio of the index (2D to ring (4D finger. However, those findings conflicted with a previous study where women with PCOS had lower right hand 2D:4D compared to healthy female controls. Both these studies used Vernier calipers to measure finger lengths - a method recently shown to be less reliable at obtaining finger length measurements than computer-assisted analysis. Methods Ninety-six women diagnosed with PCOS according to the 2003 Rotterdam criteria had their finger lengths measured with computer-assisted analysis. Participants were categorized into four recognized phenotypes of PCOS and their 2D:4D compared to healthy female controls (n = 48 and men (n = 50. Results Digit ratios assessed by computer-assisted analysis in women with PCOS did not differ from female controls, but were significantly lower in men. When subjects were stratified by PCOS phenotype, 2D:4D did not differ among phenotypes or when compared to female controls. Conclusion Computer-assisted measurements validated that digit ratios of women with PCOS do not show anatomical evidence of increased prenatal androgen exposure.

  16. A three-dimensional engineered tumour for spatial snapshot analysis of cell metabolism and phenotype in hypoxic gradients

    Science.gov (United States)

    Rodenhizer, Darren; Gaude, Edoardo; Cojocari, Dan; Mahadevan, Radhakrishnan; Frezza, Christian; Wouters, Bradly G.; McGuigan, Alison P.

    2016-02-01

    The profound metabolic reprogramming that occurs in cancer cells has been investigated primarily in two-dimensional cell cultures, which fail to recapitulate spatial aspects of cell-to-cell interactions as well as tissue gradients present in three-dimensional tumours. Here, we describe an engineered model to assemble three-dimensional tumours by rolling a scaffold-tumour composite strip. By unrolling the strip, the model can be rapidly disassembled for snapshot analysis, allowing spatial mapping of cell metabolism in concert with cell phenotype. We also show that the establishment of oxygen gradients within samples that are shaped by oxygen-dependent signalling pathways, as well as the consequential variations in cell growth, response to hypoxic gradients extending from normoxia to severe hypoxia, and therapy responsiveness, are consistent with those of tumours in vivo. Moreover, by using liquid chromatography tandem mass spectrometry, we mapped cellular metabolism and identified spatially defined metabolic signatures of cancer cells to reveal both known and novel metabolic responses to hypoxia.

  17. High-speed video gait analysis reveals early and characteristic locomotor phenotypes in mouse models of neurodegenerative movement disorders.

    Science.gov (United States)

    Preisig, Daniel F; Kulic, Luka; Krüger, Maik; Wirth, Fabian; McAfoose, Jordan; Späni, Claudia; Gantenbein, Pascal; Derungs, Rebecca; Nitsch, Roger M; Welt, Tobias

    2016-09-15

    Neurodegenerative diseases of the central nervous system frequently affect the locomotor system resulting in impaired movement and gait. In this study we performed a whole-body high-speed video gait analysis in three different mouse lines of neurodegenerative movement disorders to investigate the motor phenotype. Based on precise computerized motion tracking of all relevant joints and the tail, a custom-developed algorithm generated individual and comprehensive locomotor profiles consisting of 164 spatial and temporal parameters. Gait changes observed in the three models corresponded closely to the classical clinical symptoms described in these disorders: Muscle atrophy due to motor neuron loss in SOD1 G93A transgenic mice led to gait characterized by changes in hind-limb movement and positioning. In contrast, locomotion in huntingtin N171-82Q mice modeling Huntington's disease with basal ganglia damage was defined by hyperkinetic limb movements and rigidity of the trunk. Harlequin mutant mice modeling cerebellar degeneration showed gait instability and extensive changes in limb positioning. Moreover, model specific gait parameters were identified and were shown to be more sensitive than conventional motor tests. Altogether, this technique provides new opportunities to decipher underlying disease mechanisms and test novel therapeutic approaches. PMID:27233823

  18. pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes

    Directory of Open Access Journals (Sweden)

    Arévalo-Rodríguez Miguel

    2011-02-01

    Full Text Available Abstract Background Since publication in 1977 of plasmid pBR322, many breakthroughs in Biology have depended on increasingly sophisticated vector platforms for analysis and engineering of given bacterial strains. Although restriction sites impose a certain format in the procedures for assembling cloned genes, every attempt thus far to standardize vector architecture and nomenclature has ended up in failure. While this state of affairs may still be tolerable for traditional one-at-a-time studies of single genes, the onset of systems and synthetic biology calls for a simplification -along with an optimization- of the currently unwieldy pool of genetic tools. Results The functional DNA sequences present in the natural bacterial transposon Tn5 have been methodically edited and refactored for the production of a multi-purpose genetic tool named pBAM1, which allows a range of manipulations in the genome of Gram-negative bacteria. This all-synthetic construct enhances the power of mini-transposon vectors for either de-construction or re-construction of phenotypes á la carte by incorporating features inspired in systems engineering: modularity, re-usability, minimization, and compatibility with other genetic tools. pBAM1 bears an streamlined, restriction site-freed and narrow-host range replication frame bearing the sequences of R6K oriV, oriT and an ampicillin resistance marker. These go along with a business module that contains a host-independent and hyperactive transposition platform for in vivo or in vitro insertion of desired DNA into the genome of the target bacterium. All functional sequences were standardized for a straightforward replacement by equivalent counterparts, if required. pBAM1 can be delivered into recipient cells by either mating or electroporation, producing transposon insertion frequencies of 1.8 × 10-3 and 1.02 × 10-7, respectively in the soil bacterium Pseudomonas putida. Analyses of the resulting clones revealed a 100% of

  19. Anchor Stress Checking of Security Injection Tank

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The intention of the calculating is to check the anchor stresses of the security injection tank to know whether the stress is satisfied the code requirements on the basis of all the reaction forces gained in the static, seismic and thermal stress results.

  20. Stone anchors from Minicoy Island, Lakshadweep, India

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    at Androth, Kadmat, Kavaratti and Minicoy. In addition to these finds, in recent past an Indo-Arabian type of stone anchor has come to lime light at the Jama Mosque of Funhilol of Minicoy. In this paper an attempt has been made to describe the Indo...

  1. Predicting Anchor Links between Heterogeneous Social Networks

    CERN Document Server

    Sajadmanesh, Sina; Khodadadi, Ali

    2016-01-01

    People usually get involved in multiple social networks to enjoy new services or to fulfill their needs. Many new social networks try to attract users of other existing networks to increase the number of their users. Once a user (called source user) of a social network (called source network) joins a new social network (called target network), a new inter-network link (called anchor link) is formed between the source and target networks. In this paper, we concentrated on predicting the formation of such anchor links between heterogeneous social networks. Unlike conventional link prediction problems in which the formation of a link between two existing users within a single network is predicted, in anchor link prediction, the target user is missing and will be added to the target network once the anchor link is created. To solve this problem, we use meta-paths as a powerful tool for utilizing heterogeneous information in both the source and target networks. To this end, we propose an effective general meta-pat...

  2. Low Gravity Anchoring System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Future sampling missions to the Moon, Mars and Asteroids will likely involve drilling and in-situ analysis from mobile robotic platforms in low gravity. Past...

  3. In vitro analysis of the invasive phenotype of SUM 149, an inflammatory breast cancer cell line

    OpenAIRE

    Dharmawardhane Suranganie F; Wall Kristin M; Hoffmeyer Michaela R

    2005-01-01

    Abstract Background Inflammatory breast cancer (IBC) is the most lethal form of locally invasive breast cancer known. However, very little information is available on the cellular mechanisms responsible for manifestation of the IBC phenotype. To understand the unique phenotype of IBC, we compared the motile and adhesive interactions of an IBC cell line, SUM 149, to the non-IBC cell line SUM 102. Results Our results demonstrate that both IBC and non-IBC cell lines exhibit similar adhesive prop...

  4. A Dysmorphometric Analysis to Investigate Facial Phenotypic Signatures as a Foundation for Non-invasive Monitoring of Lysosomal Storage Disorders

    OpenAIRE

    Kung, Stefanie; Walters, Mark; Claes, Peter; Goldblatt, Jack; Le Souef, Peter; Baynam, Gareth

    2012-01-01

    Background: Some lysosomal storage disorders (LSDs), including Muccopolysaccharidosis type 1 (MPSI), are associated with characteristic facies. Methods such as three-dimensional (3D) facial scanning and geometric morphometric techniques can potentially generate detailed objective descriptions of these facial phenotypes. This approach can facilitate discriminating the inherent overlap in facial phenotypes within these disease spectra, and the non-invasive monitoring of disease progression and ...

  5. “Rolled-upness”: phenotyping leaf rolling in cereals using computer vision and functional data analysis approaches

    OpenAIRE

    Sirault, X. R. R.; Condon, A. G.; Wood, J. T.; Farquhar, G. D.; Rebetzke, G.J.

    2015-01-01

    Background The flag leaf of a wheat (Triticum aestivum L.) plant rolls up into a cylinder in response to drought conditions and then unrolls when leaf water relations improve. This is a desirable trait for extending leaf area duration and improving grain size particularly under drought. But how do we quantify this phenotype so that different varieties of wheat or different treatments can be compared objectively since this phenotype can easily be confounded with inter-genotypic differences in ...

  6. Analysis of phenotype, genotype and serotype distribution in erythromycin-resistant group B streptococci isolated from vaginal flora in Southern Ireland.

    LENUS (Irish Health Repository)

    Kiely, R A

    2010-02-01

    The screening of 2000 women of childbearing age in Cork between 2004 and 2006 produced 37 erythromycin-resistant group B streptococcus (GBS) isolates. PCR analysis was performed to determine the basis for erythromycin resistance. The ermTR gene was most frequently expressed (n = 19), followed by the ermB gene (n = 8). Four isolates harboured the mefA gene. Six isolates yielded no PCR products. Some phenotype-genotype correlation was observed. All isolates expressing the mefA gene displayed the M phenotype whilst all those expressing ermB displayed the constitutive macrolide resistance (cMLS(B)) phenotype. Of 19 isolates that expressed the ermTR gene, 16 displayed the inducible macrolide resistance (iMLS(B)) phenotype. Serotype analysis revealed that serotypes III and V predominated in these isolates. The identification of two erythromycin-resistant serotype VIII isolates among this collection represents the first reported finding of erythromycin resistance in this serotype. A single isolate was non-typable using two latex agglutination serotyping kits.

  7. Stone anchors of India: Findings, classification and significance.

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    Honolulu, Hawaii, May 12-16, 2014, Vol. 2: 973-986 973 Stone anchors of India: Findings, Classification and Significance Sila Tripati CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India Email: sila@nio.org Abstract Various.... The making of anchors from the hero stones indicates their alternative use (Sila Tripati and Patnaik, 2008). Classification Stone anchors are classified according to character, shape and region. In general stone anchors have been classified...

  8. Susceptibility to anchoring effects: How openness-to-experience influences responses to anchoring cues

    OpenAIRE

    Todd McElroy; Keith Dowd

    2007-01-01

    Previous research on anchoring has shown this heuristic to be a very robust psychological phenomenon ubiquitous across many domains of human judgment and decision-making. Despite the prevalence of anchoring effects, researchers have only recently begun to investigate the underlying factors responsible for how and in what ways a person is susceptible to them. This paper examines how one such factor, the Big-Five personality trait of openness-to-experience, influences the effect of previously p...

  9. How curved membranes recruit amphipathic helices and protein anchoring motifs

    DEFF Research Database (Denmark)

    Hatzakis, Nikos; Bhatia, Vikram Kjøller; Larsen, Jannik;

    2009-01-01

    : membrane-anchored proteins. The fact that unrelated structural motifs such as alpha-helices and alkyl chains sense MC led us to propose that MC sensing is a generic property of curved membranes rather than a property of the anchoring molecules. We therefore anticipate that MC will promote the...... redistribution of proteins that are anchored in membranes through other types of hydrophobic moieties....

  10. 33 CFR 401.14 - Anchor marking buoys.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Anchor marking buoys. 401.14 Section 401.14 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT CORPORATION, DEPARTMENT OF TRANSPORTATION SEAWAY REGULATIONS AND RULES Regulations Condition of Vessels § 401.14 Anchor marking buoys. A highly visible anchor marking...

  11. Students' Anchoring Predisposition: An Illustration from Spring Training Baseball

    Science.gov (United States)

    Mohrweis, Lawrence C.

    2014-01-01

    The anchoring tendency results when decision makers anchor on initial values and then make final assessments that are adjusted insufficiently away from the initial values. The professional literature recognizes that auditors often risk falling into the judgment trap of anchoring and adjusting (Ranzilla et al., 2011). Students may also be unaware…

  12. Comparison of zero-profile anchored spacer versus plate-cage construct in treatment of cervical spondylosis with regard to clinical outcomes and incidence of major complications: a meta-analysis

    Directory of Open Access Journals (Sweden)

    Liu WJ

    2015-09-01

    Full Text Available Weijun Liu,1,* Ling Hu,2,* Junwen Wang,1 Ming Liu,1 Xiaomei Wang3 1Department of Orthopedics, Pu Ai Hospital, Affiliated to Tongji Medical College, Huazhong University of Science and Technology, 2Department of Anesthesiology, Tianyou Hospital, Affiliated to Wuhan University of Science and Technology, 3Department of Biological Science and Technology, Wuhan Bioengineering Institute, Wuhan, People’s Republic of China *These authors contributed equally to this work Purpose: Meta-analysis was conducted to evaluate whether zero-profile anchored spacer (Zero-P could reduce complication rates, while maintaining similar clinical outcomes compared to plate-cage construct (PCC in the treatment of cervical spondylosis. Methods: All prospective and retrospective comparative studies published up to May 2015 that compared the clinical outcomes of Zero-P versus PCC in the treatment of cervical spondylosis were acquired by a comprehensive search in PubMed and EMBASE. Exclusion criteria were non-English studies, noncomparative studies, hybrid surgeries, revision surgeries, and surgeries with less than a 12-month follow-up period. The main end points including Japanese Orthopedic Association (JOA and Neck Disability Index (NDI scores, cervical lordosis, fusion rate, subsidence, and dysphagia were analyzed. All studies were analyzed with the RevMan 5.2.0 software. Publication biases of main results were examined using Stata 12.0. Results: A total of 12 studies were included in the meta-analysis. No statistical difference was observed with regard to preoperative or postoperative JOA and NDI scores, cervical lordosis, and fusion rate. The Zero-P group had a higher subsidence rate than the PCC group (P<0.05, risk difference =0.13, 95% confidence interval [CI] 0.00–0.26. However, the Zero-P group had a significantly lower postoperative dysphagia rate than the PCC group within the first 2 weeks (P<0.05, odds ratio [OR] =0.64, 95% CI 0.45–0.91, at the 6th month [P

  13. Bearing Capacity Analyses for the Great Belt East Bridge Anchor Blocks

    DEFF Research Database (Denmark)

    Sørensen, Carsten Steen; Clausen, Carl J. Frimann; Andersen, Henrik

    1993-01-01

    This paper presents a comparison between different methods of bearing capacity analyses: Upper Bound Method. Limit Equilibrium Analysis and Finite Element Analysis. For the Great Belt East Bridge anchor blocks it was concluded that these methods of calculation agree within 5%. However, for cases...

  14. The role of voltage-gated calcium channels in neurotransmitter phenotype specification: Coexpression and functional analysis in Xenopus laevis.

    Science.gov (United States)

    Lewis, Brittany B; Miller, Lauren E; Herbst, Wendy A; Saha, Margaret S

    2014-08-01

    Calcium activity has been implicated in many neurodevelopmental events, including the specification of neurotransmitter phenotypes. Higher levels of calcium activity lead to an increased number of inhibitory neural phenotypes, whereas lower levels of calcium activity lead to excitatory neural phenotypes. Voltage-gated calcium channels (VGCCs) allow for rapid calcium entry and are expressed during early neural stages, making them likely regulators of activity-dependent neurotransmitter phenotype specification. To test this hypothesis, multiplex fluorescent in situ hybridization was used to characterize the coexpression of eight VGCC α1 subunits with the excitatory and inhibitory neural markers xVGlut1 and xVIAAT in Xenopus laevis embryos. VGCC coexpression was higher with xVGlut1 than xVIAAT, especially in the hindbrain, spinal cord, and cranial nerves. Calcium activity was also analyzed on a single-cell level, and spike frequency was correlated with the expression of VGCC α1 subunits in cell culture. Cells expressing Cav 2.1 and Cav 2.2 displayed increased calcium spiking compared with cells not expressing this marker. The VGCC antagonist diltiazem and agonist (-)BayK 8644 were used to manipulate calcium activity. Diltiazem exposure increased the number of glutamatergic cells and decreased the number of γ-aminobutyric acid (GABA)ergic cells, whereas (-)BayK 8644 exposure decreased the number of glutamatergic cells without having an effect on the number of GABAergic cells. Given that the expression and functional manipulation of VGCCs are correlated with neurotransmitter phenotype in some, but not all, experiments, VGCCs likely act in combination with a variety of other signaling factors to determine neuronal phenotype specification. PMID:24477801

  15. Geodesic defect anchoring on nematic shells.

    Science.gov (United States)

    Mirantsev, Leonid V; Sonnet, André M; Virga, Epifanio G

    2012-08-01

    Nematic shells are colloidal particles coated with nematic liquid crystal molecules, which may freely glide and rotate on the colloid's surface while keeping their long axis on the local tangent plane. Molecular dynamics simulations on a nanoscopic spherical shell indicate that under appropriate adhesion conditions for the molecules on the equator, the equilibrium nematic texture exhibits at each pole a pair of +1/2 defects so close to one another to be treated as one +1 defect. Spirals connect the polar defects, though the continuum limit of the interaction potential would not feature any elastic anisotropy. A molecular averaging justifies an anchoring defect energy that feels the geodesics emanating from the defect. All our observations are explained by such a geodesic anchoring, which vanishes on flat manifolds. PMID:23005713

  16. Anchoring in a novel bimanual coordination pattern.

    Science.gov (United States)

    Maslovat, Dana; Lam, Melanie Y; Brunke, Kirstin M; Chua, Romeo; Franks, Ian M

    2009-02-01

    Anchoring in cyclical movements has been defined as regions of reduced spatial or temporal variability [Beek, P. J. (1989). Juggling dynamics. PhD thesis. Amsterdam: Free University Press] that are typically found at movement reversal points. For in-phase and anti-phase movements, synchronizing reversal points with a metronome pulse has resulted in decreased anchor point variability and increased pattern stability [Byblow, W. D., Carson, R. G., & Goodman, D. (1994). Expressions of asymmetries and anchoring in bimanual coordination. Human Movement Science, 13, 3-28; Fink, P. W., Foo, P., Jirsa, V. K., & Kelso, J. A. S. (2000). Local and global stabilization of coordination by sensory information. Experimental Brain Research, 134, 9-20]. The present experiment examined anchoring during acquisition, retention, and transfer of a 90 degrees phase-offset continuous bimanual coordination pattern (whereby the right limb lags the left limb by one quarter cycle), involving horizontal flexion about the elbow. Three metronome synchronization strategies were imposed: participants either synchronized maximal flexion of the right arm (i.e., single metronome), both flexion and extension of the right arm (i.e., double metronome within-limb), or flexion of each arm (i.e., double metronome between-limb) to an auditory metronome. In contrast to simpler in-phase and anti-phase movements, synchronization of additional reversal points to the metronome did not reduce reversal point variability or increase pattern stability. Furthermore, practicing under different metronome synchronization strategies did not appear to have a significant effect on the rate of acquisition of the pattern. PMID:18842313

  17. Molecular Conductance: Chemical Trends of Anchoring Groups

    OpenAIRE

    Ke, San-Huang; Baranger, Harold U.; Yang, Weitao

    2004-01-01

    Combining density functional theory calculations for molecular electronic structure with a Green function method for electron transport, we calculate from first principles the molecular conductance of benzene connected to two Au leads through different anchoring atoms -- S, Se, and Te. The relaxed atomic structure of the contact, different lead orientations, and different adsorption sites are fully considered. We find that the molecule-lead coupling, electron transfer, and conductance all dep...

  18. Anchor Toolkit - a secure mobile agent system

    OpenAIRE

    Mudumbai, Srilekha S.; Johnston, William; Essiari, Abdelilah

    2008-01-01

    Mobile agent technology facilitates intelligent operation in software systems with less human interaction. Major challenge to deployment of mobile agents include secure transmission of agents and preventing unauthorized access to resources between interacting systems, as either hosts, or agents, or both can act maliciously. The Anchor toolkit, designed by LBNL, handles the transmission and secure management of mobile agents in a heterogeneous distributed computing environment. It provide...

  19. Anchoring Heuristic and the Equity Premium Puzzle

    OpenAIRE

    Siddiqi, Hammad

    2015-01-01

    What happens when the anchoring and adjustment heuristic of Tversky and Kahneman (1974) is incorporated in the standard consumption-based capital asset pricing model (CCAPM)? The surprising finding is that it not only resolves the high equity-premium and low risk-free rate puzzles with a low risk-aversion coefficient, but also provides a unified framework for understanding countercyclical equity-premium, excess volatility, size, value, and momentum effects, and abnormal returns and volatiliti...

  20. Maleimide-functionalized lipids that anchor polypeptides to lipid bilayers and membranes.

    Science.gov (United States)

    Elliott, J T; Prestwich, G D

    2000-01-01

    Two maleimide-containing diacylglycerol derivatives were synthesized to permit the anchoring of short peptides and longer polypeptides to phospholipid bilayers and membranes. The maleimide was introduced at the site normally occupied by a phospholipid headgroup. The first lipid, the dipalmitoyl ester of 1-maleimido-2,3-propanediol, was developed as a membrane anchor for extracellular domains of transmembrane proteins. The second anchoring lipid, in which the 3-position contained a 6-aminohexanoate, was designed for convenient modification with amine-reactive reporter groups. Specifically, the NBD fluorophore, 7-nitrobenzo-2-oxa-1, 3-diazole-aminohexanoic-N-hydroxysuccinimide ester, was attached to give an fluorescent anchoring reagent. Next, these reagents were applied to the anchoring of a C-terminally cysteamine-modified 8 kDa polypeptide that comprises the extracellular N-terminal domain of the human thrombin receptor, a transmembrane protease-activated receptor (PAR-1). Gel filtration and fluorescence analysis showed that the fluorescent lipopolypeptide spontaneously inserted into preformed phospholipid vesicles, but it did not insert into whole cell membranes. In contrast, the dipalmitoyl derivative could only be reconstituted into artificial membranes by mixing the lipopolypeptide and phospholipid before vesicle formation. These results suggest that biophysical interactions governing the lipopolypeptide insertion into artificial and cellular membranes may differ. The thiol-reactive lipidating reagents should be valuable materials for studying the structure and function of peptides and polypeptides at phospholipid bilayer surfaces. PMID:11087332

  1. Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics

    DEFF Research Database (Denmark)

    de Angelis, Martin Hrabě; Nicholson, George; Selloum, Mohammed;

    2015-01-01

    The function of the majority of genes in the mouse and human genomes remains unknown. The mouse embryonic stem cell knockout resource provides a basis for the characterization of relationships between genes and phenotypes. The EUMODIC consortium developed and validated robust methodologies for th...

  2. GRASP: analysis of genotype–phenotype results from 1390 genome-wide association studies and corresponding open access database

    OpenAIRE

    Leslie, Richard; O’Donnell, Christopher J.; Johnson, Andrew D.

    2014-01-01

    Summary: We created a deeply extracted and annotated database of genome-wide association studies (GWAS) results. GRASP v1.0 contains >6.2 million SNP-phenotype association from among 1390 GWAS studies. We re-annotated GWAS results with 16 annotation sources including some rarely compared to GWAS results (e.g. RNAediting sites, lincRNAs, PTMs).

  3. Robotic Ankle for Omnidirectional Rock Anchors

    Science.gov (United States)

    Parness, Aaron; Frost, Matthew; Thatte, Nitish

    2013-01-01

    Future robotic exploration of near-Earth asteroids and the vertical and inverted rock walls of lava caves and cliff faces on Mars and other planetary bodies would require a method of gripping their rocky surfaces to allow mobility without gravitational assistance. In order to successfully navigate this terrain and drill for samples, the grippers must be able to produce anchoring forces in excess of 100 N. Additionally, the grippers must be able to support the inertial forces of a moving robot, as well gravitational forces for demonstrations on Earth. One possible solution would be to use microspine arrays to anchor to rock surfaces and provide the necessary load-bearing abilities for robotic exploration of asteroids. Microspine arrays comprise dozens of small steel hooks supported on individual suspensions. When these arrays are dragged along a rock surface, the steel hooks engage with asperities and holes on the surface. The suspensions allow for individual hooks to engage with asperities while the remaining hooks continue to drag along the surface. This ensures that the maximum possible number of hooks engage with the surface, thereby increasing the load-bearing abilities of the gripper. Using the microspine array grippers described above as the end-effectors of a robot would allow it to traverse terrain previously unreachable by traditional wheeled robots. Furthermore, microspine-gripping robots that can perch on cliffs or rocky walls could enable a new class of persistent surveillance devices for military applications. In order to interface these microspine grippers with a legged robot, an ankle is needed that can robotically actuate the gripper, as well as allow it to conform to the large-scale irregularities in the rock. The anchor serves three main purposes: deploy and release the anchor, conform to roughness or misalignment with the surface, and cancel out any moments about the anchor that could cause unintentional detachment. The ankle design contains a

  4. Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems.

    Science.gov (United States)

    Zhou, Lu; Lei, Xiang-He; Bochner, Barry R; Wanner, Barry L

    2003-08-01

    Two-component systems are the most common mechanism of transmembrane signal transduction in bacteria. A typical system consists of a histidine kinase and a partner response regulator. The histidine kinase senses an environmental signal, which it transmits to its partner response regulator via a series of autophosphorylation, phosphotransfer, and dephosphorylation reactions. Much work has been done on particular systems, including several systems with regulatory roles in cellular physiology, communication, development, and, in the case of bacterial pathogens, the expression of genes important for virulence. We used two methods to investigate two-component regulatory systems in Escherichia coli K-12. First, we systematically constructed mutants with deletions of all two-component systems by using a now-standard technique of gene disruption (K. A. Datsenko and B. L. Wanner, Proc. Natl. Acad. Sci. USA 97:6640-6645, 2000). We then analyzed these deletion mutants with a new technology called Phenotype MicroArrays, which permits assays of nearly 2,000 growth phenotypes simultaneously. In this study we tested 100 mutants, including mutants with individual deletions of all two-component systems and several related genes, including creBC-regulated genes (cbrA and cbrBC), phoBR-regulated genes (phoA, phoH, phnCDEFGHIJKLMNOP, psiE, and ugpBAECQ), csgD, luxS, and rpoS. The results of this battery of nearly 200,000 tests provided a wealth of new information concerning many of these systems. Of 37 different two-component mutants, 22 showed altered phenotypes. Many phenotypes were expected, and several new phenotypes were also revealed. The results are discussed in terms of the biological roles and other information concerning these systems, including DNA microarray data for a large number of the same mutants. Other mutational effects are also discussed. PMID:12897016

  5. New Insights into Genotype-phenotype Correlations in Chinese Facioscapulohumeral Muscular Dystrophy: A Retrospective Analysis of 178 Patients

    Institute of Scientific and Technical Information of China (English)

    Feng Lin; Zhi-Qiang Wang; Min-Ting Lin; Shen-Xing Murong; Ning Wang

    2015-01-01

    Background:Facioscapulohumeral muscular dystrophy (FSHD),a common autosomal dominant muscular disorder,is caused by contraction of the D4Z4 repeats on 4q35.The complicated genotype-phenotype correlation among different ethnic population remains a controversial subject.We aimed to refine this correlation in order to provide new information for genetic counseling.Methods:Here,a cohort of 136 Chinese families including 178 affected individuals and 137 unaffected members were investigated.Genetic analyses were performed using the pl3E-11,4qA and 4qB probes after pulsed field gel electrophoresis separation and southern blotting.A 10-grade FSHD clinical severity scale was adopted for clinical assessment.The genotype-phenotype correlation was established by linear regression analyses.Results:We observed a roughly inversed correlation between the short EcoRI fragment size and age-corrected clinical severity score in 154 symptomatic patients (P < 0.05).Compared to male patients,a significant higher proportion of females in both asymptomatic carriers and severe patients showed larger variation in the size of short EcoRI fragment.A high incidence (19/42,45.2%) of asymptomatic (or minimally affected) carriers was found in familial members.Conclusions:Although the number of D4Z4 repeats is known as one of the critical influences on genotype-phenotype correlation,a majority of phenotypic spectrum was still incompatible with their heterozygous contraction of the D4Z4 repeat,especial in female cases.Our results suggest that there are multi-factors synergistically modulating the phenotypic expression.

  6. Analysis of cell cycle-related proteins in gastric intramucosal differentiated-type cancers based on mucin phenotypes: a novel hypothesis of early gastric carcinogenesis based on mucin phenotype

    Directory of Open Access Journals (Sweden)

    Matsushita Hiroo

    2010-06-01

    Full Text Available Abstract Background Abnormalities of cell cycle regulators are common features in human cancers, and several of these factors are associated with the early development of gastric cancers. However, recent studies have shown that gastric cancer tumorigenesis was characterized by mucin expression. Thus, expression patterns of cell cycle-related proteins were investigated in the early phase of differentiated-type gastric cancers to ascertain any mechanistic relationships with mucin phenotypes. Methods Immunostaining for Cyclins D1, A, E, and p21, p27, p53 and β-catenin was used to examine impairments of the cell cycle in 190 gastric intramucosal differentiated-type cancers. Mucin phenotypes were determined by the expressions of MUC5AC, MUC6, MUC2 and CD10. A Ki-67 positive rate (PR was also examined. Results Overexpressions of p53, cyclin D1 and cyclin A were significantly more frequent in a gastric phenotype than an intestinal phenotype. Cyclin A was overexpressed in a mixed phenotype compared with an intestinal phenotype, while p27 overexpression was more frequent in an intestinal phenotype than in a mixed phenotype. Reduction of p21 was a common feature of the gastric intramucosal differentiated-type cancers examined. Conclusions Our results suggest that the levels of some cell cycle regulators appear to be associated with mucin phenotypes of early gastric differentiated-type cancers.

  7. Prediction of the pull-out strength of chemical anchors in natural stone

    Directory of Open Access Journals (Sweden)

    L. Contrafatto

    2014-07-01

    Full Text Available The applicability of some numerical models for the prediction of the failure mechanism and of the bearing capacity of post-installed threaded rods chemically anchored in basalt, sandstone and limestone is investigated, as well as the reliability of theoretical formulations conceived for concrete. The numerical predictions, performed by means of engineering structural analysis software and advanced numerical codes, are compared with the results of an experimental research related to chemical anchors in natural stone. The minimum embedment depth for such fastening system is identified.

  8. Fixation of a human rib by an intramedullary telescoping splint anchored by bone cement.

    Science.gov (United States)

    Liovic, Petar; Šutalo, Ilija D; Marasco, Silvana F

    2016-09-01

    A novel concept for rib fixation is presented that involves the use of a bioresorbable polymer intramedullary telescoping splint. Bone cement is used to anchor each end of the splint inside the medullary canal on each side of the fracture site. In this manner, rib fixation is achieved without fixation device protrusion from the rib, making the splint completely intramedullary. Finite element analysis is used to demonstrate that such a splint/cement composite can preserve rib fixation subjected to cough-intensity force loadings. Computational fluid dynamics and porcine rib experiments were used to study the anchor formation process required to complete the fixation. PMID:26733094

  9. Scanning electron microscopy as a tool for the analysis of colony architecture produced by phenotypic switching of a human pathogenic yeast Candida tropicalis

    International Nuclear Information System (INIS)

    Candida tropicalis has been identified as one of the most prevalent pathogenic yeast species of the Candida-non-albicans group. Phenotypic switching is a biological phenomenon related to the occurrence of spontaneous emergence of colonies with different morphologies that provides variability within colonizing populations in order to adapt to different environments. Currently, studies of the microstructure of switching variant colonies are not subject of extensive research. SEM analysis was used to verify the architecture of whole Candida colonies. The strain 49/07 exhibited a hemispherical shape character, while the strain 335/07 showed a volcano shape with mycelated-edge colony. The ring switch variant is characterized by a highly wrinkled centre and an irregular periphery. The rough phenotype exhibited a three-dimensional architecture and was characterized by the presence of deep central and peripheral depressions areas. The ultrastructural analysis also allowed the observation of the arrangement of individual cells within the colonies. The whole smooth colony consisted entirely of yeast cells. Differently, aerial filaments were found all around the colony periphery of the volcano shape colony. For this colony type the mycelated-edge consisted mainly of hyphae, although yeast cells are also seen. The ring and rough colonies phenotypes comprised mainly yeast cells with the presence of extracellular material connecting neighbouring cells. This study has shown that SEM can be used effectively to examine the microarchitecture of colonies morphotypes of the yeast C. tropicalis and further our understanding of switching event in this pathogen.

  10. Capturing phenotypes for precision medicine.

    Science.gov (United States)

    Robinson, Peter N; Mungall, Christopher J; Haendel, Melissa

    2015-10-01

    Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers that will be displayed alongside the manuscript, thereby providing a foundation for ontology-based indexing and searching of articles that contain descriptions of phenotypic abnormalities-an important step toward improving the ability of researchers and clinicians to get biomedical information that is critical for clinical care or translational research. PMID:27148566

  11. Dynamic performance of concrete undercut anchors for Nuclear Power Plants

    International Nuclear Information System (INIS)

    Graphical abstract: - Highlights: • Behavior of undercut anchors under dynamic actions simulating earthquakes. • First high frequency load and crack cycling tests on installed concrete anchors ever. • Comprehensive review of anchor qualification for Nuclear Power Plants. - Abstract: Post-installed anchors are widely used for structural and nonstructural connections to concrete. In many countries, concrete anchors used for Nuclear Power Plants have to be qualified to ensure reliable behavior even under extreme conditions. The tests required for qualification of concrete anchors are carried out at quasi-static loading rates well below the rates to be expected for dynamic actions deriving from earthquakes, airplane impacts or explosions. To investigate potentially beneficial effects of high loading rates and cycling frequencies, performance tests on installed undercut anchors were conducted. After introductory notes on anchor technology and a comprehensive literature review, this paper discusses the qualification of anchors for Nuclear Power Plants and the testing carried out to quantify experimentally the effects of dynamic actions on the load–displacement behavior of undercut anchors

  12. Automatic Spectroscopic Data Categorization by Clustering Analysis (ASCLAN): A Data-Driven Approach for Distinguishing Discriminatory Metabolites for Phenotypic Subclasses.

    Science.gov (United States)

    Zou, Xin; Holmes, Elaine; Nicholson, Jeremy K; Loo, Ruey Leng

    2016-06-01

    We propose a novel data-driven approach aiming to reliably distinguish discriminatory metabolites from nondiscriminatory metabolites for a given spectroscopic data set containing two biological phenotypic subclasses. The automatic spectroscopic data categorization by clustering analysis (ASCLAN) algorithm aims to categorize spectral variables within a data set into three clusters corresponding to noise, nondiscriminatory and discriminatory metabolites regions. This is achieved by clustering each spectral variable based on the r(2) value representing the loading weight of each spectral variable as extracted from a orthogonal partial least-squares discriminant (OPLS-DA) model of the data set. The variables are ranked according to r(2) values and a series of principal component analysis (PCA) models are then built for subsets of these spectral data corresponding to ranges of r(2) values. The Q(2)X value for each PCA model is extracted. K-means clustering is then applied to the Q(2)X values to generate two clusters based on minimum Euclidean distance criterion. The cluster consisting of lower Q(2)X values is deemed devoid of metabolic information (noise), while the cluster consists of higher Q(2)X values is then further subclustered into two groups based on the r(2) values. We considered the cluster with high Q(2)X but low r(2) values as nondiscriminatory, while the cluster with high Q(2)X and r(2) values as discriminatory variables. The boundaries between these three clusters of spectral variables, on the basis of the r(2) values were considered as the cut off values for defining the noise, nondiscriminatory and discriminatory variables. We evaluated the ASCLAN algorithm using six simulated (1)H NMR spectroscopic data sets representing small, medium and large data sets (N = 50, 500, and 1000 samples per group, respectively), each with a reduced and full resolution set of variables (0.005 and 0.0005 ppm, respectively). ASCLAN correctly identified all discriminatory

  13. Comparative Proteome Analysis of the Tuberous Roots of Six Cassava (Manihot esculenta) Varieties Reveals Proteins Related to Phenotypic Traits.

    Science.gov (United States)

    Schmitz, Gabriela Justamante Händel; de Magalhães Andrade, Jonathan; Valle, Teresa Losada; Labate, Carlos Alberto; do Nascimento, João Roberto Oliveira

    2016-04-27

    Cassava (Manihot esculenta Crantz) is a staple food and an important source of starch, and the attributes of its tuberous root largely depend on the variety. The proteome of cassava has been investigated; however, to date, no study has focused on varieties that reveal the molecular basis of phenotypical characteristics. Therefore, we aimed to compare the proteome of the tuberous roots of six cassava varieties that differed in carbohydrates, carotenoids, and resistance to diseases, among other attributes. Two-dimensional gels showed 146 differential spots between the varieties, and the functional roles of some differential proteins were correlated to phenotypic characteristics of the varieties, such as the amount of carbohydrates or carotenoids and the resistance to biotic or abiotic stresses. The results obtained here highlight elements that might help to direct the improvement of new cultivars of cassava, which is an economically and socially relevant crop worldwide. PMID:26982619

  14. Longitudinal analysis of the behavioral phenotype in a novel transgenic rat model of early stages of Alzheimer's disease

    OpenAIRE

    Galeano, Pablo; Martino Adami, Pamela V.; Do Carmo, Sonia; Blanco, Eduardo; Rotondaro, Cecilia; Capani, Francisco; Castaño, Eduardo M; Cuello, A. Claudio; Morelli, Laura

    2014-01-01

    Intraneuronal accumulation of amyloid β (iAβ) has been linked to mild cognitive impairment that may precede Alzheimer's disease (AD) onset. This neuropathological trait was recently mimicked in a novel animal model of AD, the hemizygous transgenic McGill-R-Thy1-APP (Tg(+/-)) rat. The characterization of the behavioral phenotypes in this animal model could provide a baseline of efficacy for earlier therapeutic interventions. The aim of the present study was to undertake a longitudinal study of...

  15. Tumor and reproductive traits are linked by RNA metabolism genes in the mouse ovary: a transcriptome-phenotype association analysis

    OpenAIRE

    Sharp John J; Cherry James M; Zhang Gen-Mu; Owens Garrison A; Urzúa Ulises; Munroe David J

    2010-01-01

    Abstract Background The link between reproductive life history and incidence of ovarian tumors is well known. Periods of reduced ovulations may confer protection against ovarian cancer. Using phenotypic data available for mouse, a possible association between the ovarian transcriptome, reproductive records and spontaneous ovarian tumor rates was investigated in four mouse inbred strains. NIA15k-DNA microarrays were employed to obtain expression profiles of BalbC, C57BL6, FVB and SWR adult ova...

  16. The Andean Adaptive Toolkit to Counteract High Altitude Maladaptation: Genome-Wide and Phenotypic Analysis of the Collas

    OpenAIRE

    Eichstaedt, Christina A; Antão, Tiago; Pagani, Luca; Cardona, Alexia; Kivisild, Toomas; Mormina, Maru

    2014-01-01

    During their migrations out of Africa, humans successfully colonised and adapted to a wide range of habitats, including extreme high altitude environments, where reduced atmospheric oxygen (hypoxia) imposes a number of physiological challenges. This study evaluates genetic and phenotypic variation in the Colla population living in the Argentinean Andes above 3500 m and compares it to the nearby lowland Wichí group in an attempt to pinpoint evolutionary mechanisms underlying adaptation to high...

  17. Anchoring of FRET Sensors-A Requirement for Spatiotemporal Resolution.

    Science.gov (United States)

    Ivanova, Elena V; Figueroa, Ricardo A; Gatsinzi, Tom; Hallberg, Einar; Iverfeldt, Kerstin

    2016-01-01

    FRET biosensors have become a routine tool for investigating mechanisms and components of cell signaling. Strategies for improving them for particular applications are continuously sought. One important aspect to consider when designing FRET probes is the dynamic distribution and propagation of signals within living cells. We have addressed this issue by directly comparing an anchored (taFS) to a non-anchored (naFS) cleavable FRET sensor. We chose a microtubule-associated protein tau as an anchor, as microtubules are abundant throughout the cytosol of cells. We show that tau-anchored FRET sensors are concentrated at the cytoskeleton and enriched in the neurite-like processes of cells, providing high intensity of the total signal. In addition, anchoring limits the diffusion of the sensor, enabling spatiotemporally resolved monitoring of subcellular variations in enzyme activity. Thus, anchoring is an important aspect to consider when designing FRET sensors for deeper understanding of cell signaling. PMID:27196902

  18. Adsorption phenomena and anchoring energy in nematic liquid crystals

    CERN Document Server

    Barbero, Giovanni

    2005-01-01

    Despite the large quantity of phenomenological information concerning the bulk properties of nematic phase liquid crystals, little is understood about the origin of the surface energy, particularly the surface, interfacial, and anchoring properties of liquid crystals that affect the performance of liquid crystal devices. Self-contained and unique, Adsorption Phenomena and Anchoring Energy in Nematic Liquid Crystals provides an account of new and established results spanning three decades of research into the problems of anchoring energy and adsorption phenomena in liquid crystals.The book contains a detailed discussion of the origin and possible sources of anchoring energy in nematic liquid crystals, emphasizing the dielectric contribution to the anchoring energy in particular. Beginning with fundamental surface and anchoring properties of liquid crystals and the definition of the nematic phase, the authors explain how selective ion adsorption, dielectric energy density, thickness dependence, and bias voltage...

  19. Anchor Toolkit - a secure mobile agent system

    Energy Technology Data Exchange (ETDEWEB)

    Mudumbai, Srilekha S.; Johnston, William; Essiari, Abdelilah

    1999-05-19

    Mobile agent technology facilitates intelligent operation insoftware systems with less human interaction. Major challenge todeployment of mobile agents include secure transmission of agents andpreventing unauthorized access to resources between interacting systems,as either hosts, or agents, or both can act maliciously. The Anchortoolkit, designed by LBNL, handles the transmission and secure managementof mobile agents in a heterogeneous distributed computing environment. Itprovides users with the option of incorporating their security managers.This paper concentrates on the architecture, features, access control anddeployment of Anchor toolkit. Application of this toolkit in a securedistributed CVS environment is discussed as a case study.

  20. Starting point anchoring effects in choice experiments

    DEFF Research Database (Denmark)

    Ladenburg, Jacob; Olsen, Søren Bøye

    Anchoring is acknowledged as a potential source of considerable bias in Dichotomous Choice Contingent Valuation studies. Recently, another stated preference method known as Choice Experiments has gained in popularity as well as the number of applied studies. However, as the elicitation of...... subjectivity in the present study is gender dependent, pointing towards, that female respondents are prone to be affected by the price levels employed. Male respondents, on the other hand, are not sensitive towards these prices levels. Overall, this implicates that female respondents, when employing a low...

  1. The bone-anchored hearing aid

    DEFF Research Database (Denmark)

    Foghsgaard, Søren

    2014-01-01

    The bone-anchored hearing aid (Baha) was introduced in 1977 by Tjellström and colleagues and has now been used clinically for over 30 years. Generally, the outcomes are good, and several studies have shown improved audiological- and quality of life outcomes. The principle of the Baha is, that sound...... vibrations are led directly to the inner ear via the mastoid bone, bypassing the middle ear. This is achieved via an osseointegrated implant and a skin-penetrating abutment. Studies report high success rates and a majority of complications as typically minor in nature....

  2. Nominal Anchor Exchange Rate Policies as a Domestic Distortion

    OpenAIRE

    Anne O. Krueger

    1997-01-01

    This paper analyzes a nominal anchor exchange rate policy as a domestic distortion, in the tradition of international trade theory. It is shown that, in addition to the problems of sustainability and exit pinpointed in the exchange rate literature, a nominal anchor exchange rate policy, while in force, drives a wedge between the domestic and the international intertemporal marginal rates of substitution. The welfare cost of the Mexican use of the nominal anchor exchange rate policy prior to D...

  3. The impact of anchoring bias in the UK equity market

    OpenAIRE

    Koskinen, Matti

    2013-01-01

    PURPOSE OF THE STUDY The purpose of this thesis is to study how the anchoring bias, a cognitive bias, affects equity analysts' forecasts and what kind of implications this bias has for investors and managers of listed companies in the UK stock market. I test whether industry median forecast earnings per share can work as an anchor when analysts are estimating companies' future earnings and how this potential anchoring affects forecast errors, future stock returns, earnings surprises and s...

  4. Degradation theories of concrete and development of a new deviatoric model in incremental tangent formulation: limit analysis applied to case of anchor bolts embedded in concrete; Theorie de degradation du beton et developpement d'un nouveau modele d'endommagement en formulation incrementale tangente: calcul a la rupture applique au cas des chevilles de fixation ancrees dans le beton

    Energy Technology Data Exchange (ETDEWEB)

    Ung Quoc, H

    2003-12-15

    This research is achieved in the general framework of the study of the concrete behaviour. It has for objective the development of a new behaviour model satisfying to the particular requirements for an industrial exploitation. After the analysis of different existent models, a first development has concerned models based on the smeared crack theory. A new formulation of the theory permitted to overcome the stress locking problem. However, the analysis showed the persistence of some limits inert to this approach in spite of this improvement. Then, an analysis of the physical mechanisms of the concrete degradation has been achieved and permitted to develop the new damage model MODEV. The general formulation of this model is based on the theory of the thermodynamics and applied to the case of the heterogeneous and brittle materials. The MODEV model considers two damage mechanisms: extension and sliding. The model considers also that the relative tangent displacement between microcracks lips is responsible of the strain irreversibility. Thus, the rate of inelastic strain becomes function of the damage and the heterogeneity index of the material. The unilateral effect is taken in account as an elastic hardening or softening process according to re-closing or reopening of cracks. The model is written within the framework of non standard generalised materials in incremental tangent formulation and implemented in the general finite element code SYMPHONIE. The validation of the model has been achieved on the basis of several tests issued from the literature. The second part of this research has concerned the development of the CHEVILAB software. This simulation tool based on the limit analysis approach permit the evaluation of the ultimate load capacity of anchors bolts. The kinematics approach of the limit analysis has been adapted to the problem of anchors while considering several specific failure mechanisms. This approach has been validated then by comparison with the

  5. Finding our way through phenotypes.

    Directory of Open Access Journals (Sweden)

    Andrew R Deans

    2015-01-01

    Full Text Available 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.

  6. Finding our way through phenotypes.

    Science.gov (United States)

    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

  7. Illusion of Relevance: Anchoring in Economic and Financial Knowledge

    Directory of Open Access Journals (Sweden)

    Andrey Kudryavtse

    2010-12-01

    Full Text Available Contemporary research documents various psychological aspects of economic thought and decision-making. The main goal of our study is to analyze the role of the anchoring (bias(Tversky and Kahneman, 1974 in perceiving economic and financial information, and, in particular, the effect of perceived relevance of the anchors on the degree of the bias. Anchoring bias refers to people's tendency to form their estimates for different categories, starting from a particular available, and often irrelevant, value and insufficiently adjusting their final judgments from this starting value. We carry out an experiment involving a group of MBA students, asking them to recall a number of recent economic and financial indicators (stock and bond market index returns, rates of inflation, currency exchange rates, etc., with half of the participants receiving actual information about some unrelated indicators (anchors, before answering the questions. We document that significant anchoring bias is exhibited, on average, for each of our experimental questions and by vast majority of the participants, the degree of the bias being higher for women and older participants. Furthermore, in the context of the effect of anchors' perceived relevance, we find that people exhibit significantly stronger bias in cases when the anchor is presented as a similar category. Our findings indicate that if, at least at the first glance, an anchor bears some similarity to the target question, then the resulting answer may be more assimilated towards the anchor

  8. Molecular analysis of chromosome 21 in a patient with a phenotype of down syndrome and apparently normal karyotype

    Energy Technology Data Exchange (ETDEWEB)

    Ahlbom, B.E.; Wadelius, C.; Zech, L.; Anneren, G. [Uppsala Univ. (Sweden)] [and others

    1996-06-28

    Down syndrome (DS) is caused in most cases by the presence of an extra chromosome 21. It has been shown that the DS phenotype is produced by duplication of only a small part of the long arm of chromosome 21, the 21q22 region, including and distal to locus D21S55. We present molecular investigations on a woman with clinically typical DS but apparently normal chromosomes. Her parents were consanguineous and she had a sister with a DS phenotype, who died at the age of 15 days. Repeated cytogenetic investigations (G-banding and high resolution banding) on the patient and her parents showed apparently normal chromosomes. Autoradiographs of quantitative Southern blots of DNAs from the patient, her parents, trisomy 21 patients, and normal controls were analyzed after hybridization with unique DNA sequences regionally mapped on chromosome 21. Sequences D21S59, D21S1, D21S11, D21S8, D21S17, D21S55, ERG, D21S15, D21S112, and COL6A1 were all found in two copies. Fluorescent in situ hybridization with a chromosome 21-specific genomic library showed no abnormalities and only two copies of chromosome 21 were detected. Nineteen markers from the critical region studied with polymerase chain reaction amplification of di- and tetranucleotide repeats did not indicate any partial trisomy 21. From his study we conclude that the patient does not have any partial submicroscopic trisomy for any segment of chromosome 21. It seems reasonable to assume that she suffers from an autosomal recessive disorder which is phenotypically indistinguishable from DS. 23 refs., 6 figs., 3 tabs.

  9. Temporal discrimination thresholds in adult-onset primary torsion dystonia: an analysis by task type and by dystonia phenotype.

    LENUS (Irish Health Repository)

    Bradley, D

    2012-01-01

    Adult-onset primary torsion dystonia (AOPTD) is an autosomal dominant disorder with markedly reduced penetrance. Sensory abnormalities are present in AOPTD and also in unaffected relatives, possibly indicating non-manifesting gene carriage (acting as an endophenotype). The temporal discrimination threshold (TDT) is the shortest time interval at which two stimuli are detected to be asynchronous. We aimed to compare the sensitivity and specificity of three different TDT tasks (visual, tactile and mixed\\/visual-tactile). We also aimed to examine the sensitivity of TDTs in different AOPTD phenotypes. To examine tasks, we tested TDT in 41 patients and 51 controls using visual (2 lights), tactile (non-painful electrical stimulation) and mixed (1 light, 1 electrical) stimuli. To investigate phenotypes, we examined 71 AOPTD patients (37 cervical dystonia, 14 writer\\'s cramp, 9 blepharospasm, 11 spasmodic dysphonia) and 8 musician\\'s dystonia patients. The upper limit of normal was defined as control mean +2.5 SD. In dystonia patients, the visual task detected abnormalities in 35\\/41 (85%), the tactile task in 35\\/41 (85%) and the mixed task in 26\\/41 (63%); the mixed task was less sensitive than the other two (p = 0.04). Specificity was 100% for the visual and tactile tasks. Abnormal TDTs were found in 36 of 37 (97.3%) cervical dystonia, 12 of 14 (85.7%) writer\\'s cramp, 8 of 9 (88.8%) blepharospasm, 10 of 11 (90.1%) spasmodic dysphonia patients and 5 of 8 (62.5%) musicians. The visual and tactile tasks were found to be more sensitive than the mixed task. Temporal discrimination threshold results were comparable across common adult-onset primary torsion dystonia phenotypes, with lower sensitivity in the musicians.

  10. Detection of AmpC beta-lactamase in Escherichia coli: comparison of three phenotypic confirmation assays and genetic analysis

    OpenAIRE

    Peter-Getzlaff, S.; Polsfuss, S; Poledica, M.; Hombach, M; Giger, J; Böttger, E.C.; R. Zbinden; Bloemberg, G V

    2011-01-01

    Two mechanisms account for AmpC activity in Escherichia coli, namely, mutations in the ampC promoter and attenuator regions resulting in ampC overexpression and acquisition of plasmid-carried ampC genes. In this study, we analyzed 51 clinical E. coli isolates with reduced susceptibility to amoxicillin-clavulanic acid, piperacillin-tazobactam, or extended-spectrum cephalosporins for the presence of AmpC production. Three phenotypic AmpC confirmation assays (cefoxitin-cloxacillin disk diffusion...

  11. Global Phenotype Screening and Transcript Analysis Outlines the Inhibitory Mode(s) of Action of Two Amphibian-Derived, α-Helical, Cationic Peptides on Saccharomyces cerevisiae▿ †

    OpenAIRE

    Morton, C Oliver; Hayes, Andrew; Wilson, Michael; Rash, Bharat M.; Oliver, Stephen G.; Coote, Peter

    2007-01-01

    Dermaseptin S3(1-16) [DsS3(1-16)] and magainin 2 (Mag 2) are two unrelated, amphibian-derived cationic peptides that adopt an α-helical structure within microbial membranes and have been proposed to kill target organisms via membrane disruption. Using a combination of global deletion mutant library phenotypic screening, expression profiling, and physical techniques, we have carried out a comprehensive in vitro analysis of the inhibitory action of these two peptides on the model fungus Sacchar...

  12. Dynamic calculation model and seismic response for frame supporting structure with prestressed anchors

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A dynamic calculation model of frame supporting structures with prestressed anchors for the slope stability is proposed. The frame and soil are closely contacted in the role of prestressed anchors and they cannot be separated along the whole slope. The lateral displacement of frame and soil is nearly in phase. The movement characteristic satisfies the theory of elastic foundation beam. The frame is treated with elastic foundation beam in this model. The influence of prestressed anchors is simplified as linear spring and damped system related with velocity. Under the condition of horizontal earthquake excitation, the equation of vibration response is established by using the model of dynamic Winkler beam and the analytical solutions are obtained for simple harmonic vibration. This method is applied to a case record for illustration of its capability, in order to verify the method, 3D nonlinear FEM (ADINA) is used to analyze the seismic performance of this case, the comparative results show that the design and the analysis are safe and credible by using the proposed method. The calculation model provides a new way for earthquake analysis and seismic design of slope stability supported by frame structure with prestressed anchors.

  13. A locus-specific database for mutations in GDAP1 allows analysis of genotype-phenotype correlations in Charcot-Marie-Tooth diseases type 4A and 2K

    Directory of Open Access Journals (Sweden)

    Cassereau Julien

    2011-12-01

    Full Text Available Abstract Background The ganglioside-induced differentiation-associated protein 1 gene (GDAP1, which is involved in the Charcot-Marie-Tooth disease (CMT, the most commonly inherited peripheral neuropathy, encodes a protein anchored to the mitochondrial outer membrane. The phenotypic presentations of patients carrying GDAP1 mutations are heterogeneous, making it difficult to determine genotype-phenotype correlations, since the majority of the mutations have been found in only a few unrelated patients. Locus-specific databases (LSDB established in the framework of the Human Variome Project provide powerful tools for the investigation of such rare diseases. Methods and Results We report the development of a publicly accessible LSDB for the GDAP1 gene. The GDAP1 LSDB has adopted the Leiden Open-source Variation Database (LOVD software platform. This database, which now contains 57 unique variants reported in 179 cases of CMT, offers a detailed description of the molecular, clinical and electrophysiological data of the patients. The usefulness of the GDAP1 database is illustrated by the finding that GDAP1 mutations lead to primary axonal damage in CMT, with secondary demyelination in the more severe cases of the disease. Conclusion Findings of this nature should lead to a better understanding of the pathophysiology of CMT. Finally, the GDAP1 LSDB, which is part of the mitodyn.org portal of databases of genes incriminated in disorders involving mitochondrial dynamics and bioenergetics, should yield new insights into mitochondrial diseases.

  14. Photoacoustic analysis of the solubilization kinetics of pulmonary secretions from cystic fibrosis patients - secretor and non-secretor phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Barja, P R; Coelho, C C; Paiva, R F [Research and Development Institute, UNIVAP, Av. Shishima Hifumi 2911, Sao Jose dos Campos, SP (Brazil); Barboza, M A; Matos, L C; Matos, C C B [Faculty of Medicine of Sao Jose do Rio Preto (FAMERP), Sao Jose do Rio Preto, SP (Brazil); Oliveira, L V F, E-mail: barja@univap.b [Rehabilitation Sciences Master' s Program, Nove de Julho University (UNINOVE), Sao Paulo, SP (Brazil)

    2010-03-01

    Cystic fibrosis (CF) is an autosomal recessive inherited disease that increases viscoelasticity of pulmonary secretions. Affected patients are required to use therapeutic aerosols continuously. The expression of ABH glycoconjugates in exocrine secretions determines the nature of part of the carbohydrates present in these secretions, allowing the classification of individuals into the so-called 'secretor' and 'non secretor' phenotypes. The aim of this work was to employ photoacoustic (PA) measurements to monitor the solubilization kinetics of pulmonary secretions from CF patients, analyzing the influence of the secretor status in the solubilization kinetics of samples nebulized with different therapeutic aerosols. Sputum samples were obtained by spontaneous expectoration from positive and negative secretor CF patients. Each sample was nebulized with i) tobramycin, ii) alpha dornase, and iii) N-acetylcysteine in a PA cell; fitting of the data with the Boltzmann equation led to the determination of t{sub 0} (typical interaction time) and {Delta}t (solubilization interval) for each curve. Differences between the secretor and non-secretor phenotypes were statistically significant in the groups for tobramycin and alpha dornase, but not for N-acetylcysteine. Results show that the secretor status influences the solubilization of pulmonary mucus of CF patients nebulized with tobramycin and alpha dornase.

  15. Development of a porcine skeletal muscle cDNA microarray: analysis of differential transcript expression in phenotypically distinct muscles

    Directory of Open Access Journals (Sweden)

    Stear Michael

    2003-03-01

    Full Text Available Abstract Background Microarray profiling has the potential to illuminate the molecular processes that govern the phenotypic characteristics of porcine skeletal muscles, such as hypertrophy or atrophy, and the expression of specific fibre types. This information is not only important for understanding basic muscle biology but also provides underpinning knowledge for enhancing the efficiency of livestock production. Results We report on the de novo development of a composite skeletal muscle cDNA microarray, comprising 5500 clones from two developmentally distinct cDNA libraries (longissimus dorsi of a 50-day porcine foetus and the gastrocnemius of a 3-day-old pig. Clones selected for the microarray assembly were of low to moderate abundance, as indicated by colony hybridisation. We profiled the differential expression of genes between the psoas (red muscle and the longissimus dorsi (white muscle, by co-hybridisation of Cy3 and Cy5 labelled cDNA derived from these two muscles. Results from seven microarray slides (replicates correctly identified genes that were expected to be differentially expressed, as well as a number of novel candidate regulatory genes. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray. Conclusion We have developed a porcine skeletal muscle cDNA microarray and have identified a number of candidate genes that could be involved in muscle phenotype determination, including several members of the casein kinase 2 signalling pathway.

  16. Growth Curve Models for the Analysis of Phenotype Arrays for a Systems Biology Overview of Yersinia pestis

    Energy Technology Data Exchange (ETDEWEB)

    Fodor, I K; Holtz-Morris, A E; McCutchen-Maloney, S L

    2005-09-08

    The Phenotype MicroArray technology of Biolog, Inc. (Hayward, CA) measures the respiration of cells as a function of time in thousands of microwells simultaneously, and thus provides a high-throughput means of studying cellular phenotypes. The microwells contain compounds involved in a number of biochemical pathways, as well as chemicals that test the sensitivity of cells against antibiotics and stress. While the PM experimental workflow is completely automated, statistical methods to analyze and interpret the data are lagging behind. To take full advantage of the technology, it is essential to develop efficient analytical methods to quantify the information in the complex datasets resulting from PM experiments. We propose the use of statistical growth-curve models to rigorously quantify observed differences in PM experiments, in the context of the growth and metabolism of Yersinia pestis cells grown under different physiological conditions. The information from PM experiments complement genomic and proteomic results and can be used to identify gene function and in drug development. Successful coupling of phenomics results with genomics and proteomics will lead to an unprecedented ability to characterize bacterial function at a systems biology level.

  17. Photoacoustic analysis of the solubilization kinetics of pulmonary secretions from cystic fibrosis patients - secretor and non-secretor phenotypes

    Science.gov (United States)

    Barja, P. R.; Coelho, C. C.; Paiva, R. F.; Barboza, M. A.; Matos, L. C.; Matos, C. C. B.; Oliveira, L. V. F.

    2010-03-01

    Cystic fibrosis (CF) is an autosomal recessive inherited disease that increases viscoelasticity of pulmonary secretions. Affected patients are required to use therapeutic aerosols continuously. The expression of ABH glycoconjugates in exocrine secretions determines the nature of part of the carbohydrates present in these secretions, allowing the classification of individuals into the so-called "secretor" and "non secretor" phenotypes. The aim of this work was to employ photoacoustic (PA) measurements to monitor the solubilization kinetics of pulmonary secretions from CF patients, analyzing the influence of the secretor status in the solubilization kinetics of samples nebulized with different therapeutic aerosols. Sputum samples were obtained by spontaneous expectoration from positive and negative secretor CF patients. Each sample was nebulized with i) tobramycin, ii) alpha dornase, and iii) N-acetylcysteine in a PA cell; fitting of the data with the Boltzmann equation led to the determination of t0 (typical interaction time) and Δt (solubilization interval) for each curve. Differences between the secretor and non-secretor phenotypes were statistically significant in the groups for tobramycin and alpha dornase, but not for N-acetylcysteine. Results show that the secretor status influences the solubilization of pulmonary mucus of CF patients nebulized with tobramycin and alpha dornase.

  18. Photoacoustic analysis of the solubilization kinetics of pulmonary secretions from cystic fibrosis patients - secretor and non-secretor phenotypes

    International Nuclear Information System (INIS)

    Cystic fibrosis (CF) is an autosomal recessive inherited disease that increases viscoelasticity of pulmonary secretions. Affected patients are required to use therapeutic aerosols continuously. The expression of ABH glycoconjugates in exocrine secretions determines the nature of part of the carbohydrates present in these secretions, allowing the classification of individuals into the so-called 'secretor' and 'non secretor' phenotypes. The aim of this work was to employ photoacoustic (PA) measurements to monitor the solubilization kinetics of pulmonary secretions from CF patients, analyzing the influence of the secretor status in the solubilization kinetics of samples nebulized with different therapeutic aerosols. Sputum samples were obtained by spontaneous expectoration from positive and negative secretor CF patients. Each sample was nebulized with i) tobramycin, ii) alpha dornase, and iii) N-acetylcysteine in a PA cell; fitting of the data with the Boltzmann equation led to the determination of t0 (typical interaction time) and Δt (solubilization interval) for each curve. Differences between the secretor and non-secretor phenotypes were statistically significant in the groups for tobramycin and alpha dornase, but not for N-acetylcysteine. Results show that the secretor status influences the solubilization of pulmonary mucus of CF patients nebulized with tobramycin and alpha dornase.

  19. Optimizing the phenotyping of rodent ASD models: Enrichment analysis of mouse and human neurobiological phenotypes associated with high-risk autism genes identifies morphological, electrophysiological, neurological, and behavioral features.

    OpenAIRE

    Buxbaum Joseph D; Betancur Catalina; Bozdagi Ozlem; Dorr Nate P; Elder Gregory A; Hof Patrick R

    2012-01-01

    Abstract Background There is interest in defining mouse neurobiological phenotypes useful for studying autism spectrum disorders (ASD) in both forward and reverse genetic approaches. A recurrent focus has been on high-order behavioral analyses, including learning and memory paradigms and social paradigms. However, well-studied mouse models, including for example Fmr1 knockout mice, do not show dramatic deficits in such high-order phenotypes, raising a question as to what constitutes useful ph...

  20. Stable isotope phenotyping via cluster analysis of NanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment

    Directory of Open Access Journals (Sweden)

    Katherine S Dawson

    2016-05-01

    Full Text Available Stable isotope probing (SIP is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS, allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S and elemental ratio (C/CN and S/CN profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs into 5 distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.

  1. Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment

    Science.gov (United States)

    Dawson, Katherine S.; Scheller, Silvan; Dillon, Jesse G.; Orphan, Victoria J.

    2016-01-01

    Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs) into five distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.

  2. 30 CFR 57.9311 - Anchoring stationary sizing devices.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Anchoring stationary sizing devices. 57.9311 Section 57.9311 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND... Dumping Sites § 57.9311 Anchoring stationary sizing devices. Grizzlies and other stationary sizing...

  3. 30 CFR 56.9311 - Anchoring stationary sizing devices.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Anchoring stationary sizing devices. 56.9311 Section 56.9311 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND... Dumping Sites § 56.9311 Anchoring stationary sizing devices. Grizzlies and other stationary sizing...

  4. Understanding Rasch Measurement: Partial Credit Model and Pivot Anchoring.

    Science.gov (United States)

    Bode, Rita K.

    2001-01-01

    Describes the Rasch measurement partial credit model, what it is, how it differs from other Rasch models, and when and how to use it. Also describes the calibration of instruments with increasingly complex items. Explains pivot anchoring and illustrates its use and describes the effect of pivot anchoring on step calibrations, item hierarchy, and…

  5. Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population

    Directory of Open Access Journals (Sweden)

    Walsh Tom

    2006-01-01

    Full Text Available Abstract Recessively inherited phenotypes are frequent in the Palestinian population, as the result of a historical tradition of marriages within extended kindreds, particularly in isolated villages. In order to characterise the genetics of inherited hearing loss in this population, we worked with West Bank schools for the deaf to identify children with prelingual, bilateral, severe to profound hearing loss not attributable to infection, trauma or other known environmental exposure. Of 156 families enrolled, hearing loss in 17 families (11 per cent was due to mutations in GJB2 (connexin 26, a smaller fraction of GJB2-associated deafness than in other populations. In order to estimate how many different genes might be responsible for hearing loss in this population, we evaluated ten families for linkage to all 36 known human autosomal deafness-related genes, fully sequencing hearing-related genes at any linked sites in informative relatives. Four families harboured four novel alleles of TMPRSS3 (988ΔA = 352stop, otoancorin (1067A >T = D356V and pendrin (716T > A = V239D and 1001G > T = 346stop. In each family, all affected individuals were homozygous for the critical mutation. Each allele was specific to one or a few families in the cohort; none were widespread. Since epidemiological tests of association of mutations with deafness were not feasible for such rare alleles, we used functional and bioinformatics approaches to evaluate their consequences. In six other families, hearing loss was not linked to any known gene, suggesting that these families harbour novel genes responsible for this phenotype. We conclude that inherited hearing loss is highly heterogeneous in this population, with most extended families acting as genetic isolates in this context. We also conclude that the same genes are responsible for hearing loss in this population as elsewhere, so that gene discovery in these families informs the genetics of hearing loss worldwide.

  6. Breaking anchored droplets in a microfluidic Hele-Shaw cell

    CERN Document Server

    Amselem, Gabriel; Gallaire, François; Baroud, Charles N

    2015-01-01

    We study microfluidic self digitization in Hele-Shaw cells using pancake droplets anchored to surface tension traps. We show that above a critical flow rate, large anchored droplets break up to form two daughter droplets, one of which remains in the anchor. Below the critical flow velocity for breakup the shape of the anchored drop is given by an elastica equation that depends on the capillary number of the outer fluid. As the velocity crosses the critical value, the equation stops admitting a solution that satisfies the boundary conditions; the drop breaks up in spite of the neck still having finite width. A similar breaking event also takes place between the holes of an array of anchors, which we use to produce a 2D array of stationary drops in situ.

  7. Operative treatment of acromioclavicular joint dislocation: a new technique with suture anchors

    Directory of Open Access Journals (Sweden)

    Zhang Jingwei

    2014-07-01

    Full Text Available 【Abstract】Objective: To evaluate clinical outcome of suture anchors in strengthening both acromioclavicular and coracoclavicular ligaments in the surgical treatment of acromioclavicular joint dislocation. Methods: Twenty-eight patients with acute traumatic Rockwood III, IV and V dislocations of the acromioclavicular joint surgically treated at our institute between October 2010 and January 2012 were recruited. All patients underwent open reduction combined with suture anchors. Function was evaluated using the ConstantMurley shoulder score. Clinical and radiographic shoulder ratings were evaluated using Taft criteria at 3, 6 and 12 months. Results:Two cases with fixation loosening were not included in final statistical analysis. Other patients obtained full joint reposition on immediate postoperative radiographs. Follow-up was performed with an average of 15.6 months (range, 12-19. After early range of motion exercises, 96.2% of the patients (25/26 could abduct and elevate their shoulders more than 90 degrees within postoperative 3 months. There was no infection. Average Constant-Murley score was 96.3 points (range, 94-100 and mean Taft shoulder rating was 10.7 points (range, 8-12 at 12 months. Conclusion: The suture anchor is a relatively simple technique and can avoid screw removal which is helpful in reconstructing both acromioclavicular and coracoclavicular ligaments in acute traumatic acromioclavicular joint dislocation. Key words: Acromioclavicular joint; Dislocations; Surgery; Suture anchors

  8. Analysis of genetic distance between Peruvian Alpaca (Vicugna Pacos showing two distinct fleece phenotypes, Suri and Huacaya, by means of microsatellite markers

    Directory of Open Access Journals (Sweden)

    Carlo Renieri

    2011-10-01

    Full Text Available Two coat phenotypes exist in Alpaca, Huacaya and Suri. The two coats show different fleece structure, textile characteristics and prices on the market. Although present scientific knowledge suggests a simple genetic model of inheritance, there is a tendency to manage and consider the two phenotypes as two different breeds. A 13 microsatellite panel was used in this study to assess genetic distance between Suri and Huacaya alpacas in a sample of non-related animals from two phenotypically pure flocks at the Illpa-Puno experimental station in Quimsachata, Peru. The animals are part of a germplasm established approximately 20 years ago and have been bred separately according to their coat type since then. Genetic variability parameters were also calculated. The data were statistically analyzed using the software Genalex 6.3, Phylip 3.69 and Fstat 2.9.3.2. The sample was tested for Hardy-Weinberg equilibrium (HWE and after strict Bonferroni correction only one locus (LCA37 showed deviation from equilibrium (Ploci associations showed significant disequilibrium. Observed heterozygosis (Ho= 0.766; SE=0.044, expected heterozygosis (He=0.769; SE=0.033, number of alleles (Na=9.667, SE=0.772 and Fixation index (F=0.004; SE=0.036 are comparable to data from previous studies. Measures of genetic distance were 0.06 for Nei’s and 0.03 for Cavalli-Sforza’s. The analysis of molecular variance reported no existing variance between populations. Considering the origin of the animals, their post domestication evolution and the reproductive practices in place, the results do not show genetic differentiation between the two populations for the studied loci.

  9. Comparative analysis of gingival phenotype in animal and human experimental models using optical coherence tomography in a non-invasive approach

    Science.gov (United States)

    Mota, Cláudia C. B. O.; Fernandes, Luana O.; Melo, Luciana S. A.; Feitosa, Daniela S.; Cimões, Renata; Gomes, Anderson S. L.

    2015-06-01

    Imaging methods are widely used in diagnostic and among the diversity of modalities, optical coherence tomography (OCT) is nowadays commercially available and considered the most innovative technique used for imaging applications, in both medical and non-medical applications. In this study, we exploit the OCT technique in the oral cavity for identification and differentiation between free and attached gingiva, as well as determining the gingival phenotype, an important factor to determination of periodontal prognosis in patients. For the animal studies, five porcine jaws were analyzed using a Swept Source SS-OCT system operating at 1325nm and stereomicroscope, as gold pattern. The SSOCT at 1325nm was chosen due to the longer central wavelength, that allows to deeper penetration imaging, and the faster image acquisition, an essential factor for clinical setting. For the patient studies, a total of 30 males and female were examined using the SS-OCT at 1325nm and computer controlled periodontal probing. 2D and 3D images of tooth/gingiva interface were performed, and quantitative measurements of the gingival sulcus could be noninvasively obtained. Through the image analysis of the animals jaws, it was possible to quantify the free gingiva and the attached gingiva, the calculus deposition over teeth surface and also the subgingival calculus. For the patient's studies, we demonstrated that the gingival phenotype could be measured without the periodontal probe introduction at the gingival sulcus, confirming that OCT can be potentially useful in clinic for direct observation and quantification of gingival phenotype in a non-invasive approach.

  10. Analysis and test research on mechanical performance for steel-concrete composite anchor structure of cable- stayed bridge pylon%斜拉桥索塔钢混组合锚固结构力学性能分析和试验研究

    Institute of Scientific and Technical Information of China (English)

    俞先林; 张奇志

    2009-01-01

    采用自平衡式加载反力架对苏通大桥索塔钢混组合锚固结构进行足尺模型试验,观测模型的应力、裂缝分布和变形情况.采用ANSYS有限元软件对模型进行数值分析.试验和分析结果表明:索孔出口面上方的混凝土表面最易出现裂缝;钢混结合面表现为弯剪共同作用的特性,顶推荷载水平分力主要由钢锚箱结构承担,混凝土亦承担一小部分,竖向分力可全部由剪力钉传递给混凝土承受;单节段模型的有限元计算结果比多节段模型的计算结果偏大,用单节段模型试验结果代表实桥受力状况偏于安全.%Full-scale model test on steel-concrete composite anchor structure for pylon of sutong bridge was done by a self-balanced loading reaction frame to observe the stress,crack distribution and deformation of the model. Also numerical simulation was conducted by the finite element software ANSYS. The results of analysis and test show that cracks most easily occur on concrete surface at upperpart of cable anchor duct export. The steel-concrete contacting surface undertakes mutual action of bending moment and shear. Most horizontal component of pushing load is balanced by steel anchor box and only a small part by concrete,while vertical component of pushing load is all transferred to concrete by shear studs. Since numerical simulation data from single segment model test is larger than that from multi-segmental model test,it's conservative to adopt single segment mode test data instead of actual bridge stress status.

  11. Sustained productivity in recombinant Chinese Hamster Ovary (CHO) cell lines: proteome analysis of the molecular basis for a process-related phenotype

    LENUS (Irish Health Repository)

    Meleady, Paula

    2011-07-24

    Abstract Background The ability of mammalian cell lines to sustain cell specific productivity (Qp) over the full duration of bioprocess culture is a highly desirable phenotype, but the molecular basis for sustainable productivity has not been previously investigated in detail. In order to identify proteins that may be associated with a sustained productivity phenotype, we have conducted a proteomic profiling analysis of two matched pairs of monoclonal antibody-producing Chinese hamster ovary (CHO) cell lines that differ in their ability to sustain productivity over a 10 day fed-batch culture. Results Proteomic profiling of inherent differences between the two sets of comparators using 2D-DIGE (Difference Gel Electrophoresis) and LC-MS\\/MS resulted in the identification of 89 distinct differentially expressed proteins. Overlap comparisons between the two sets of cell line pairs identified 12 proteins (AKRIB8, ANXA1, ANXA4, EIF3I, G6PD, HSPA8, HSP90B1, HSPD1, NUDC, PGAM1, RUVBL1 and CNN3) that were differentially expressed in the same direction. Conclusion These proteins may have an important role in sustaining high productivity of recombinant protein over the duration of a fed-batch bioprocess culture. It is possible that many of these proteins could be useful for future approaches to successfully manipulate or engineer CHO cells in order to sustain productivity of recombinant protein.

  12. HDR syndrome: a follow-up genotype-phenotype analysis of a de novo missense Thr272Ile mutation in exon 4 of GATA3.

    Science.gov (United States)

    Gomes, T S; Gortner, L; Dockter, G; Leitner, D; Thakker, R V; Rohrer, T

    2012-11-01

    Hypoparathyroidism, sensorineural deafness and renal dysplasia (HDR) syndrome (MIM 146255) is a rare autosomal dominant disorder caused by mutations in the gene encoding GATA3, a dual zinc-finger transcription factor involved in vertebrate embryonic development. In this clinical case study we report on a follow-up of a phenotype associated with a GATA3 mutation. HDR syndrome was clinically diagnosed at age of 1.5 years in a boy with a de novo heterozygous missense (c.815C→T) mutation, Thr272Ile, in exon 4 of the GATA3 gene. Both parents were negative for Thr272Ile.At age of 17 months, the patient had a weight of 10.7, a body length of 78 cm, and a head circumference of 47.5 cm. By the age of 7 years, growth is age-appropriate, severe bilateral hearing loss (dB 60) was corrected by hearing aids. However, cognitive development (auditory sensory me-mory and language abilities) is at the lower ends of the test scores.In conclusion, a mildly impaired clinical course was achieved by the age of 7 years in a patient with HDR syndrome; this report adds to the body of data on genotype-phenotype analysis in HDR syndrome. · PMID:23203342

  13. Allogeneic hematopoietic stem cell transplantation for adult patients with mixed phenotype acute leukemia: results of a matched-pair analysis.

    Science.gov (United States)

    Shimizu, Hiroaki; Saitoh, Takayuki; Machida, Shinichiro; Kako, Shinichi; Doki, Noriko; Mori, Takehiko; Sakura, Toru; Kanda, Yoshinobu; Kanamori, Heiwa; Miyawaki, Shuichi; Okamoto, Shinichiro

    2015-11-01

    Adult patients with mixed phenotype acute leukemia (MPAL) have a poor prognosis, and the therapeutic role of allogeneic stem cell transplantation (allo-SCT) for MPAL remains to be elucidated. Thus, we retrospectively assessed the efficacy of allo-SCT for MPAL. Eighteen patients with MPAL were identified from the transplant outcome database of Kanto Study Group for Cell Therapy (KSGCT). We also selected 215 patients with acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) as control cohorts using an optimal matching method. The 5-yr overall survival (OS) rate of patients with MPAL was 48.1%, and patients in remission at the time of transplant showed significantly better survival than those not in remission (5-yr OS: 71.8% vs. 0%, P = 0.001). No significant differences were seen in OS when stratifying patients according to immunophenotype, cytogenetic abnormalities, or the type of induction therapy. The 5-yr OS rate of patients with MPAL was not significantly different compared with AML control patients (48.1% vs. 48.1%; P = 0.855) or ALL control patients (48.1% vs. 37.8%; P = 0.426). These results suggested that allo-SCT is an effective treatment for MPAL, especially early in the disease course, and innovative transplant approaches are warranted to improve the transplant outcome of patients with MPAL who are not in remission. PMID:25605541

  14. Measurement of the risk for substance use disorders: phenotypic and genetic analysis of an index of common liability.

    Science.gov (United States)

    Vanyukov, Michael M; Kirisci, Levent; Moss, Lisa; Tarter, Ralph E; Reynolds, Maureen D; Maher, Brion S; Kirillova, Galina P; Ridenour, Ty; Clark, Duncan B

    2009-05-01

    The inability to quantify the risk for disorders, such as substance use disorders (SUD), hinders etiology research and development of targeted intervention. Based on the concept of common transmissible liability to SUD related to illicit drugs, a method enabling quantification of this latent trait has been developed, utilizing high-risk design and item response theory. This study examined properties of a SUD transmissible liability index (TLI) derived using this method. Sons of males with or without SUD were studied longitudinally from preadolescence to young adulthood. The properties of TLI, including its psychometric characteristics, longitudinal risk assessment and ethnic variation, were examined. A pilot twin study was conducted to analyze the composition of TLI's phenotypic variance. The data suggest that TLI has concurrent, incremental, predictive and discriminant validity, as well as ethnic differences. The data suggest a high heritability of the index in males. The results suggest applicability of the method for genetic and other etiology-related research, and for evaluation of individual risk. PMID:19377872

  15. Array-based FMR1 sequencing and deletion analysis in patients with a fragile X syndrome-like phenotype.

    Directory of Open Access Journals (Sweden)

    Stephen C Collins

    Full Text Available BACKGROUND: Fragile X syndrome (FXS is caused by loss of function mutations in the FMR1 gene. Trinucleotide CGG-repeat expansions, resulting in FMR1 gene silencing, are the most common mutations observed at this locus. Even though the repeat expansion mutation is a functional null mutation, few conventional mutations have been identified at this locus, largely due to the clinical laboratory focus on the repeat tract. METHODOLOGY/PRINCIPAL FINDINGS: To more thoroughly evaluate the frequency of conventional mutations in FXS-like patients, we used an array-based method to sequence FMR1 in 51 unrelated males exhibiting several features characteristic of FXS but with normal CGG-repeat tracts of FMR1. One patient was identified with a deletion in FMR1, but none of the patients were found to have other conventional mutations. CONCLUSIONS/SIGNIFICANCE: These data suggest that missense mutations in FMR1 are not a common cause of the FXS phenotype in patients who have normal-length CGG-repeat tracts. However, screening for small deletions of FMR1 may be of clinically utility.

  16. 自锚式悬索桥钢混组合主梁施工预拱度分析%Construction pre-camber analysis on steel-concrete composite beam of self-anchored suspension bridge

    Institute of Scientific and Technical Information of China (English)

    孙永明; 何晓东; 李文东

    2015-01-01

    对自锚式悬索桥的主梁施工方法进行了总结与评价,指出顶推施工的钢混组合主梁即使在均匀成桥吊杆的作用下,其成桥线形仍会在最大跨临时墩范围内发生局部凹陷的情况,而主梁施工预拱度也不能采取圆曲线或二次抛物线在各跨径内统一布置。鉴于此,本文基于有限单元法对一座自锚式悬索桥的施工过程进行正装模拟分析,计算结果表明,钢混组合梁截面性质改变是引起主梁成桥线形存在凹陷的本质原因;同时将成桥状态的主梁简化为承受竖向均布荷载和梁端集中水平力作用的三跨连续梁结构,并采用力法推导了各跨跨中位置竖向位移的简化计算公式;经算例验证,本文提出的施工预拱度简化计算公式能够有效计入主梁截面性质改变对主梁成桥线形的影响,较准确地预测出主梁累计竖向位移,其计算精度满足工程需求,而本文的研究结论将对同类桥型的主梁施工预拱度设计有较强的指导意义和参考价值。%This paper summarized and evaluated the main beam construction methods of self‐anchored suspension bridge ,pointed out that the main‐beam line would have a local depression between the largest span temporary pier when the steel‐concrete composite beams were constructed by the incremental launching construction method ,even if the main beam were withstand uniform boom‐forces ,moreover , the construction pre‐camber curve of the main girder could not be arranged as a circle curve or quadratic parabola within the entire span .In view of this ,the entire construction process of a self‐anchored suspen‐sion bridge was analyzed by the finite element method ,The results showed that the cross‐section proper‐ty changes of steel‐concrete composite beam were the nature reason of the local depression on the main‐beam line;T he completed main beam w as simplified into a three‐span continuous

  17. Phenotypic Diversity Analysis of Oil Palm (Elaeis guineensis Jacq.) Germplasm Cameroon Origin Based on Vegetative and Physiologic Characteristic

    OpenAIRE

    Lubis, Mahmud Irfan; Putri, Lollie Agustina P.; Purba, Abdul Razak

    2016-01-01

    Forty seven accessions as a part of of oil palm germplasm Cameroon Origin is planted at Adolina, an estate of PT Perkebunan Nusantara IV were evaluated for the variability based on their early vegetative and physiology characteristics. Mean data from these accessions were analysed by Multivarite Analysis consist of Principal Component Analysis (PCA), revealing their variability and distribution. Results demonstrated that principal component analysis obtained two main components to contribute ...

  18. Neurostimulation leads, intrathecal catheters and anchoring devices evolution

    Directory of Open Access Journals (Sweden)

    Laura Demartini

    2015-03-01

    Full Text Available Many scientific studies highlight the usefulness of spinal cord stimulation and intrathecal therapy for the management of chronic pain syndromes resistant to pharmacological or less invasive interventional therapies. One of the possible complications of these techniques, reported in literature, is migration of the lead or catheter; thus the use of an anchoring system is considered mandatory. Every company that produces devices for neurostimulation or neuromodulation provides various anchoring devices evolved over time. In the study, the authors discuss about the most common anchoring devices based on their clinical experience.

  19. Considerations on the design of through-wall anchors

    International Nuclear Information System (INIS)

    Connections to existing buildings are often the most difficult planning challenge for the realization of construction measures in case of piping system replacements in nuclear power plants. This is due to restricted space or limited load reserves of the building structure. Usually the realization of support connections to the existing buildings is achieved by anchor bolts. But in critical cases the preferred alternative solution uses through-wall anchors. Up to now uniform assessment thresholds are not available, no technical guidelines or regulations for construction variants exist. Through-wall anchors allow significantly higher load capacities for tensile and shear loads but require enhanced planning and realization efforts.

  20. Cellular analysis of the phenotypic correction of the genetically controlled low immune response to the polyproline determinant by macrophages

    International Nuclear Information System (INIS)

    SJL mice are high responders to the polyproline region of poly(Tyr,Glu)-polyPro-polyLys, (T,G)-Pro-L and of poly(Phe,Glu)-polyPro-polyLys, (Phe,G)-Pro-L, whereas DBA/l mice are the low responders to this moiety. The low responsiveness of DBA/l mice to polyproline could be enhanced by immunization with (T,G)-Pro-L 4 days after stimulation of peritoneal cells by thioglycolate. The same effect was observed when DBA/l mice were immunized with 107 syngeneic peritoneal exudate cells (PEC) preincubated in vitro with the immunogen. Similar treatments of SJL mice did not enhance the high response to polyproline, nor did it enhance low responses to other synthetic polypeptides tested. The enhancing effect of PEC on immunocompetent cells was established by transferring graded numbers of spleen cells together with 107 PEC into irradiated syngeneic DBA/l recipients. The effective cell type in the PEC was found to be the macrophage as the same results were observed with the adherent-cell population. Furthermore, the effect was not abolished after in vitro irradiation of PEC with 5000 R or by anti-theta treatment. In vivo irradiation of the PEC donors 2 days before the cells were harvested also did not influence the phenotypic correction of the low responsiveness. Transfer experiments in which graded inocula of either marrow cells or thymocytes from DBA/l donors were transferred into syngeneic recipients in the presence of an excess of the complementary cell type together with PEC indicated that the enhancing effect was reflected in the bone-marrow-cell population only

  1. Maxillary sinus perforation by orthodontic anchor screws.

    Science.gov (United States)

    Motoyoshi, Mitsuru; Sanuki-Suzuki, Rina; Uchida, Yasuki; Saiki, Akari; Shimizu, Noriyoshi

    2015-06-01

    To facilitate safe placement of orthodontic anchor screws (miniscrews), we investigated the frequency of maxillary sinus perforation after screw placement and the effect of sinus perforation on screw stability. Maxillary sinus perforations involving 82 miniscrews (diameter, 1.6 mm; length, 8 mm) were evaluated using cone-beam computed tomography. All miniscrews were placed in maxillary alveolar bone between the second premolar and first molar for anchorage for anterior retraction in patients undergoing first premolar extraction. The placement torque and screw mobility of each implant were determined using a torque tester and a Periotest device, and variability in these values in relation to sinus perforation was evaluated. Eight of the 82 miniscrews perforated the maxillary sinus. There was no case of sinusitis in patients with miniscrew perforation and no significant difference in screw mobility or placement torque between perforating and non-perforating miniscrews. The sinus floor was significantly thinner in perforated cases than in non-perforated cases. A sinus floor thickness of 6.0 mm or more is recommended in order to avoid miniscrew perforation of the maxillary sinus. PMID:26062857

  2. Anchored boundary conditions for locally isostatic networks

    Science.gov (United States)

    Theran, Louis; Nixon, Anthony; Ross, Elissa; Sadjadi, Mahdi; Servatius, Brigitte; Thorpe, M. F.

    2015-11-01

    Finite pieces of locally isostatic networks have a large number of floppy modes because of missing constraints at the surface. Here we show that by imposing suitable boundary conditions at the surface the network can be rendered effectively isostatic. We refer to these as anchored boundary conditions. An important example is formed by a two-dimensional network of corner sharing triangles, which is the focus of this paper. Another way of rendering such networks isostatic is by adding an external wire along which all unpinned vertices can slide (sliding boundary conditions). This approach also allows for the incorporation of boundaries associated with internal holes and complex sample geometries, which are illustrated with examples. The recent synthesis of bilayers of vitreous silica has provided impetus for this work. Experimental results from the imaging of finite pieces at the atomic level need such boundary conditions, if the observed structure is to be computer refined so that the interior atoms have the perception of being in an infinite isostatic environment.

  3. A biospectroscopic analysis of human prostate tissue obtained from different time periods points to a trans-generational alteration in spectral phenotype.

    Science.gov (United States)

    Theophilou, Georgios; Lima, Kássio M G; Briggs, Matthew; Martin-Hirsch, Pierre L; Stringfellow, Helen F; Martin, Francis L

    2015-01-01

    Prostate cancer is the most commonly-diagnosed malignancy in males worldwide; however, there is marked geographic variation in incidence that may be associated with a Westernised lifestyle. We set out to determine whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) or Raman spectroscopy combined with principal component analysis-linear discriminant analysis or variable selection techniques employing genetic algorithm or successive projection algorithm could be utilised to explore differences between prostate tissues from differing years. In total, 156 prostate tissues from transurethral resection of the prostate procedures for benign prostatic hyperplasia from 1983 to 2013 were collected. These were distributed to form seven categories: 1983-1984 (n = 20), 1988-1989 (n = 25), 1993-1994 (n = 21), 1998-1999 (n = 21), 2003-2004 (n = 21), 2008-2009 (n = 20) and 2012-2013 (n = 21). Ten-μm-thick tissue sections were floated onto Low-E (IR-reflective) slides for ATR-FTIR or Raman spectroscopy. The prostate tissue spectral phenotype altered in a temporal fashion. Examination of the two categories that are at least one generation (30 years) apart indicated highly-significant segregation, especially in spectral regions containing DNA and RNA bands (≈1,000-1,490 cm(-1)). This may point towards alterations that have occurred through genotoxicity or through epigenetic modifications. Immunohistochemical studies for global DNA methylation supported this. This study points to a trans-generational phenotypic change in human prostate. PMID:26310632

  4. Effect of GBA Mutations on Phenotype of Parkinson’s Disease: A Study on Chinese Population and a Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Yuan Zhang

    2015-01-01

    Full Text Available GBA has been identified as a genetic risk factor for PD. Whether the clinical manifestations of PD patients with or without GBA mutations are different has still not reached a consensus. We firstly detected the GBA mutation L444P in 1147 Chinese PD patients and simultaneously evaluated their corresponding clinical data. Then we compared the phenotypes between 646 PD patients with GBA mutations and 10344 PD patients without GBA mutations worldwide through meta-analysis. Through the method of meta-analysis, there was significant difference in age at onset (MD = −3.10 [95% CI: −4.88, −1.32], bradykinesia as an initial symptom (OR = 1.49 [95% CI: 1.15, 1.94], having family history (OR = 1.50 [95% CI: 1.18, 1.91], and dementia (OR = 3.21 [95% CI: 1.97, 5.24] during the comparison between PD patients with and without GBA mutations. While, in the aspect of tremor as an initial symptom (OR = 0.81 [95% CI: 0.64, 1.03], the severity of motor symptoms such as H-Y (MD = 0.06 [95% CI: −0.06, 0.17] and UPDRS-III (MD = 1.61 [95% CI: −0.65, 3.87] and having dyskinesia (OR = 1.60 [95% CI: 0.90, 2.84] during the comparison between the two groups revealed no statistical differences. Our results suggested that the phenotypes of PD patients with GBA mutations are different from GBA noncarriers.

  5. The Effect of the Trabecular Microstructure on the Pullout Strength of Suture Anchors

    OpenAIRE

    Yakacki, Christopher M.; Poukalova, Mariya; Guldberg, Robert E.; Lin, Angela; Saing, Minn; Gillogly, Scott; Gall, Ken

    2010-01-01

    This study investigates how the microstructural properties of trabecular bone affect suture anchor performance. Seven fresh-frozen humeri were tested for pullout strength with a 5 mm Arthrex Corkscrew in the greater tuberosity, lesser tuberosity, and humeral head. Micro-computed tomography analysis was performed in the three regions of interest directly adjacent to individual pullout experiments. The morphometric properties of bone mineral density (BMD), structural model index (SMI), trabecul...

  6. Identification of a lipid-anchored heparan sulfate proteoglycan in Schwann cells

    OpenAIRE

    1990-01-01

    Schwann cells synthesize both hydrophobic and peripheral cell surface heparan sulfate proteoglycans (HSPGs). Previous analysis of the kinetics of radiolabeling suggested the peripheral HSPGs are derived from the membrane-anchored forms (Carey, D., and D. Evans. 1989. J. Cell Biol. 108:1891-1897). Peripheral cell surface HSPGs were purified from phytic acid extracts of cultured neonatal rat sciatic nerve Schwann cells by anion exchange, gel filtration, and laminin-affinity chromatography. Appr...

  7. Longitudinal analysis of the behavioral phenotype in a novel transgenic rat model of early stages of Alzheimer’s disease

    Directory of Open Access Journals (Sweden)

    Pablo Galeano

    2014-09-01

    Full Text Available Intraneuronal accumulation of amyloid β (iAβ has been linked to mild cognitive impairment that may precede Alzheimer’s disease (AD onset. This neuropathological trait was recently mimicked in a novel animal model of AD, the hemizygous transgenic McGill-R-Thy1-APP (Tg+/- rat. The characterization of the behavioral phenotypes in this animal model could provide a baseline of efficacy for earlier therapeutic interventions. The aim of the present study was to undertake a longitudinal study of Aβ accumulation and a comprehensive behavioral evaluation of this transgenic rat model. We assessed exploratory activity, anxiety-related behaviors, recognition memory, working memory, spatial learning and reference memory at 3, 6 and 12 months of age. In parallel, we measured Aβ by ELISA, Western blots and semiquantitative immunohistochemistry in hippocampal samples. SDS-soluble Aβ peptide accumulated at low levels (~9 pg/mg without differences among ages. However, Western blots showed SDS-resistant Aβ oligomers (~30 kDa at 6 and 12 months, but not at 3 months. When compared to wild-type (WT, male Tg+/- rats exhibited a spatial reference memory deficit in the Morris Water Maze (MWM as early as 3 months of age, which persisted at 6 and 12 months. In addition, Tg+/- rats displayed a working memory impairment in the Y-maze and higher anxiety levels in the Open Field (OF at 6 and 12 months of age, but not at 3 months. Exploratory activity in the OF was similar to that of WT at all time points. Spatial learning in the MWM and the recognition memory, as assessed by the Novel Object Recognition Test, were unimpaired at any time point. The data from the present study demonstrate that the hemizygous transgenic McGill-R-Thy1-APP rat has a wide array of behavioral and cognitive impairments from young adulthood to middle-age. The low Aβ burden and early emotional and cognitive deficits in this transgenic rat model supports its potential use for drug discovery

  8. Analysis of common PTPN1 gene variants in type 2 diabetes, obesity and associated phenotypes in the French population

    Directory of Open Access Journals (Sweden)

    Marre Michel

    2006-05-01

    Full Text Available Abstract Background The protein tyrosine phosphatase-1B, a negative regulator for insulin and leptin signalling, potentially modulates glucose and energy homeostasis. PTP1B is encoded by the PTPN1 gene located on chromosome 20q13 showing linkage with type 2 diabetes (T2D in several populations. PTPN1 gene variants have been inconsistently associated with T2D, and the aim of our study was to investigate the effect of PTPN1 genetic variations on the risk of T2D, obesity and on the variability of metabolic phenotypes in the French population. Methods Fourteen single nucleotide polymorphisms (SNPs spanning the PTPN1 locus were selected from previous association reports and from HapMap linkage disequilibrium data. SNPs were evaluated for association with T2D in two case-control groups with 1227 cases and 1047 controls. Association with moderate and severe obesity was also tested in a case-control study design. Association with metabolic traits was evaluated in 736 normoglycaemic, non-obese subjects from a general population. Five SNPs showing a trend towards association with T2D, obesity or metabolic parameters were investigated for familial association. Results From 14 SNPs investigated, only SNP rs914458, located 10 kb downstream of the PTPN1 gene significantly associated with T2D (p = 0.02 under a dominant model; OR = 1.43 [1.06–1.94] in the combined sample set. SNP rs914458 also showed association with moderate obesity (allelic p = 0.04; OR = 1.2 [1.01–1.43]. When testing for association with metabolic traits, two strongly correlated SNPs, rs941798 and rs2426159, present multiple consistent associations. SNP rs2426159 exhibited evidence of association under a dominant model with glucose homeostasis related traits (p = 0.04 for fasting insulin and HOMA-B and with lipid markers (0.02 = p = 0.04. Moreover, risk allele homozygotes for this SNP had an increased systolic blood pressure (p = 0.03. No preferential transmission of alleles was observed

  9. Stone anchors from the Okhamandal region, Gujarat Coast, India

    Digital Repository Service at National Institute of Oceanography (India)

    Sundaresh; Gaur, A.S.; Gudigar, P.; Tripati, S.; Vora, K.H.; Bandodkar, S.N.

    Dwarka and Armada yielded a number of stone anchors which suggest that Okhamandal area was major concentration of maritime activities in Saurashtra region in the past. Among these three sites, Bet Dwarka has clear evidence on the settlement of Harappan...

  10. The utilisation of a career conversation framework based on Schein’s career anchors model

    Directory of Open Access Journals (Sweden)

    Magda Bezuidenhout

    2013-01-01

    Full Text Available Orientation: This  study  constituted  and  reported  on  the  outcomes  of  a  structured  career conversation  framework  based  on  Schein’s  eight  career  anchors  in  an  open  distance  and e-learning (ODeL university in South Africa.Research purpose: The purpose of the research was to report on the utilisation of a structured career conversation framework based on Schein’s career anchors model.Motivation for the study: The rationale for the study was the paucity of studies investigating career anchors in South Africa’s multicultural organisational context.Research design, approach and method: A quantitative approach was adopted in the study. The population consisted of 4200 employees at a university in South Africa. Statistical analysis was performed using one-way analysis of variance (ANOVA as well as a Scheffe post hoc test.Main  findings: The  findings  of  this  study  suggest  that  career  conversation  has  a  dynamic nature (i.e. it changes over a period of time. Consequently, career development interventions in the workplace need to approach the workforce holistically.Practical/managerial implications: The findings and results will assist managers, practitioners and  career  development  specialists  in  the  practical  implementation  of  the  career  anchor concept.Contribution/value-add: The career conversation framework based on Schein’s career anchors has expanded the existing theory to find the right balance between career conversations and career anchors to keep people motivated to perform optimally in an organisation.

  11. Liquid crystal director fluctuations and surface anchoring by molecular simulation

    OpenAIRE

    Andrienko, D.; Germano, G; Allen, M. P.

    2002-01-01

    We propose a simple and reliable method to measure the liquid crystal surface anchoring strength by molecular simulation. The method is based on the measurement of the long-range fluctuation modes of the director in confined geometry. As an example, molecular simulations of a liquid crystal in slab geometry between parallel walls with homeotropic anchoring have been carried out using the Monte Carlo technique. By studying different slab thicknesses, we are able to calculate separately the pos...

  12. Neurostimulation leads, intrathecal catheters and anchoring devices evolution

    OpenAIRE

    Laura Demartini; Gianluca Conversa; Luciana Armiento; Lucia Angelini; Cesare Bonezzi

    2015-01-01

    Many scientific studies highlight the usefulness of spinal cord stimulation and intrathecal therapy for the management of chronic pain syndromes resistant to pharmacological or less invasive interventional therapies. One of the possible complications of these techniques, reported in literature, is migration of the lead or catheter; thus the use of an anchoring system is considered mandatory. Every company that produces devices for neurostimulation or neuromodulation provides various anchoring...

  13. Monetary sterilization and dual nominal anchors: some Caribbean examples

    OpenAIRE

    Khemraj, Tarron; Pasha, Sukrishnalall

    2011-01-01

    This paper notes that a high sterilization coefficient plus a de facto pegged exchange rate indicates the existence of dual nominal anchors. The econometric evidence presented shows that several Caribbean economies with fixed exchange rate regimes also possess high sterilization coefficients. Given open capital accounts in the various economies, the paper argues that this finding contravenes the money neutrality thesis, which holds that only one nominal anchor can prevail in the long-term. Th...

  14. Epidermolysis Bullosa Acquisita: Autoimmunity to Anchoring Fibril Collagen

    OpenAIRE

    Chen, Mei; Kim, Gene H; Prakash, Lori; Woodley, David T.

    2011-01-01

    Epidermolysis bullosa acquisita (EBA) is a rare and acquired autoimmune subepidermal bullous disease of the skin and mucosa. EBA includes various distinct clinical manifestations resembling Bullous Pemphigus, Brunsting-Perry pemphigoid, or cicatricial pemphigoid. These patients have autoantibodies against type VII collagen, an integral component of anchoring fibrils, which are responsible for attaching the dermis to the epidermis. Destruction or perturbation of the normally functioning anchor...

  15. Transosseous Acetabular Labral Repair as an Alternative to Anchors

    OpenAIRE

    Pérez-Carro, Luis; Cabello, Andres Gonzalez; Rakha, Mohamed Ibrahim; Patnaik, Sarthak; Centeno, Elias; Miranda, Victor; Fernández, Ana Alfonso

    2015-01-01

    Labral tears are the most common pathology in patients undergoing hip arthroscopy and the most common cause of mechanical hip symptoms. Labral repair techniques have been described in the literature using suture anchors placed as close as possible to the acetabular rim without penetrating the articular surface. Optimal surgical technique for labral repair is very important, and an inappropriate entry point and guide angulation may lead to intra-articular penetration of the anchor, chondral da...

  16. The Effect of Anchoring Sutures on Medicinal Leech Mortality

    OpenAIRE

    Davila, Victor J.; Hoppe, Ian C.; Landi, Rocco; Ciminello, Frank S.

    2009-01-01

    Objective: The implementation of leech therapy for surgical flaps is not always logistically easy or comfortable for patients or healthcare providers. We examine different methods of placing sutures in the medicinal leech, Hirudo medicinalis, to make the implementation of leech therapy easier. Methods: Sixteen leeches were randomly divided into 3 groups: a control group, a deep anchoring suture group, and a superficial anchoring suture group. The leeches were observed to determine if either o...

  17. Anchor stud monotonic and cyclic shear tests. Final report

    International Nuclear Information System (INIS)

    In a prestressed concrete reactor vessel (PCRV), the main cavity liner and other cavity liners with large diameter/thickness (D/t) ratios are anchored to the concrete by anchor studs. These anchor studs are subject to shear loading resulting from prestressing, pressurization, temperature, and creep of the PCRV. The test program discussed in this report consists of both monotonic and cyclic testing of models simulating the prototype anchor stud/concrete assembly. The tests determined the shear stiffness characteristics of the 3/4-in.-diameter, one-piece Nelson anchor stud embedded in concrete and established its low-cycle fatigue life under displacement-controlled loading. The previously obtained results of Phase I and Phase II tests on two-piece anchor studs, along with high-cyclic fatigue data taken from the literature, are discussed and are plotted with the current, Phase III, results to form a displacement versus cycles to failure curve covering a useful range of design applications

  18. Evaluation of mitral valve replacement anchoring in a phantom

    Science.gov (United States)

    McLeod, A. Jonathan; Moore, John; Lang, Pencilla; Bainbridge, Dan; Campbell, Gordon; Jones, Doug L.; Guiraudon, Gerard M.; Peters, Terry M.

    2012-02-01

    Conventional mitral valve replacement requires a median sternotomy and cardio-pulmonary bypass with aortic crossclamping and is associated with significant mortality and morbidity which could be reduced by performing the procedure off-pump. Replacing the mitral valve in the closed, off-pump, beating heart requires extensive development and validation of surgical and imaging techniques. Image guidance systems and surgical access for off-pump mitral valve replacement have been previously developed, allowing the prosthetic valve to be safely introduced into the left atrium and inserted into the mitral annulus. The major remaining challenge is to design a method of securely anchoring the prosthetic valve inside the beating heart. The development of anchoring techniques has been hampered by the expense and difficulty in conducting large animal studies. In this paper, we demonstrate how prosthetic valve anchoring may be evaluated in a dynamic phantom. The phantom provides a consistent testing environment where pressure measurements and Doppler ultrasound can be used to monitor and assess the valve anchoring procedures, detecting pararvalvular leak when valve anchoring is inadequate. Minimally invasive anchoring techniques may be directly compared to the current gold standard of valves sutured under direct vision, providing a useful tool for the validation of new surgical instruments.

  19. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination

    OpenAIRE

    Gang Li; Hillier, LaDeana W; Grahn, Robert A.; Zimin, Aleksey V; David, Victor A.; Marilyn Menotti-Raymond; Rondo Middleton; Steven Hannah; Sher Hendrickson; Alex Makunin; O’Brien, Stephen J; Pat Minx; Wilson, Richard K.; Lyons, Leslie A.; Warren, Wesley C.

    2016-01-01

    High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands o...

  20. Pyramidal anchor stone from Baga waters of Goa, west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    . Pyramidal anchor stones have an apex hole which goes up to the round hole, however Goa anchor stone has no such perforation, but, instead has a rectangular cutting on the apex. The anchor stone is compared with Greek pyramidal anchor stones, and probably...

  1. Phenotypic Characterization of Toxic Compound Effects on Liver Spheroids Derived from iPSC Using Confocal Imaging and Three-Dimensional Image Analysis.

    Science.gov (United States)

    Sirenko, Oksana; Hancock, Michael K; Hesley, Jayne; Hong, Dihui; Cohen, Avrum; Gentry, Jason; Carlson, Coby B; Mann, David A

    2016-09-01

    Cell models are becoming more complex to better mimic the in vivo environment and provide greater predictivity for compound efficacy and toxicity. There is an increasing interest in exploring the use of three-dimensional (3D) spheroids for modeling developmental and tissue biology with the goal of accelerating translational research in these areas. Accordingly, the development of high-throughput quantitative assays using 3D cultures is an active area of investigation. In this study, we have developed and optimized methods for the formation of 3D liver spheroids derived from human iPS cells and used those for toxicity assessment. We used confocal imaging and 3D image analysis to characterize cellular information from a 3D matrix to enable a multi-parametric comparison of different spheroid phenotypes. The assay enables characterization of compound toxicities by spheroid size (volume) and shape, cell number and spatial distribution, nuclear characterization, number and distribution of cells expressing viability, apoptosis, mitochondrial potential, and viability marker intensities. In addition, changes in the content of live, dead, and apoptotic cells as a consequence of compound exposure were characterized. We tested 48 compounds and compared induced pluripotent stem cell (iPSC)-derived hepatocytes and HepG2 cells in both two-dimensional (2D) and 3D cultures. We observed significant differences in the pharmacological effects of compounds across the two cell types and between the different culture conditions. Our results indicate that a phenotypic assay using 3D model systems formed with human iPSC-derived hepatocytes is suitable for high-throughput screening and can be used for hepatotoxicity assessment in vitro. PMID:27494736

  2. Communication: Electrical rectification of C59N: The role of anchoring and doping sites

    International Nuclear Information System (INIS)

    Based on the nonequilibrium Green’s function formalism and density-functional theory, we investigate the onset of electrical rectification in a single C59N molecule in conjunction with gold electrodes. Our calculations reveal that rectification is dependent upon the anchoring of the Au atom on C59N; when the Au electrode is singly bonded to a C atom (labeled here as A), the system does not exhibit rectification, whereas when the electrode is connected to the C–C bridge site between two hexagonal rings (labeled here as B), transmission asymmetry is observed, where the rectification ratio reaches up to 2.62 at ±1 V depending on the N doping site relative to the anchoring site. Our analysis of the transmission mechanism shows that N doping of the B configuration causes rectification because more transmission channels are available for transmission in the B configuration than in the A configuration

  3. Communication: Electrical rectification of C{sub 59}N: The role of anchoring and doping sites

    Energy Technology Data Exchange (ETDEWEB)

    Tawfik, Sherif Abdulkader, E-mail: sherif.abbas@sydney.edu.au; Stampfl, C. [School of Physics, The University of Sydney, Sydney, New South Wales 2006 (Australia); Cui, X. Y.; Ringer, S. P. [Australian Centre for Microscopy and Microanalysis, and School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, New South Wales 2006 (Australia)

    2016-01-14

    Based on the nonequilibrium Green’s function formalism and density-functional theory, we investigate the onset of electrical rectification in a single C{sub 59}N molecule in conjunction with gold electrodes. Our calculations reveal that rectification is dependent upon the anchoring of the Au atom on C{sub 59}N; when the Au electrode is singly bonded to a C atom (labeled here as A), the system does not exhibit rectification, whereas when the electrode is connected to the C–C bridge site between two hexagonal rings (labeled here as B), transmission asymmetry is observed, where the rectification ratio reaches up to 2.62 at ±1 V depending on the N doping site relative to the anchoring site. Our analysis of the transmission mechanism shows that N doping of the B configuration causes rectification because more transmission channels are available for transmission in the B configuration than in the A configuration.

  4. Flapping states of an el astically anchored wing in a uniform flow

    CERN Document Server

    Orchini, A; Guerrero, J; Festa, R; Boragno, C

    2012-01-01

    Linear stability analysis of an elastically anchored wing in a uniform flow is investigated both analytically and numerically. The analytical formulation explicitly takes into account the effect of the wake on the wing by means of Theodorsen's theory. Three different parameters non-trivially rule the observed dynamics: mass density ratio between wing and fluid, spring elastic constant and distance between the wing center of mass and the spring anchor point on the wing. We found relationships between these parameters which rule the transition between stable equilibrium and fluttering. The shape of the resulting marginal curve has been successfully verified by high Reynolds number direct numerical simulations. Our findings are of interest in applications related to energy harvesting by fluid-structure interaction, a problem which has recently attracted a great deal of attention. The main aim in that context is to identify the optimal physical/geometrical system configuration leading to large sustained motion, w...

  5. Palladium nanoparticle anchored polyphosphazene nanotubes: preparation and catalytic activity on aryl coupling reactions

    Indian Academy of Sciences (India)

    V Devi; A Ashok Kumar; S Sankar; K Dinakaran

    2015-06-01

    Highly accessible-supported palladium (Pd) nanoparticles anchored polyphosphazene (PPZ) nanotubes (NTs) having average diameter of 120 nm were synthesized rapidly at room temperature and homogeneously decorated with Pd nanoparticles. The resultant PPZ–Pd nanocomposites were morphologically and structurally characterized by means of transmission electron microscope equipped with energy-dispersive X-ray spectroscopy and X-ray diffraction analysis. Characterization results showed that the Pd nanoparticles with good dispersibility could be well anchored onto the surfaces of the PPZ NTs. The PPZ–Pd NTs show enhanced catalytic activity for the Suzuki coupling of aryl bromides with arylboronic acid. In addition, these PPZ–Pd NTs show excellent behaviour as reusable catalysts of the Suzuki and Heck coupling reactions.

  6. Dynamic interaction between the soil and an anchored sheet pile during seismic excitation

    Science.gov (United States)

    Degrande, G.; Praet, E.; van Zegbroeck, B.; van Marcke, P.

    2002-05-01

    A subdomain approach for dynamic soil-structure interaction is proposed for the linear elastic seismic analysis of an anchored sheet pile, retaining a horizontally layered soil on rigid bedrock. A hybrid solution technique is used, employing a finite element formulation for the generalized sheet pile, a thin layer formulation for the soil and a direct stiffness formulation for the tieback; the displacement vectors of the sheet pile and the soil are decomposed, using the eigenmodes of the sheet pile and the propagating or decaying modes in the soil. The discretization can be limited to the interface(s), where pointwise continuity of the displacements is enforced, whereas a weak variational formulation is used for the stress equilibrium. The solution technique is illustrated by means of a numerical example, where the harmonic response of a flexible anchored sheet pile is considered and compared to the case where no tieback is present.

  7. Communication: Electrical rectification of C59N: The role of anchoring and doping sites.

    Science.gov (United States)

    Tawfik, Sherif Abdulkader; Cui, X Y; Ringer, S P; Stampfl, C

    2016-01-14

    Based on the nonequilibrium Green's function formalism and density-functional theory, we investigate the onset of electrical rectification in a single C59N molecule in conjunction with gold electrodes. Our calculations reveal that rectification is dependent upon the anchoring of the Au atom on C59N; when the Au electrode is singly bonded to a C atom (labeled here as A), the system does not exhibit rectification, whereas when the electrode is connected to the C-C bridge site between two hexagonal rings (labeled here as B), transmission asymmetry is observed, where the rectification ratio reaches up to 2.62 at ±1 V depending on the N doping site relative to the anchoring site. Our analysis of the transmission mechanism shows that N doping of the B configuration causes rectification because more transmission channels are available for transmission in the B configuration than in the A configuration. PMID:26772547

  8. Coexpression network analysis in abdominal and gluteal adipose tissue reveals regulatory genetic loci for metabolic syndrome and related phenotypes

    DEFF Research Database (Denmark)

    Min, Josine L; Nicholson, George; Halgrimsdottir, Ingileif; Almstrup, Kristian; Petri, Andreas; Barrett, Amy; Travers, Mary; Rayner, Nigel W; Mägi, Reedik; Pettersson, Fredrik H; Broxholme, John; Neville, Matt J; Wills, Quin F; Cheeseman, Jane; Allen, Maxine; Holmes, Chris C; Spector, Tim D; Fleckner, Jan; McCarthy, Mark I; Karpe, Fredrik; Lindgren, Cecilia M; Zondervan, Krina T

    2012-01-01

    Metabolic Syndrome (MetS) is highly prevalent and has considerable public health impact, but its underlying genetic factors remain elusive. To identify gene networks involved in MetS, we conducted whole-genome expression and genotype profiling on abdominal (ABD) and gluteal (GLU) adipose tissue, ...... interactions influence complex traits such as MetS, integrated analysis of genotypes and coexpression networks across multiple tissues relevant to clinical traits is an efficient strategy to identify novel associations....

  9. Multi-dimensional Likelihood Estimation Techniques in conjunction with the Method of Anchored Distributions (MAD)

    Science.gov (United States)

    Over, M. W.; Murakami, H.; Hahn, M. S.; Yang, Y.; Rubin, Y.

    2010-12-01

    The method of anchored distributions (MAD, Rubin et al., Water Resour. Res., 2010) is a Bayesian inversion technique that combines geostatistical concepts with a strategy for localization of data that is indirectly related to the target variables, using anchors. Anchors are statistical distributions of the target variables (e.g., the hydraulic conductivity) at specific locations The variable field is described by the statistical distributions of structural parameters that characterize global features and by anchor distributions that intend to capture local effects. The posterior distributions of structural and anchor parameter sets are used to update the approximate spatial distribution of target variable and are generated by re-sampling the parameter sets using their normalized likelihood estimates as the probability of being selected. Increasing the dimension of the data, to include additional information in the likelihood estimate, increases the computational burden. Two measures are taken to accommodate the advantageous additional data without spurious side effects. (1) Partitioning parameter sets into hypercubes, based upon the similarity of the structural parameter values. (2) Principal component analysis, to reduce the dimensionality by discarding a certain percentage of principal components. As an additional feature for large sample sets, or faster calculation, a ‘bundling’ regime can be implemented. Bundling is employed immediately after partitioning the parameter sets into hypercubes. Bundling identifies spatial patterns amongst the realizations generated from the distributions defining the anchor parameters. The added organizational step allows data with reduced sample sizes to be passed to the PCA algorithm. The division of the data set allows for simple parallelization of the computation and our case study achieved a three-fold dimension reduction. Because of the high dimension involved in the calculation, without absurdly large sample sizes, it is

  10. Econophysical anchoring of unimodal power-law distributions

    International Nuclear Information System (INIS)

    The sciences are abundant with size distributions whose densities have a unimodal shape and power-law tails both at zero and at infinity. The quintessential examples of such unimodal and power-law (UPL) distributions are the sizes of income and wealth in human societies. While the tails of UPL distributions are precisely quantified by their corresponding power-law exponents, their bulks are only qualitatively characterized as unimodal. Consequently, different statistical models of UPL distributions exist, the most popular considering lognormal bulks. In this paper we present a general econophysical framework for UPL distributions termed ‘the anchoring method’. This method: (i) universally approximates UPL distributions via three ‘anchors’ set at zero, at infinity, and at an intermediate point between zero and infinity (e.g. the mode); (ii) is highly versatile and broadly applicable; (iii) encompasses the existing statistical models of UPL distributions as special cases; (iv) facilitates the introduction of new statistical models of UPL distributions and (v) yields a socioeconophysical analysis of UPL distributions. (paper)

  11. Integrated method for adaptability and phenotypic stability analysis = Método integrado para análise de adaptabilidade e estabilidade fenotipica

    Directory of Open Access Journals (Sweden)

    Edmar Soares de Vasconcelos

    2011-04-01

    Full Text Available The objectives of this study were a description of the Centroid Method, which is used to investigate the phenotypic adaptability of genotypes and the inclusion of new ideotypes therein, creating the Integrated Method for adaptability and phenotypic stability analysis, as well as a comparison of the two methods in a study example. As an applied example of the new proposal, grain yield data of 14 soybean genotypes from experiments at four locations in the state of Minas Gerais were used. In a comparison, the qualitative and quantitative gains of the Centroid Method with seven ideotypes were higher than of the Centroid Method with only four ideotypes for adaptability analysis. With the incorporation of the new ideotypes into theCentroid Method other concepts for the adaptability and phenotypic stability analysis are represented and the modified method was designated “Integrated Method of Adaptability and Stability Analysis”. CS 801 genotype was classified as the genotype with best adaptability to the environments Viçosa, Florestal, São Gotardo and Rio Paranaiba. The stability of the genotypes CAC 1, CS 741, Splendor, UFV 16, UFV 19, UFVP IV-6, UFVP IV-8, UFVP V-15, UFVP V-7,and UFV98700739 was classified as general.Os objetivos deste trabalho foram apresentar uma modificação ao método original do Centróide inserindo novos ideótipos, gerando uma proposta denominada Método Integrado para análise adaptabilidade e estabilidade fenotípica e comparar as duas metodologias. Como exemplo de aplicação da nova proposta foi utilizado dados de produtividade de grãos de quatorze genótipos de soja obtidos em experimentos conduzidos em quatro locais, no Estado de Minas Gerais. O novo método do Centróide com sete ideótipos propiciou ganhos qualitativos e quantitativos perante o método original do Centróide que possuía apenas quatro ideótipos para análise de adaptabilidade. Os novos ideótipos inseridos ao método do Centróide original

  12. Perceptual anchoring in preschool children: not adultlike, but there.

    Directory of Open Access Journals (Sweden)

    Karen Banai

    Full Text Available BACKGROUND: Recent studies suggest that human auditory perception follows a prolonged developmental trajectory, sometimes continuing well into adolescence. Whereas both sensory and cognitive accounts have been proposed, the development of the ability to base current perceptual decisions on prior information, an ability that strongly benefits adult perception, has not been directly explored. Here we ask whether the auditory frequency discrimination of preschool children also improves when given the opportunity to use previously presented standard stimuli as perceptual anchors, and whether the magnitude of this anchoring effect undergoes developmental changes. METHODOLOGY/PRINCIPAL FINDINGS: Frequency discrimination was tested using two adaptive same/different protocols. In one protocol (with-reference, a repeated 1-kHz standard tone was presented repeatedly across trials. In the other (no-reference, no such repetitions occurred. Verbal memory and early reading skills were also evaluated to determine if the pattern of correlations between frequency discrimination, memory and literacy is similar to that previously reported in older children and adults. Preschool children were significantly more sensitive in the with-reference than in the no-reference condition, but the magnitude of this anchoring effect was smaller than that observed in adults. The pattern of correlations among discrimination thresholds, memory and literacy replicated previous reports in older children. CONCLUSIONS/SIGNIFICANCE: The processes allowing the use of context to form perceptual anchors are already functional among preschool children, albeit to a lesser extent than in adults. Nevertheless, immature anchoring cannot fully account for the poorer frequency discrimination abilities of young children. That anchoring is present among the majority of typically developing preschool children suggests that the anchoring deficits observed among individuals with dyslexia represent a

  13. [Effect of gametocidal chromosome 4S' on the phenotype segregation ratio in genetic analysis of common wheat lines].

    Science.gov (United States)

    Vdovichenko, Zh V; Antoniuk, M Z; Ternovskaia, T K

    2003-01-01

    Using experimental data on genetic analysis of introgressive lines for the character "hairy leaf sheath" controlled by the "cuckoo" chromosome 4S1, the algorithm for calculation of the theoretical segregation ratio in F2 was developed. Segregation distortion is caused by non-viability of the majority of gametes lacking the chromosome 4S1. The frequency of functioning gametes without the chromosome 4S1 is determined by the probability p versus the theoretically expected ratio 7 nonviable: 9 viable ones. Since segregation involves two characters, gamete viability and hairiness, the ratio 15 hairy: 1 hairless was used as a basis for search of the frequency p by maximum-likelihood method using 16 populations F2 from crossing the lines differing in the character studied. PMID:14650327

  14. Integrative Functional Genomics Analysis of Sustained Polyploidy Phenotypes in Breast Cancer Cells Identifies an Oncogenic Profile for GINS2

    Directory of Open Access Journals (Sweden)

    Juha K. Rantala

    2010-11-01

    Full Text Available Aneuploidy is among the most obvious differences between normal and cancer cells. However, mechanisms contributing to development and maintenance of aneuploid cell growth are diverse and incompletely understood. Functional genomics analyses have shown that aneuploidy in cancer cells is correlated with diffuse gene expression signatures and aneuploidy can arise by a variety of mechanisms, including cytokinesis failures, DNA endoreplication, and possibly through polyploid intermediate states. To identify molecular processes contributing to development of aneuploidy, we used a cell spot microarray technique to identify genes inducing polyploidy and/or allowing maintenance of polyploid cell growth in breast cancer cells. Of 5760 human genes screened, 177 were found to induce severe DNA content alterations on prolonged transient silencing. Association with response to DNA damage stimulus and DNA repair was found to be the most enriched cellular processes among the candidate genes. Functional validation analysis of these genes highlighted GINS2 as the highest ranking candidate inducing polyploidy, accumulation of endogenous DNA damage, and impairing cell proliferation on inhibition. The cell growth inhibition and induction of polyploidy by suppression of GINS2 was verified in a panel of breast cancer cell lines. Bioinformatic analysis of published gene expression and DNA copy number studies of clinical breast tumors suggested GINS2 to be associated with the aggressive characteristics of a subgroup of breast cancers in vivo. In addition, nuclear GINS2 protein levels distinguished actively proliferating cancer cells suggesting potential use of GINS2 staining as a biomarker of cell proliferation as well as a potential therapeutic target.

  15. Metabolomic phenotyping of af cloned pig model

    DEFF Research Database (Denmark)

    Clausen, Morten Rahr; Christensen, Kirstine Lykke; Hedemann, Mette Skou;

    2011-01-01

    Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and...... possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal...... outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n...

  16. Anchoring of Expectations: The Role of Credible Targets in a Game Experiment

    Directory of Open Access Journals (Sweden)

    Bodo Herzog

    2015-10-01

    Full Text Available This paper provides new evidence on the formation and anchoring of inflation expectations. I conduct a game experiment and analyze the adjustment as well as the impact of credible targets on expectations. In addition, I evaluate the idiosyncratic determinants on the formation of expectations. The analysis reveals six results: First, I find evidence that long-term inflation expectations are firmly anchored to a credible target. Second, a temporary deviation due to unexpected monetary policy might trigger a decline in credibility, and third a de-anchoring of expectations due to uncertainty. Fourth, I find that people change their expectations little if a credible target exists. Fifth, expectations exhibit a large degree of time-variance only in environments without a target. Sixth, the dynamic adjustment to an ‘incomplete’ equilibrium, which is theoretically unstable, is nevertheless rapid and persistent in case of credible targets. All in all, I demonstrate a unique game setup with contributions to both experimental and monetary economics.

  17. Electrical properties and mechanical stability of anchoring groups for single-molecule electronics

    Directory of Open Access Journals (Sweden)

    Riccardo Frisenda

    2015-07-01

    Full Text Available We report on an experimental investigation of transport through single molecules, trapped between two gold nano-electrodes fabricated with the mechanically controlled break junction (MCBJ technique. The four molecules studied share the same core structure, namely oligo(phenylene ethynylene (OPE3, while having different aurophilic anchoring groups: thiol (SAc, methyl sulfide (SMe, pyridyl (Py and amine (NH2. The focus of this paper is on the combined characterization of the electrical and mechanical properties determined by the anchoring groups. From conductance histograms we find that thiol anchored molecules provide the highest conductance; a single-level model fit to current–voltage characteristics suggests that SAc groups exhibit a higher electronic coupling to the electrodes, together with better level alignment than the other three groups. An analysis of the mechanical stability, recording the lifetime in a self-breaking method, shows that Py and SAc yield the most stable junctions while SMe form short-lived junctions. Density functional theory combined with non-equlibrium Green’s function calculations help in elucidating the experimental findings.

  18. Role of suture anchors in management of fractures of inferior pole of patella

    Directory of Open Access Journals (Sweden)

    Anand Ashish

    2010-01-01

    Full Text Available Background: The traditional recommendation for displaced comminuted inferior pole fractures is excision of the comminuted pole followed by reattachment of the patellar tendon with transosseous suture. To the best of our knowledge there has been no previous published study mentioning the use of suture anchors for fracture inferior pole of patella. We present a retrospective analysis of five cases of patients doing well at final follow-up of two years. Materials and Methods: Five patients treated at our institute using suture anchors for repair of comminuted inferior pole fractures of patella between January 2007 to March 2007. (range 28 years-55 years. There were three males and two females. Results: The average follow-up was 25 months (range 24 months-26 months. The patients were evaluated for range of motion, strength, patellofemoral scores and any alteration of patellar height. The outcome of the procedure was assessed with use of the patellofemoral scoring system of Noyes et al, 5 as adapted by Saltzman et al. 6 The final patellofemoral score (maximum 100 points was 94.6 (range 93-96. Conclusion: We believe it is a novel extended indication of the use of suture anchors and should be in the armament of every trauma surgeon.

  19. High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation

    Science.gov (United States)

    Anandapadamanaban, Madhanagopal; Andresen, Cecilia; Helander, Sara; Ohyama, Yoshifumi; Siponen, Marina I.; Lundström, Patrik; Kokubo, Tetsuro; Ikura, Mitsuhiko; Moche, Martin; Sunnerhagen, Maria

    2016-01-01

    The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 Å) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 when bound to yeast TBP, together with mutational data. The yTAF1-TAND1, which in itself acts as a transcriptional activator, binds into the DNA-binding TBP concave surface by presenting similar anchor residues to TBP as E. coli Mot1 but from a distinct structural scaffold. Furthermore, we show how yTAF1-TAND2 employs an aromatic and acidic anchoring pattern to bind a conserved yTBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides compelling insight into the competitive multiprotein TBP interplay critical to transcriptional regulation. PMID:23851461

  20. Secreted form of the human interleukin 2 receptor encoded by an anchor minus cDNA

    International Nuclear Information System (INIS)

    The DNA sequence encoding all of the putative intracytoplasmic domain and most of the trans-membrane domain of the huma IL 2 receptor was detected from a full length receptor cDNA. After expression in mouse L cells, the resultant anchor minus cDNA was found to direct the synthesis of a secreted rather than membrane-associated form of the IL 2 receptor. The secreted receptor protein (44,000 to 46,000 M/sub r/) retained the capacity to bind both IL 2 and the monoclonal anti-Tac antibody, as evidenced by (1) retention on IL 2 and anti-Tac affinity columns, (2) inhibition of [3H]-antiTac binding to HUT 102B2 cells, and (3) partial inhibition of IL 2-induced CTLL proliferation. Removal of these domains from the IL 2 receptor did not alter the post-translational processing or rate of export of the truncated receptor protein. These data confirm the proposed membrane orientation of the IL 2 receptor (NH2 terminus out, COOH terminus in) and underscore the anchoring function of this carboxy terminal receptor segment. The availability of such anchor minus receptor cDNA constructs may facilitate purification of large quantities of receptor protein for further analysis of receptor structure, valency, and localization of the IL 2 binding site(s)

  1. Evaluation of postoperative results from videoarthroscopic treatment for recurrent shoulder dislocation using metal anchors

    Directory of Open Access Journals (Sweden)

    Éder Menegassi Martel

    2016-02-01

    Full Text Available ABSTRACT OBJECTIVE: To clinically and radiologically evaluate the results from videoarthroscopic treatment using metal anchors in patients with recurrent shoulder dislocation and its complications. METHODS: This was a retrospective study on 47 patients (47 shoulders operated by the shoulder group of the orthopedic hospital between February 2010 and February 2012. A questionnaire, interview and physical and radiographic examinations were used, with the classification of Samilson and Pietro. The mean postoperative follow-up was 33 months (range 12-47 months. The statistical analysis consisted of using Fisher's exact test through the IBM SPSS 22 statistical software. The significance level used was 5%. RESULTS: Recurrence was observed in nine cases. The patients were, on average, 26.5 years old at the first episode, and 19.1% were aged 20 years or under. Among these, 55.6% presented recurrence. In relation to age at the time of the surgical procedure, the average age was 27 years, and 12.8% were aged 20 years or under. Nineteen patients presented prominent anchors and, of these, 21% manifested arthrosis. CONCLUSION: There was a statistically identified correlation between the recurrence rate and age less than or equal to 20 years at the times of first dislocation and the surgical procedure. Further studies should be conducted in order to compare the use of absorbable anchors, which despite higher cost, may provide lower risk of developing glenohumeral arthrosis in some cases.

  2. Stresses induced by post-tensioned anchor in jointed rock mass

    Institute of Scientific and Technical Information of China (English)

    Alan Showkati; Parviz Maarefvand; Hossein Hassani

    2015-01-01

    A new analytical study on stresses around a post-tensioned anchor in rocks with two perpendicular joint sets is presented. The assumptions of orthotropic elastic rock with plane strain conditions are made in derivation of the formulations. A tri-linear bond-slip constitutive law is used for modeling the tendon-grout interface behavior and debonding of this interface. The bearing plate width is also considered in the analysis. The obtained solutions are in the integral forms and numerical techniques that have been used for evaluation. In the illustrative example given, the major principal stress is compressive in the anchor free zone and compressive stress concentrations of 815 kPa and 727 kPa (for the anchor load of 300 kN) are observed under the bearing plate and the bond length proximal end, respectively. However, large values of tensile stresses with the maximum of−434 kPa are formed at the bond length distal end. The results obtained using the proposed solution are compared very those of numerical method (FEM).

  3. Operative treatment of acromioclavicular joint dislocation:a new technique with suture anchors

    Institute of Scientific and Technical Information of China (English)

    Zhang Jingwei; Li Min; He Xianfeng; Yu Yihui; Zhu Limei

    2014-01-01

    Objective:To evaluate clinical outcome of suture anchors in strengthening both acromioclavicular and coracoclavicular ligaments in the surgical treatment of acromioclavicular joint dislocation.Methods:Twenty-eight patients with acute traumatic Rockwood Ⅲ,Ⅳ and Ⅴ dislocations of the acromioclavicular joint surgically treated at our institute between October 2010 and January 2012 were recruited.All patients underwent open reduction combined with suture anchors.Function was evaluated using the ConstantMurley shoulder score.Clinical and radiographic shoulder ratings were evaluated using Taft criteria at 3,6 and 12 months.Results:Two cases with fixation loosening were not included in final statistical analysis.Other patients obtained full joint reposition on immediate postoperative radiographs.Follow-up was performed with an average of 15.6 months (range,12-19).After early range of motion exercises,96.2% of the patients (25/26) could abduct and elevate their shoulders more than 90 degrees within postoperative 3 months.There was no infection.Average Constant-Murley score was 96.3 points (range,94-100)and mean Taft shoulder rating was 10.7 points (range,8-12) at 12 months.Conclusion:The suture anchor is a relatively simple technique and can avoid screw removal which is helpful in reconstructing both acromioclavicular and coracoclavicular ligaments in acute traumatic acromioclavicular joint dislocation.

  4. Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae).

    Science.gov (United States)

    Muir, Christopher D; Pease, James B; Moyle, Leonie C

    2014-12-01

    Adaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL sign test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large-effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs support a functional hypothesis that the distribution of stomata affects the resistance to CO2 diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes and demonstrates that some trait transitions between species could have involved few, large-effect genetic changes, allowing rapid responses to new environmental conditions. PMID:25298519

  5. Employees’ work engagement and job commitment: The moderating role of career anchors

    Directory of Open Access Journals (Sweden)

    Melinde Coetzee

    2014-02-01

    Full Text Available Orientation: Organisations continue to focus on human resource initiatives for enhancingemployee commitment, satisfaction and engagement in order to gain a competitive edge in adynamic and fast-changing marketplace.Research purpose: The objective of the present study was to assess whether individuals’career anchors (measured by the career orientations inventory significantly moderate therelationship between their work engagement (measured by the Utrecht work engagementscale and job commitment (measured by the organisation-related commitment scale.Motivation for the study: Although the literature review suggests that people’s workengagement and job commitment may be influenced by their career anchors, there seems to bea paucity of research examining the interaction effects between these three variables.Research approach, design and method: A cross-sectional quantitative survey approach wasused. A non-probability purposive sample of adults (N = 318 employed in a human resourcecapacity in the South African service industry participated in the study. Stepwise hierarchicalmoderated regression analysis was performed to achieve the objective of the study.Main findings: The results showed that the work engagement-job commitment relationshipwas generally stronger for high career anchor preferences than for low career anchorpreferences.Practical/managerial implications: The results of the study can be useful when human resourceinterventions for enhancing employees’ engagement and commitment are developed.Contribution: The results of the study add new insights to the career literature by showing thatpeople’s career self-concepts (as reflected by their career anchors are important to consider inenhancing their work engagement and job commitment.

  6. Decay accelerating factor of complement is anchored to cells by a C-terminal glycolipid

    International Nuclear Information System (INIS)

    Membrane-associated decay accelerating factor (DAF) of human erythrocytes (E/sup hu/) was analyzed for a C-terminal glycolipid anchoring structure. Automated amino acid analysis of DAF following reductive radiomethylation revealed ethanolamine and glucosamine residues in proportions identical with those present in the E/sup hu/ acetylcholinesterase (AChE) anchor. Cleavage of radiomethylated 70-kilodalton (kDa) DAF with papain released the labeled ethanolamine and glucosamine and generated 61- and 55-kDa DAF products that retained all labeled Lys and labeled N-terminal Asp. Incubation of intact E/sup hu/ with phosphatidylinositol-specific phospholipase C (PI-PLC), which cleaves the anchors in trypanosome membrane form variant surface glycoproteins (mfVSGs) and murine thymocyte Thy-1 antigen, released 15% of the cell-associated DAF antigen. The released 67-kDa PI-PLC DAF derivative retained its ability to decay the classical C3 convertase C4b2a but was unable to membrane-incorporate and displayed physicochemical properties similar to urine DAF, a hydrophilic DAF form that can be isolated for urine. Nitrous acid deamination cleavage of E/sup hu/ DAF at glucosamine following labeling with the lipophilic photoreagent 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine ([125I]TID) released the [125I]TID label in a parallel fashion as from [125I]TID-labeled AChE. Biosynthetic labeling of HeLa cells with [3H] ethanolamine resulted in rapid 3H incorporation into both 48-kDa pro-DAF and 72-kDa mature epithelial cell DAF. The findings indicate that DAF and AChE are anchored in E/sup hu/ by the same or a similar glycolipid structure and that, like VSGs, this structure is incorporated into DAF early in DAF biosynthesis prior to processing of pro-DAF in the Golgi

  7. Seismic response of unanchored and partially anchored liquid-storage tanks. Final report

    International Nuclear Information System (INIS)

    Ground-mounted vertical storage tanks are important components of nuclear plant safety systems. A systematic study is made of the principal effects of base uplifting on the seismic response of laterally excited, unanchored and partially anchored cylindrical liquid-storage tanks. The study consists of two parts: the first deals with the static uplifting resistance of the flexible base plate, and the second deals with the dynamic response of the uplifting system. An insight into the behavior of the uplifting base plate is first gained with the help of a prismatic beam solution. In Section 2, the solution is implemented exactly, whereas in Section 3 it is implemented approximately by use of the Ritz energy procedure. Solutions are next presented for axisymmetrically and asymmetrically uplifted base plate of tanks, in Section 4. For the axisymmetric case the solution is implemented exactly, as well as approximately by modeling the plate by a series of semiinfinite prismatic beams. The accuracy of the latter approach is confirmed by comparing its predictions with those of the former. In Section 5, a highly efficient and rational method is presented for the dynamic response analysis of uplifting tanks. Both unanchored tanks and partially anchored tanks, for which the number of anchor bolts at the base is insufficient to ensure full fixity, are considered. It is shown that base uplifting may reduce significantly the hydrodynamic pressures, but these reductions may be associated with increased axial compressive stresses in the tank wall and large plastic rotations at the plate-shell junction. For partially anchored tanks, energy loss due to bolt yielding is found to be small

  8. Is hexamerin receptor a GPI-anchored protein in Achaea janata (Lepidoptera: Noctuidae)?

    Indian Academy of Sciences (India)

    Madhusudhan Budatha; Thuirei Jacob Ningshen; Aparna Dutta-Gupta

    2011-08-01

    The process of uptake of hexamerins during metamorphosis from insect haemolymph by fat body cells is reminiscent of receptor-mediated endocytosis. Previously, we had identified a hexamerin-binding protein (HBP) and reported for the first time that uptake of hexamerins is dependent on the phosphorylation of HBP partly by a tyrosine kinase, which is, in turn, activated by 20-hydroxyecdysone (20E). However, the exact nature of HBP and the mechanism of interaction are still unknown. Here we report the possibility of HBP being a GPI-anchored protein in the fat body of Achaea janata and its role in the tyrosine-kinase-mediated phosphorylation signalling. Digestion of fat body membrane preparation with bacterial phosphatidylinositol-specific phospholipase C (PI-PLC), and the subsequent recognition by antibodies specific for the cross-reacting determinant (CRD), revealed that HBP is glycosylphosphatidylinositol (GPI)-anchored protein and, further, that the hexamerin binding to HBP was inhibited after digestion. Hexamerin overlay assay (HOA) of co-immunoprecipitated in vitro phosphorylated HBP showed exclusive binding to ∼120 kDa protein. Lectin-binding analysis of hexamerins revealed the presence of -acetylgalactosamine (GalNAc) and -acetylglucosamine (GluNAc), whereas HBP showed the presence of GalNac alone. Mild chemical deglycosylation studies and binding interaction in the presence of sugars revealed that glycan moieties are possibly not involved in the interaction between HBP and hexamerins. Taken together, these results suggest that HBP may be a GPI-anchored protein, and interaction and activation of HBP is through lipid-linked non-receptor src tyrosine kinases. However, additional studies are needed to prove that HBP is a GPI-anchored protein.

  9. Effects of Anchor Bolts Failures in Steam Explosion Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seung Hyun; Chang, Yoon-Suk [Kyung Hee University, Yongin (Korea, Republic of); Song, Sungchu; Cho, Yong-Jin [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2015-05-15

    Steam explosion may occur in a nuclear power plant by molten core-coolant interactions when the external reactor vessel cooling strategy is failed. This phenomenon can threat the integrity of reactor cavity, penetration piping and support structures. Even though extensive researches have been performed to predict influences of the steam explosion, due to complexity of physical phenomena and environmental thermal hydraulic conditions, it is remained as one of possible hazards. A steam explosion can cause intensive and rapid heat transfer, and lead to the formation of pressure waves and production of missiles that may endanger surrounding reactor cavity wall and associate components due to resulting dynamic effects. The goal of this research is to examine structural integrity of RPV (Reactor Pressure Vessel) support structures and anchor bolts under typical ex-vessel steam explosion conditions through FE analyses. Particularly, influence due to the failure of anchor bolts connecting RPV and support structures was evaluated. In this paper, influence of RPV and support structure due to the anchor bolt failure were evaluated under typical steam explosion conditions and the following conclusions were derived. The highest maximum stresses were calculated at the support structures under the steam explosion condition with the SVF and anchor bolts non-failure. The all stress values did not exceed their yield strengths. The displacements were high under anchor bolt failure conditions. However, the vertical movements of major components were small comparing to the overall dimensions of them.

  10. FINITE ELEMENT ANALYSIS OF SEISMIC BEHAVIOR OF RC FRAME JOINTS INDIRECTLY STRENGTHENED WITH TIED AND LOCK-ANCHORED CFRP SHEETS%系锚碳纤维布间接加固混凝土框架节点抗震性能有限元分析

    Institute of Scientific and Technical Information of China (English)

    贺学军; 余晓光; 周朝阳; 刘澍; 吴绪康

    2015-01-01

    系锚碳纤维布(简称CFRP)间接加固混凝土框架节点方法能够有效避免直接粘贴加固CFRP易剥离、难以在实际工程中实施等缺陷。通过对5个系锚CFRP间接加固节点在滞回曲线、节点承载力和延性系数等方面的有限元数值模拟对比分析,探讨节点梁端箍筋配箍率、纵向CFRP条带用量及横向CFRP条箍用量等参数对节点抗震性能的影响。分析结果表明:梁柱端间接加固的系锚CFRP能明显改善节点的抗震性能,其极限承载能力和梁端位移延性系数提高幅度分别达到19.8%和55.5%;在其他参数相同的情况下,增加梁端纵向CFRP条带的配置率能同时提高加固节点的抗震延性和承载能力,梁端箍筋配箍率能显著改善其抗震延性,梁柱端横向CFRP条箍配置率对加固节点的抗震延性和承载能力的提高作用不大,但能有效延缓纵筋的屈服和黏结滑移。%The method of indirectly strengthening RC frame joints with tied and lock-anchored carbon fiber reinforced polymer ( CFRP ) sheets can effectively avoid debonding of CFRP and infeasibility in practice which exist in strengthening directly.Based on the numerical simulation comparative analysis of the five strengthened joints'hysteresis curves, bearing capacity and ductility coefficient, the influence of the parameters on the seismic performance of the joints strengthened with tied and lock-anchored CFRP sheets was discussed.The influencing parameters included the ratio of stirrup , longitudinal CFRP sheets at the beam end and the amount of lateral shear CFRP at the beam and column end.The results showed that the tied and lock-anchored CFRP sheets could significantly improve the seismic performance of the joints.The maximum increase in ultimate bearing capacity and ductility coefficient of beam end was up to19.8% and 55.5% respectively.When others remained invariable, increasing the ratio of longitudinal CFRP sheets at the

  11. Analysis of caffeine and paraxanthine in human saliva with ultra-high-performance liquid chromatography for CYP1A2 phenotyping.

    Science.gov (United States)

    Jordan, Nan Yeun; Mimpen, Jolet Y; van den Bogaard, Willie J M; Flesch, Frits M; van de Meent, Michiel H M; Torano, Javier Sastre

    2015-07-15

    Cytochrome P450 1A2 (CYP1A2) plays an important role in drug metabolism. Caffeine (CAF) is converted into paraxanthine (PX) by this enzyme and is used as a xenobiotic substrate to determine the CYP1A2 phenotype in humans. A method for the quantification of CAF and PX in saliva was developed using liquid-liquid extraction with ethyl acetate and analysis with ultra-high-performance liquid chromatography. Peaks from CAF, PX and internal standard were resolved within 6min. The method was validated from 0.05 to 5μgmL(-1) CAF and 0.025-2.5μgmL(-1) PX. Inter- and intra-day accuracies ranged from 91.2 to 107.2% with precisions <13.5%. The limits of detection were 0.16 and 0.63 ngmL(-1) for PX and CAF, respectively. PX/CAF concentration ratios from volunteers were 0.26-1.09 with mean ratios of 0.78±0.26 and 0.38±0.10 for regular and light/non-coffee drinkers, respectively. PMID:26038236

  12. Meta-analysis of the influence of TM6SF2 E167K variant on Plasma Concentration of Aminotransferases across different Populations and Diverse Liver Phenotypes.

    Science.gov (United States)

    Sookoian, Silvia; Pirola, Carlos J

    2016-01-01

    A nonsynonymous E167K (rs58542926 C/T) variant in TM6SF2 gene was recently associated with nonalcoholic fatty liver disease (NAFLD). We explored the association between E167K and plasma concentrations of alanine (ALT) and aspartate (AST) aminotransferases through a meta-analysis. We also estimated the strength of the effect across diverse liver phenotypes, including NAFLD and chronic viral hepatitis; fourteen studies were included. We found that ALT (p = 3.2 × 10(-6), n = 94,414) and AST (p = 0007, n = 93,809) levels were significantly associated with rs58542926 in NAFLD. By contrast, rs58542926 was not associated with either ALT (p = 0.24, n = 4187) or AST (p = 0.17, n = 2678) levels in four studies on chronic hepatitis. In conclusion, the results of the pooled estimates in patients with NAFLD showed that carriers of the T allele (EK + KK), when compared with homozygous subjects for the C allele (EE genotype) have increased levels of aminotransferases; however, this increase represents -2.5 (9.8%) and 1.2 (5%) IU/L of ALT and AST respectively, which is fairly small compared with the large effect of PNPLA3- rs738409-G allele that is associated with a -28% increase in serum ALT. PMID:27278285

  13. Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells

    International Nuclear Information System (INIS)

    Metastasis is a major cancer-related cause of death. Recent studies have described metastasis pathways. However, the exact contribution of each pathway remains unclear. Another key feature of a tumor is the presence of hypoxic areas caused by a lack of oxygen at the center of the tumor. Hypoxia leads to the expression of pro-metastatic genes as well as the repression of anti-metastatic genes. As many Affymetrix datasets about metastasis and hypoxia are publicly available and not fully exploited, this study proposes to re-analyze these datasets to extract new information about the metastatic phenotype induced by hypoxia in different cancer cell lines. Affymetrix datasets about metastasis and/or hypoxia were downloaded from GEO and ArrayExpress. AffyProbeMiner and GCRMA packages were used for pre-processing and the Window Welch t test was used for processing. Three approaches of meta-analysis were eventually used for the selection of genes of interest. Three complementary approaches were used, that eventually selected 183 genes of interest. Out of these 183 genes, 99, among which the well known JUNB, FOS and TP63, have already been described in the literature to be involved in cancer. Moreover, 39 genes of those, such as SERPINE1 and MMP7, are known to regulate metastasis. Twenty-one genes including VEGFA and ID2 have also been described to be involved in the response to hypoxia. Lastly, DAVID classified those 183 genes in 24 different pathways, among which 8 are directly related to cancer while 5 others are related to proliferation and cell motility. A negative control composed of 183 random genes failed to provide such results. Interestingly, 6 pathways retrieved by DAVID with the 183 genes of interest concern pathogen recognition and phagocytosis. The proposed methodology was able to find genes actually known to be involved in cancer, metastasis and hypoxia and, thus, we propose that the other genes selected based on the same methodology are of prime interest in

  14. Metabolomic phenotyping of a cloned pig model

    Directory of Open Access Journals (Sweden)

    Callesen Henrik

    2011-08-01

    Full Text Available Abstract Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5 was for the first time elucidated by nuclear magnetic resonance (NMR-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6 by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals.

  15. Optical Fiber Grating Sensor for Force Measurement of Anchor Cable

    Institute of Scientific and Technical Information of China (English)

    JIANG Desheng; FU Jinghua; LIU Shengchun; SUI Lingfeng; FU Rong

    2006-01-01

    The development of the sensor suitable for measuring large load stress to the anchor cable becomes an important task in bridge construction and maintenance. Therefore, a new type of optical fiber sensor was developed in the laboratory - optical fiber grating sensor for force measurement of anchor cable (OFBFMAC). No similar report about this kind of sensor has been found up to now in China and other countries. This sensor is proved to be an effective way of monitoring in processes of anchor cable installation, cable cutting, cable force regulation, etc, with the accurate and repeatable measuring results. Its successful application in the tie bar cable force safety monitoring for Wuhan Qingchuan bridge is a new exploration of optical fiber grating sensing technology in bridge tie bar monitoring system.

  16. Plate anchored stirrup; Pureto teichakugata sendan hokyo tekkin

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, T.; Tanaka, Y.; Nakano, K.; Yamamoto, T. [Taisei Construction Co. Ltd., Tokyo (Japan)

    1998-09-01

    After the Great Hanshin Earthquake, the use of edge form of stirrups of semicircular hook or acute-angled hook which functions sufficiently even after exfoliation of concrete cover is proposed instead of right angle hook. However, when these stirrups are used in plate structures requiring hooks on two ends or in columns as connection reinforcement of hoop, the construction of these stirrups is so complicated that brings higher cost. The authors proposes stirrups to anchor by plate for stirrups of planar members. Anchorage capacity of these plate anchored stirrups and hooks after exfoliation of concrete cover was examined by experiments and the anchorage capacity was confirmed to be larger than that of semicircular hooks. The plate anchored stirrups are effective and easy to construct with low cost. 7 refs., 13 figs., 4 tabs.

  17. Addition of lipid substituents of mammalian protein glycosylphosphoinositol anchors.

    OpenAIRE

    Singh, N.; Zoeller, R A; Tykocinski, M. L.; Lazarow, P B; Tartakoff, A M

    1994-01-01

    A single metabolic path leading to synthesis of ether lipids is known in animal cells, the major products of which are plasmalogens. To learn whether this peroxisomal path is also responsible for the synthesis of base-resistant lipid components of glycosylphosphoinositol (GPI)-anchored membrane proteins, we have investigated the structure of anchor precursor mannolipids both in wild-type cells (CHO-K1 and a macrophage-like line, RAW 264.7) and in two corresponding mutant cells in which ether ...

  18. GEE for GWAS using Longitudinal Phenotype Data

    OpenAIRE

    Sitlani, Colleen M.; Rice, Kenneth M.; Lumley, Thomas; McKnight, Barbara; Cupples, L. Adrienne; Avery, Christy L; Noordam, Raymond; Stricker, Bruno H. C.; Whitsel, Eric A.; Psaty, Bruce M.

    2014-01-01

    Many longitudinal cohort studies have both genome-wide measures of genetic variation and repeated measures of phenotypes and environmental exposures. Genome-wide association study analyses have typically used only cross-sectional data to evaluate quantitative phenotypes and binary traits. Incorporation of repeated measures may increase power to detect associations, but also requires specialized analysis methods. Here we discuss one such method – generalized estimating equations...

  19. Current status of frameless anchored IUD for immediate intracesarean insertion.

    Science.gov (United States)

    Wildemeersch, Dirk; Goldstuck, Norman D; Hasskamp, Thomas

    2016-01-01

    Immediate postpartum intrauterine device (IUD) insertion deserves great attention as it can provide immediate, timely and convenient contraception plus the added benefit of preventing repeat unintended pregnancies. Although women post vaginal delivery can benefit from immediate post-placenta contraception, women undergoing Cesarean section clearly need contraception, as an inter-delivery interval shorter than 18 months places them at a high risk for uterine rupture. The main drawback of currently available framed IUD devices for immediate postpartum insertion of an IUD is their high expulsion and displacement rates when inserted immediately postpartum after both vaginal and Cesarean delivery. Current research suggests that a brief window of opportunity exists of 10 minutes for insertion of conventional IUDs after which time expulsion rates both immediately and over time are greatly enhanced. This paper summarizes the current research conducted to overcome the expulsion problems associated with conventional T-shaped devices as well as through the use of an anchored frameless device. In the 1970s and 1980s, attempts were made to solve the expulsion problem by modifying existing devices, such as adding absorbable sutures (Delta-T) or additional appendages. These attempts proved to be clinically unsuccessful as the catgut suture added to the transverse arms did not provide sufficient resistance to prevent downward displacement and expulsion. An anchoring technique to suspend a copper IUD to the fundus of the uterus was developed in Belgium in the 1980s and has been the subject of extensive ongoing clinical research since 1985. Recently the frameless copper releasing anchor IUD, GyneFix, has been tested for postplacental insertion. Initially, the anchor was modified by the inclusion of a biodegradable cone which was added below the anchoring knot. Clinical studies confirmed the adequacy of this approach suggesting that it was technically possible to anchor an IUD

  20. [Dactylogyrids (Monogenea: Dactylogyridea) with an unusual number of anchors, their origin and phylogenetic significance. Reference data].

    Science.gov (United States)

    Gerasev, P I

    2002-01-01

    It is considered that in Anacanthorinae, Markewitschiana and Pseudacolpenteron pavlovskii (Dactylogyridae s. s.) the anchors are absent originally. In the other dactylogyrids (s. l.) without anchors (Pseudacolpenteron ignotus; Acolpenteron; Anonchohaptor-Icelanchohaptor; Kritskyia-Telethecium-Pavanelliela) these structures are lost. In related genera Rhinoxenus and Nanotrema the dorsal pair of anchors is transformed into the "spikes"; in Heteronchocleidinae there is one anchor; in Trinigyrus and Schilbetrematoides are two anchors; and in Urogyrus three anchors are reduced. But in Rhinonaster, Cacatyocotyle, Callceostomella, Neocalseostoma elongatum and Pseudodactylogyridae the presence of one pair of ventral "peduncular" or "haptoral" anchors appear to be the original state. For Anacanthorinae and Dactylogyridae s. s. the presence of 18-16 hooks, original lacking of anchors, appearance of one pair of them, evolutionary development and subsequent reduction of these structures are characteristic. In the dactylogyrids (s. l.) having two pairs of anchors and 14 hooks, one pair of the anchors is present originally, then usually the second dorsal pair grows up, and finally, the reduction of a part of anchors or all the anchors is possible. In the 16-hooked dactylogyrids (s. l.) having two pairs of anchors (Tetraonchinea, Amphibdellainea, Neodactylodiscinea) the original lacking or reduction of the anchors is not reported. The author considers, that it is unwarranted to unite all dactylogyrids (s. l.) without anchors into the superorder Ananchorea Malmberg, 1990 or to postulate the original presence of the two pairs of ventral anchors in this group. It is also impossible to unit all dactylogyrids (s. l.) having 0-4 anchors and 18-14 hooks into Dactylogyridae sensu Boeger et Kritsky, 1993. PMID:12070963

  1. SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species.

    OpenAIRE

    Rebekah E Oliver; Tinker, Nicholas A.; Lazo, Gerard R.; Shiaoman Chao; Jellen, Eric N.; Martin L. Carson; Rines, Howard W; Donald E Obert; Lutz, Joseph D.; Irene Shackelford; Korol, Abraham B.; Charlene P. Wight; Gardner, Kyle M.; Jiro Hattori; Beattie, Aaron D

    2013-01-01

    A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources wer...

  2. Cluster analysis of bone microarchitecture from high resolution peripheral quantitative computed tomography demonstrates two separate phenotypes associated with high fracture risk in men and women.

    Science.gov (United States)

    Edwards, M H; Robinson, D E; Ward, K A; Javaid, M K; Walker-Bone, K; Cooper, C; Dennison, E M

    2016-07-01

    Osteoporosis is a major healthcare problem which is conventionally assessed by dual energy X-ray absorptiometry (DXA). New technologies such as high resolution peripheral quantitative computed tomography (HRpQCT) also predict fracture risk. HRpQCT measures a number of bone characteristics that may inform specific patterns of bone deficits. We used cluster analysis to define different bone phenotypes and their relationships to fracture prevalence and areal bone mineral density (BMD). 177 men and 159 women, in whom fracture history was determined by self-report and vertebral fracture assessment, underwent HRpQCT of the distal radius and femoral neck DXA. Five clusters were derived with two clusters associated with elevated fracture risk. "Cluster 1" contained 26 women (50.0% fractured) and 30 men (50.0% fractured) with a lower mean cortical thickness and cortical volumetric BMD, and in men only, a mean total and trabecular area more than the sex-specific cohort mean. "Cluster 2" contained 20 women (50.0% fractured) and 14 men (35.7% fractured) with a lower mean trabecular density and trabecular number than the sex-specific cohort mean. Logistic regression showed fracture rates in these clusters to be significantly higher than the lowest fracture risk cluster [5] (pfemoral neck areal BMD was significantly lower than cluster 5 in women in cluster 1 and 2 (p<0.001 for both), and in men, in cluster 2 (p<0.001) but not 1 (p=0.220). In conclusion, this study demonstrates two distinct high risk clusters in both men and women which may differ in etiology and response to treatment. As cluster 1 in men does not have low areal BMD, these men may not be identified as high risk by conventional DXA alone. PMID:27130873

  3. Characterization of Regenerative Phenotype of Unrestricted Somatic Stem Cells (USSC) from Human Umbilical Cord Blood (hUCB) by Functional Secretome Analysis.

    Science.gov (United States)

    Schira, Jessica; Falkenberg, Heiner; Hendricks, Marion; Waldera-Lupa, Daniel M; Kögler, Gesine; Meyer, Helmut E; Müller, Hans Werner; Stühler, Kai

    2015-10-01

    Stem cell transplantation is a promising therapeutic strategy to enhance axonal regeneration after spinal cord injury. Unrestricted somatic stem cells (USSC) isolated from human umbilical cord blood is an attractive stem cell population available at GMP grade without any ethical concerns. It has been shown that USSC transplantation into acute injured rat spinal cords leads to axonal regrowth and significant locomotor recovery, yet lacking cell replacement. Instead, USSC secrete trophic factors enhancing neurite growth of primary cortical neurons in vitro. Here, we applied a functional secretome approach characterizing proteins secreted by USSC for the first time and validated candidate neurite growth promoting factors using primary cortical neurons in vitro. By mass spectrometric analysis and exhaustive bioinformatic interrogation we identified 1156 proteins representing the secretome of USSC. Using Gene Ontology we revealed that USSC secretome contains proteins involved in a number of relevant biological processes of nerve regeneration such as cell adhesion, cell motion, blood vessel formation, cytoskeleton organization and extracellular matrix organization. We found for instance that 31 well-known neurite growth promoting factors like, e.g. neuronal growth regulator 1, NDNF, SPARC, and PEDF span the whole abundance range of USSC secretome. By the means of primary cortical neurons in vitro assays we verified SPARC and PEDF as significantly involved in USSC mediated neurite growth and therewith underline their role in improved locomotor recovery after transplantation. From our data we are convinced that USSC are a valuable tool in regenerative medicine as USSC's secretome contains a comprehensive network of trophic factors supporting nerve regeneration not only by a single process but also maintained its regenerative phenotype by a multitude of relevant biological processes. PMID:26183719

  4. 76 FR 10627 - Assumption Buster Workshop: Trust Anchors Are Invulnerable

    Science.gov (United States)

    2011-02-25

    ...) Committee, an interagency working group that coordinates cyber security research activities in support of... confident that they are immune from the attacks.'' This assertion underlies significant cyber security research and development that is aimed at developing and implementing invulnerable trust anchors,...

  5. When Does Scale Anchoring Work? A Case Study

    Science.gov (United States)

    Sinharay, Sandip; Haberman, Shelby J.; Lee, Yi-Hsuan

    2011-01-01

    Providing information to test takers and test score users about the abilities of test takers at different score levels has been a persistent problem in educational and psychological measurement. Scale anchoring, a technique which describes what students at different points on a score scale know and can do, is a tool to provide such information.…

  6. The importance of anchor text for ad hoc search revisited

    NARCIS (Netherlands)

    M. Koolen; J. Kamps

    2010-01-01

    It is generally believed that propagated anchor text is very important for effective Web search as offered by the commercial search engines. "Google Bombs" are a notable illustration of this. However, many years of TREC Web retrieval research failed to establish the effectiveness of link evidence fo

  7. Ten Anchor Points for Teaching Principles of Marketing

    Science.gov (United States)

    Tomkovick, Chuck

    2004-01-01

    Effective marketing instructors commonly share a love for their students, an affinity for the subject matter, and a devotion to continuous quality improvement. The purpose of this article is to highlight 10 anchor points for teaching Principles of Marketing, which are designed to better engage students in the learning process. These anchor…

  8. A+: Adjusted anchored neighborhood regression for fast super-resolution

    OpenAIRE

    Timofte, Radu; De Smet, Vincent; Van Gool, Luc

    2015-01-01

    Timofte R., De Smet V., Van Gool L., ''A+: Adjusted anchored neighborhood regression for fast super-resolution'', Lecture notes in computer science, vol. 9006, part IV, pp. 111-126, 2015 (12th Asian conference on computer vision - ACCV 2014, November 1-5, 2014, Singapore).

  9. Analytical Model for Hook Anchor Pull-Out

    DEFF Research Database (Denmark)

    Brincker, Rune; Ulfkjær, J. P.; Adamsen, P.;

    1995-01-01

    A simple analytical model for the pull-out of a hook anchor is presented. The model is based on a simplified version of the fictitious crack model. It is assume that the fracture process is the pull-off of a cone shaped concrete part, simplifying the problem by assuming pure rigid body motions...

  10. Analytical Model for Hook Anchor Pull-out

    DEFF Research Database (Denmark)

    Brincker, Rune; Ulfkjær, J. P.; Adamsen, P.;

    A simple analytical model for the pull-out of a hook anchor is presented. The model is based on a simplified version of the fictitious crack model. It is assumed that the fracture process is the pull-off of a cone shaped concrete part, simplifying the problem by assuming pure rigid body motions...

  11. Impact of Enhanced Anchored Instruction in Inclusive Math Classrooms

    Science.gov (United States)

    Bottge, Brian A.; Toland, Michael D.; Gassaway, Linda; Butler, Mark; Choo, Sam; Griffen, Ann Katherine; Ma, Xin

    2015-01-01

    The Common Core State Standards for Mathematics will place more pressure on special education and math teachers to raise the skill levels of all students, especially those with disabilities in math (MD). The purpose of this study was to assess the effects of enhanced anchored instruction (EAI) on students with and without MD in co-taught general…

  12. Experience-based, body-anchored qualitative research interviewing

    DEFF Research Database (Denmark)

    Stelter, Reinhard

    2010-01-01

    -anchored interviewing, and second, by an interview guide that explores a research participant's personal experience with mindfulness meditation. An excerpt from an interview is discussed to illustrate the advantages of this interview form, namely its value as a methodological instrument for qualitative research in...

  13. Fullerene-based Anchoring Groups for Molecular Electronics

    DEFF Research Database (Denmark)

    Martin, Christian A.; Ding, Dapeng; Sørensen, Jakob Kryger;

    2008-01-01

    We present results on a new fullerene-based anchoring group for molecular electronics. Using lithographic mechanically controllable break junctions in vacuum we have determined the conductance and stability of single-molecule junctions of 1,4-bis(fullero[c]pyrrolidin-1-yl)benzene. The compound can...

  14. Analysis of β-lactamase phenotypes and carriage of selected β-lactamase genes among Escherichia coli strains obtained from Kenyan patients during an 18-year period

    Directory of Open Access Journals (Sweden)

    Kiiru John

    2012-07-01

    Full Text Available Abstract Background Although β-lactam antibiotics are heavily used in many developing countries, the diversity of β-lactamase genes (bla is poorly understood. We screened for major β-lactamase phenotypes and diversity of bla genes among 912 E. coli strains isolated from clinical samples obtained between 1992 and 2010 from hospitalized and non-hospitalized patients. Results None of the isolates was resistant to carbapenems but 30% of all isolates were susceptible to cefepime, cephamycins and piperacillin-tazobactam. Narrow spectrum β-lactamase (NSBL phenotype was observed in 278 (30% isolates that contained blaTEM-1 (54% or blaSHV-1 (35% or both (11%. Extended Spectrum β-lactamase (ESBL phenotype was detected in 247 (27% isolates which carried blaCTX-M-14 (29%, blaCTX-M-15 (24%, blaCTX-M-9 (2%, blaCTX-M-8 (4%, blaCTX-M-3 (11%, blaCTX-M-1 (6%, blaSHV-5 (3%, blaSHV-12 (5%, and blaTEM-52 (16%. Complex Mutant TEM-like (CMT phenotype was detected in 220 (24% isolates which carried blaTEM-125 (29%, while blaTEM-50, blaTEM-78, blaTEM-109, blaTEM −152 and blaTEM-158 were detected in lower frequencies of between 7% and 11%. Majority of isolates producing a combination of CTX-M-15 + OXA-1 + TEM-1 exhibited resistance phenotypes barely indistinguishable from those of CMT-producers. Although 73 (8% isolates exhibited Inhibitor Resistant TEM-like (IRT phenotype, blaTEM-103 was the only true IRT-encoding gene identified in 18 (25% of strains with this phenotype while the rest produced a combination of TEM-1 + OXA-1. The pAmpCs-like phenotype was observed in 94 (10% isolates of which 77 (82% carried blaCMY-2 while 18% contained blaCMY-1. Isolates from urine accounted for 53%, 53%, 74% and 72% of strains exhibiting complex phenotypes such as IRT, ESBL, CMT or pAmpC respectively. On the contrary, 55% isolates from stool exhibited the relatively more susceptible NSBL-like phenotype. All the phenotypes, and majority of the bla genes, were

  15. A Single-hole stone anchor from Kottapatnam: Early historic port site of Andhra Pradesh, India

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.; Rao, K.P.; Kumari, S.; Imsong, O.; Vanlalhruaitluangi, V.

    broken piece of polished stone celt in addition to other findings. The recent explorations brought to light a Vijayanagar period coin, pottery and a single hole stone anchor. The finding of the stone anchor throws light on the maritime activities...

  16. Serum Biochemical Phenotypes in the Domestic Dog

    Science.gov (United States)

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A.

    2016-01-01

    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  17. Estimation of maximum axial force of anchor bolts in consideration of random bolt failures

    International Nuclear Information System (INIS)

    This paper proposes a method for structural reliability analysis of anchor bolts used in the support skirt of a reactor vessel. The method is based on the conservative assumption that a few anchor bolts within the skirt's inner-wall may fail in a random nature. Under the assumption, the maximum axial forces in the intact bolts are estimated. To reflect the uncertainty, random numbers are generated to simulate the possible failed bolts among a total of 60 bolts, which are circumferentially arranged along the inner side of the wall. Then the outcome of failed bolts together with their locations for every 60 bolts is defined as an experiment of a sample. The locations of failed bolt can significantly affect the stress analysis and its random outcomes require an efficient calculation scheme. In this paper we propose a rapid calculation algorithm, thus the direction of bending moment that causes the worst scenario in the stress analysis of bolts for each experiment can be rapidly found. Taking into consideration of design loads, the finite element method is further employed to calculate the maximum axial bolt force of each experiment. After statistical analysis of maximum axial forces from all experiments, the average maximum axial-force interval that the remaining bolts can withstand under a given random condition is estimated with a 95% confidence level. This interval can be used in conjunction with various results of structural integrity assessment to ensure the structural safety and reliability of a nuclear power plant component

  18. Anchoring a Leviathan: How the Nuclear Membrane Tethers the Genome

    Directory of Open Access Journals (Sweden)

    Rafal eCzapiewski

    2016-05-01

    Full Text Available It is well established that the nuclear envelope has many distinct direct connections to chromatin that contribute to genome organization. The functional consequences of genome organization on gene regulation are less clear. Even less understood is how interactions of lamins and nuclear envelope transmembrane proteins (NETs with chromatin can produce anchoring tethers that can withstand the physical forces of and on the genome. Chromosomes are the largest molecules in the cell, making megadalton protein structures like the nuclear pore complexes and ribosomes seem small by comparison. Thus to withstand strong forces from chromosome dynamics an anchoring tether is likely to be much more complex than a single protein-protein or protein-DNA interaction. Here we will briefly review known NE-genome interactions that likely contribute to spatial genome organization, postulate in the context of experimental data how these anchoring tethers contribute to gene regulation, and posit several hypotheses for the physical nature of these tethers that need to be investigated experimentally. Significantly, disruption of these anchoring tethers and the subsequent consequences for gene regulation could explain how mutations in nuclear envelope proteins cause diseases ranging from muscular dystrophy to lipodystrophy to premature ageing progeroid syndromes. The two favored hypotheses for nuclear envelope protein involvement in disease are 1 weakening nuclear and cellular mechanical stability, and 2 disrupting genome organization and gene regulation. Considerable experimental support has been obtained for both. The integration of both mechanical and gene expression defects in the disruption of anchoring tethers could provide a unifying hypothesis consistent with both.

  19. Characterizing the flow of stirred vessels with anchor type impellers

    Directory of Open Access Journals (Sweden)

    Peixoto S.M.C.

    2000-01-01

    Full Text Available Despite its importance in chemical industries, there are few works which studies anchor type impellers and only a fraction of the works investigate these systems under a computational approach. The great majority refers to turbine impellers, specially Rushton turbines, under turbulent flow. Anchor impellers are used specially for highly viscous flow, typical of polymer reactions. The viscosity is normally in the range 1000-10000 cp. Since this range of viscosity describe highly viscous flows, the reactions for anchor agitated systems are normally carried out under laminar flow. This work presents a detailed computational fluid dynamics (CFD approach to study the behaviour of stirred vessels using anchor impellers. The axial plane of the tank, which is being modelled, is divided into small control volumes, which collectively is referred to as the mesh, or grid. In each of these cells the momentum balance, energy and mass conservation, which describes the model, are rewritten algebraically using the finite volumes method to relate such variables as velocity, pressure and temperature to values in neighbouring cells. The equations are then solved numerically, and the results yield the flow corresponding to the model. Since the geometry of a vessel with anchor impellers strictly calls for a three dimensional method, an approximation is made to account for the effect of the blades (Kuncewics, 1992. The main objective of this work is to give a detailed description of the flow generated by this axial impeller with a view to indicate ways in which the design and operation of these systems can be improved.

  20. Phenotypic profiles of Armenian grape cultivars

    Directory of Open Access Journals (Sweden)

    Aroutiounian Rouben

    2015-01-01

    Full Text Available The conservation and sustainable use of grapevine biodiversity in Armenia is particularly important due to the large number of traditional local varieties. Being partially different from European grapevine gene pool, the material of Armenian local cultivars significantly contributes to the understanding of the genetic variation and is valuable source for target selection. During last years many Armenian grapevine cultivars have been already described and their genotypes determined, but some local varieties and wild accessions remain unidentified and their phenotypic characteristics overlooked. The comprehensive analysis of phenotypes is essential for research, including genetic association studies, cultivar evaluation and selection. The goal of our research was the phenotyping on the base of reproductive, carpological and analytical characteristics of 80 Armenian aboriginal and new grape cultivars. Description of phenotypic profiles is important step towards identification and conservation of genetic resources of Armenian grapes. In future, these data can be applied for breeding of improved grape varieties targeted to fresh consumption and wine production.

  1. Mining skeletal phenotype descriptions from scientific literature.

    Directory of Open Access Journals (Sweden)

    Tudor Groza

    Full Text Available Phenotype descriptions are important for our understanding of genetics, as they enable the computation and analysis of a varied range of issues related to the genetic and developmental bases of correlated characters. The literature contains a wealth of such phenotype descriptions, usually reported as free-text entries, similar to typical clinical summaries. In this paper, we focus on creating and making available an annotated corpus of skeletal phenotype descriptions. In addition, we present and evaluate a hybrid Machine Learning approach for mining phenotype descriptions from free text. Our hybrid approach uses an ensemble of four classifiers and experiments with several aggregation techniques. The best scoring technique achieves an F-1 score of 71.52%, which is close to the state-of-the-art in other domains, where training data exists in abundance. Finally, we discuss the influence of the features chosen for the model on the overall performance of the method.

  2. An Investigation to Determine the Career Anchors Which Affect the Career Decision of Tourism Students

    OpenAIRE

    GEZEN, Tuba; Köroğlu, Özlem

    2014-01-01

    AbstractAlthough career anchors are used as a career tool in organizations, are examined in many limited researches. The purpose of this study is to determine the career anchors which affect the job and career decision of the tourism students. Therefore, Tourism and Hotel Management students who attend four-year programs/departments of Balikesir University have been conducted surveys. The Career Anchors Scale developed by Schein (1990) has been used to determine the career anchors of the tour...

  3. Developments, expectations of wave energy converters and mooring anchors in the UK

    Science.gov (United States)

    Huang, Ming; Aggidis, G. A.

    2008-02-01

    The paper introduces the important developments of Wave Energy Converters (WECs) in the UK, and the generic anchor types for WECs and similar structures. Several WECs and their characteristics are introduced to explain the development direction. The anchors are discussed in relation to the behaviour and performance of WECs, and comparisons are made with similar aspects of the offshore industry. Typical and desirable features of anchors for WECs are summarized. Additionally, expectations and research suggestions for WECs and their anchor design are presented.

  4. Cement grouting during installation of ground anchors in non-cohesive soils

    OpenAIRE

    Domes, Xenia A. L.

    2015-01-01

    Pressure grouting during installation of grouted ground anchors is known to increase anchor capacity in non-cohesive soils, but little information is available on correlations between applied grouting pressures, duration of grouting, ground conditions and increase of anchor pull-out capacity. The presented PhD study is concerned with processes taking place during installation of grouted ground anchors in non-cohesive soils, where filtration of the cement grout is assumed. It...

  5. A group of 20 stone anchors from the waters of Dwarka, on the Gujarat Coast, India

    Digital Repository Service at National Institute of Oceanography (India)

    Gaur, A; Sundaresh; Tripati, S.; Gudigar, P.; Vora, K.H.; Bandodkar, S.N.

    A large number of stone anchors were discovered in a water depth of 10-14 m off Dwarka during the 1998-99 season. The seabed near the anchors consists of a ledge with an average height of 1 m. Several anchors were found trapped between the rocks...

  6. 33 CFR 401.83 - Reporting position at anchor, wharf, etc.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Reporting position at anchor, wharf, etc. 401.83 Section 401.83 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT... § 401.83 Reporting position at anchor, wharf, etc. A vessel anchoring in a designated anchorage area,...

  7. Biomimetic Mussel Adhesive Inspired Clickable Anchors Applied to the Functionalization of Fe3O4 Nanoparticles

    NARCIS (Netherlands)

    Goldmann, Anja S.; Schoedel, Christine; Walther, Andreas; Yuan, Jiayin; Loos, Katja; Mueller, Axel H. E.; Müller, Axel H.E.

    2010-01-01

    The functionalization of magnetite (Fe3O4) nanoparticles with dopamine-derived clickable biomimetic anchors is reported. Herein, an alkyne-modified catechol-derivative is employed as the anchor, as i) the catechol-functional anchor groups possess irreversible covalent binding affinity to Fe3O4 nanop

  8. Display of GPI-anchored anti-EGFR nanobodies on extracellular vesicles promotes tumour cell targeting

    Directory of Open Access Journals (Sweden)

    Sander A. A. Kooijmans

    2016-03-01

    Full Text Available Background: Extracellular vesicles (EVs are attractive candidate drug delivery systems due to their ability to functionally transport biological cargo to recipient cells. However, the apparent lack of target cell specificity of exogenously administered EVs limits their therapeutic applicability. In this study, we propose a novel method to equip EVs with targeting properties, in order to improve their interaction with tumour cells. Methods: EV producing cells were transfected with vectors encoding for anti-epidermal growth factor receptor (EGFR nanobodies, which served as targeting ligands for tumour cells, fused to glycosylphosphatidylinositol (GPI anchor signal peptides derived from decay-accelerating factor (DAF. EVs were isolated using ultrafiltration/size-exclusion liquid chromatography and characterized using western blotting, Nanoparticle Tracking Analysis, and electron microscopy. EV–tumour cell interactions were analyzed under static conditions using flow cytometry and under flow conditions using a live-cell fluorescence microscopy-coupled perfusion system. Results: V analysis showed that GPI-linked nanobodies were successfully displayed on EV surfaces and were highly enriched in EVs compared with parent cells. Display of GPI-linked nanobodies on EVs did not alter general EV characteristics (i.e. morphology, size distribution and protein marker expression, but greatly improved EV binding to tumour cells dependent on EGFR density under static conditions. Moreover, nanobody-displaying EVs showed a significantly improved cell association to EGFR-expressing tumour cells under flow conditions. Conclusions: We show that nanobodies can be anchored on the surface of EVs via GPI, which alters their cell targeting behaviour. Furthermore, this study highlights GPI-anchoring as a new tool in the EV toolbox, which may be applied for EV display of a variety of proteins, such as antibodies, reporter proteins and signaling molecules.

  9. Influence of anchor behaviour on the earthquake response of liquid storage tanks

    International Nuclear Information System (INIS)

    The dynamic response of thin liquid storage tanks to earthquakes is a very complicated phenomenon, because it can be highly non linear. Among others, one can meet material and geometric non linearities of the tank shell leading eventually to static or dynamic buckling non linear behavior of anchor bolts, contact non-linearities due to the uplift of the tank base and to the unilateral character of the fluid pressure on the shell and high amplitude fluid oscillations. Moreover, linear or non linear soil structure interaction affects considerably the response of the fluid structure system under consideration. In this paper we focus attention on problems related only to the base uplift and anchors plastification. We study a tank similar to the Hualien project tank, but we neglect the soil structure interaction. The studied tank is representative of medium height to radius ratio ratio tanks with relatively thick bottom plate. The contact is simulated via a simple discrete penalty method in order to facilitate the calculation of the impact forces. Modal coordinates calculated for various Fourier harmonics are used for the dynamic analysis and the coupled modal equations of motion are solved with an explicit time integration algorithm. Obviously, this approach is less precise than a direct finite element analysis on the nodal basis but is less expensive. The scope of this paper is to discuss the efficiency of the proposed method to deal with problems like those aforementioned and to give some qualitative results concerning the influence of anchor bolts behaviour on the earthquake response of tanks. (author). 2 refs., 7 figs., 1 tab

  10. Mixed phenotype acute leukemia

    Institute of Scientific and Technical Information of China (English)

    Ye Zixing; Wang Shujie

    2014-01-01

    Objective To highlight the current understanding of mixed phenotype acute leukemia (MPAL).Data sources We collected the relevant articles in PubMed (from 1985 to present),using the terms "mixed phenotype acute leukemia","hybrid acute leukemia","biphenotypic acute leukemia",and "mixed lineage leukemia".We also collected the relevant studies in WanFang Data base (from 2000 to present),using the terms "mixed phenotype acute leukemia" and "hybrid acute leukemia".Study selection We included all relevant studies concerning mixed phenotype acute leukemia in English and Chinese version,with no limitation of research design.The duplicated articles are excluded.Results MPAL is a rare subgroup of acute leukemia which expresses the myeloid and lymphoid markers simultaneously.The clinical manifestations of MPAL are similar to other acute leukemias.The World Health Organization classification and the European Group for Immunological classification of Leukaemias 1998 cdteria are most widely used.MPAL does not have a standard therapy regimen.Its treatment depends mostly on the patient's unique immunophenotypic and cytogenetic features,and also the experience of individual physician.The lack of effective treatment contributes to an undesirable prognosis.Conclusion Our understanding about MPAL is still limited.The diagnostic criteria have not been unified.The treatment of MPAL remains to be investigated.The prognostic factor is largely unclear yet.A better diagnostic cdteria and targeted therapeutics will improve the therapy effect and a subsequently better prognosis.

  11. Phenotypic Resistance to Antibiotics

    Directory of Open Access Journals (Sweden)

    Jose L. Martinez

    2013-04-01

    Full Text Available The development of antibiotic resistance is usually associated with genetic changes, either to the acquisition of resistance genes, or to mutations in elements relevant for the activity of the antibiotic. However, in some situations resistance can be achieved without any genetic alteration; this is called phenotypic resistance. Non-inherited resistance is associated to specific processes such as growth in biofilms, a stationary growth phase or persistence. These situations might occur during infection but they are not usually considered in classical susceptibility tests at the clinical microbiology laboratories. Recent work has also shown that the susceptibility to antibiotics is highly dependent on the bacterial metabolism and that global metabolic regulators can modulate this phenotype. This modulation includes situations in which bacteria can be more resistant or more susceptible to antibiotics. Understanding these processes will thus help in establishing novel therapeutic approaches based on the actual susceptibility shown by bacteria during infection, which might differ from that determined in the laboratory. In this review, we discuss different examples of phenotypic resistance and the mechanisms that regulate the crosstalk between bacterial metabolism and the susceptibility to antibiotics. Finally, information on strategies currently under development for diminishing the phenotypic resistance to antibiotics of bacterial pathogens is presented.

  12. Fc block treatment, dead cells exclusion, and cell aggregates discrimination concur to prevent phenotypical artifacts in the analysis of subpopulations of tumor-infiltrating CD11b(+) myelomonocytic cells.

    Science.gov (United States)

    Kuonen, Francois; Touvrey, Cedric; Laurent, Julien; Ruegg, Curzio

    2010-11-01

    It is well established that cancer cells can recruit CD11b(+) myeloid cells to promote tumor angiogenesis and tumor growth. Increasing interest has emerged on the identification of subpopulations of tumor-infiltrating CD11b(+) myeloid cells using flow cytometry techniques. In the literature, however, discrepancies exist on the phenotype of these cells (Coffelt et al., Am J Pathol 2010;176:1564-1576). Since flow cytometry analysis requires particular precautions for accurate sample preparation and trustable data acquisition, analysis, and interpretation, some discrepancies might be due to technical reasons rather than biological grounds. We used the syngenic orthotopic 4T1 mammary tumor model in immunocompetent BALB/c mice to analyze and compare the phenotype of CD11b(+) myeloid cells isolated from peripheral blood and from tumors, using six-color flow cytometry. We report here that the nonspecific antibody binding through Fc receptors, the presence of dead cells and cell doublets in tumor-derived samples concur to generate artifacts in the phenotype of tumor-infiltrating CD11b(+) subpopulations. We show that the heterogeneity of tumor-infiltrating CD11b(+) subpopulations analyzed without particular precautions was greatly reduced upon Fc block treatment, dead cells, and cell doublets exclusion. Phenotyping of tumor-infiltrating CD11b(+) cells was particularly sensitive to these parameters compared to circulating CD11b(+) cells. Taken together, our results identify Fc block treatment, dead cells, and cell doublets exclusion as simple but crucial steps for the proper analysis of tumor-infiltrating CD11b(+) cell populations. PMID:20824631

  13. Prognosis of complicated clinical course of varicose veins of lower extremities on the basis of analysis of phenotypic characteristics of connective tissue dysplasia

    Directory of Open Access Journals (Sweden)

    Tsarev О.А.

    2015-12-01

    Full Text Available Aim: to identify the phenotypic characteristics of indeterminate connective tissue dysplasia, which help to predict the progression of varicose veins of lower extremities and disease recurrence after surgery. Material and Methods. The long-term results of surgical treatment of 60 patients with varicose veins of lower extremities in a 5-year period after phlebectomy were analyzed. The phenotypic characteristics of indeterminate connective tissue dysplasia were researched. 24 patients had recurrence of varicose veins of lower extremities associated with disease progression; 36 patients did not have recurrence of varicose veins of lower extremities. Results. All the patients demonstrated the signs of indeterminate connective tissue dysplasia, whereas their frequency was different. There were specified nine phenotypic characteristics of indeterminate connective tissue dysplasia, which were significantly more frequent for patients with recurrence of varicose vein disease of lower extremities: 1 postural abnormality, 2 flat foot, 3 skin pallor, 4 hyperextension of skin, 5 positive "wrist test", 6 positive "pollex test", 7 diastasis recti abdominis, 8 myopia, 9 hematomas which form quickly. Conclusion. The determined sum of phenotypic characters of indeterminate connective tissue dysplasia allows to predict progression of varicose vein disease of lower extremities, and offers new opportunities for improving the results of surgical treatment via developing special therapeutic measures aimed at improving lifestyle and dysplasia treatment.

  14. Iron anchors of Northern Odisha, east coast India: Maritime contacts with European countries

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.; Patnaik, S.K.; Acharya, S.B.

    at Siraf. Second Interim Report. Iran 8: 1–17. 12    List of Figures Figure 1. Iron anchor find sites, ports and trade centres of Odisha. Figure 2. Iron anchor found at Balaramgadi, Northern Odisha (Photo: Sila Tripati) Figure 2a. Iron anchor found... at Balaramgadi, Northern Odisha (S.B. Chitari & Rudra Behera). Figure 3. Iron anchor found at Chandabali on the mouth of the River Baitarani (OMISEAS, Bhubaneswar). Figure 4. Iron anchor found at Chandabali on the mouth of the River Baitarani (Photo: Sila...

  15. Stability Testing of a Wide Bone-Anchored Device after Surgery without Skin Thinning

    Directory of Open Access Journals (Sweden)

    Malou Hultcrantz

    2015-01-01

    Full Text Available Objective. To longitudinally follow the osseointegration using Resonance Frequency Analysis (RFA for different lengths of abutment on a new wide bone-anchored implant, introduced with the non-skin thinning surgical technique. Study Design. A single-center, prospective 1 year study following adults with bone-anchored hearing implants. Materials and Methods. Implantation was performed and followed for a minimum of 1 year. All patients were operated on according to the tissue preserving technique. A 4.5 mm wide fixture (Oticon Medical with varying abutments (9 to 12 mm was used and RFA was tested 1 week, 7 weeks, 6 months, and 12 months later. Implant Stability Quotient (ISQ, was measured from 1 to 100. Stability was compared to a group of patients (N=7 implanted with another brand (Cochlear BI400 of 4.5 mm fixtures. Results. All 10 adults concluded the study. None of the participants lost their implant during the test period indicating a good anchoring of abutments to the wide fixture tested. Stability testing was shown to vary depending on abutment length and time after surgery and with higher values for shorter abutments and increasing values over the first period of time. One patient changed the abutment from 12 to 9 mm and another from a 9 to a 12 during the year. No severe skin problems, numbness around the implant, or cosmetic problems arose. Conclusion. After 1 year of follow-up, combination of a wide fixture implant and the non-skin thinning surgical technique indicates a safe procedure with good stability and no abutment losses.

  16. Mobile Anchor Assisted Node Localization for Wireless Sensor Networks

    CERN Document Server

    Chen, Hongyang; Huang, Pei; Poor, H Vincent; Sezaki, Kaoru

    2009-01-01

    In this paper, a cooperative localization algorithm is proposed that considers the existence of obstacles in mobilityassisted wireless sensor networks (WSNs). In this scheme, a mobile anchor (MA) node cooperates with static sensor nodes and moves actively to refine location performance. The localization accuracy of the proposed algorithm can be improved further by changing the transmission range of mobile anchor node. The algorithm takes advantage of cooperation betweenMAs and static sensors while, at the same time, taking into account the relay node availability to make the best use of beacon signals. For achieving high localization accuracy and coverage, a novel convex position estimation algorithm is proposed, which can effectively solve the localization problem when infeasible points occur because of the effects of radio irregularity and obstacles. This method is the only range-free based convex method to solve the localization problem when the feasible set of localization inequalities is empty. Simulatio...

  17. Simulation study of liquid crystal anchoring at a polymer surface

    Science.gov (United States)

    Hamaneh, Mehdi

    2005-03-01

    The process of rubbing a polymer substrate to induce planar anchoring has two effects. It aligns the polymer chains and also creates grooves in the surface. We have investigated which one of these effects is more important by conducting a series of simulations of molecules of 5CB in contact with a poly(vinyl alcohol) surface. The polymer surface was constructed from a set of parallel straight chains. It was then distorted to mimic the effect of grooves in a direction perpendicular to the chain direction, thus causing two opposing anchoring effects. It was found that the 5CB molecules ordered preferentially along the chain direction when the depth of the grooves was less than 20 percent of the distance between grooves. For grooves whose walls were more steeply pitched, the nematic ordering aligned with the grooves.

  18. Graphene nanoribbons anchored to SiC substrates

    Science.gov (United States)

    Le, Nam B.; Woods, Lilia M.

    2016-09-01

    Graphene nanoribbons are quasi-one-dimensional planar graphene allotropes with diverse properties dependent on their width and types of edges. Graphene nanoribbons anchored to substrates is a hybrid system, which offers novel opportunities for property modifications as well as experimental control. Here we present electronic structure calculations of zigzag graphene nanoribbons chemically attached via the edges to the Si or C terminated surfaces of a SiC substrate. The results show that the edge characteristics are rather robust and the properties are essentially determined by the individual nanoribbon. While the localized spin polarization of the graphene nanoribbon edge atoms is not significantly affected by the substrate, secondary energy gaps in the highest conduction and lowest valence region may emerge in the anchored structures. The van der Waals interaction together with the electrostatic interactions due to the polarity of the surface bonds are found to be important for the structure parameters and energy stability.

  19. Graphene nanoribbons anchored to SiC substrates.

    Science.gov (United States)

    Le, Nam B; Woods, Lilia M

    2016-09-14

    Graphene nanoribbons are quasi-one-dimensional planar graphene allotropes with diverse properties dependent on their width and types of edges. Graphene nanoribbons anchored to substrates is a hybrid system, which offers novel opportunities for property modifications as well as experimental control. Here we present electronic structure calculations of zigzag graphene nanoribbons chemically attached via the edges to the Si or C terminated surfaces of a SiC substrate. The results show that the edge characteristics are rather robust and the properties are essentially determined by the individual nanoribbon. While the localized spin polarization of the graphene nanoribbon edge atoms is not significantly affected by the substrate, secondary energy gaps in the highest conduction and lowest valence region may emerge in the anchored structures. The van der Waals interaction together with the electrostatic interactions due to the polarity of the surface bonds are found to be important for the structure parameters and energy stability. PMID:27392014

  20. Organization, 'Anchoring' of Knowledge, and Innovative Activity in Construction

    DEFF Research Database (Denmark)

    Drejer, Ina; Vinding, Anker Lund

    2006-01-01

    The construction industry is characterised by the widespread use of project organisation. It has been suggested that the relatively low level of innovative activity in the industry can be explained by the temporary nature of firm boundary-crossing projects. Survey data from the Danish construction...... industry is used to investigate the importance of learning and 'anchoring' of project-specific knowledge at the firm level for participation in innovative activities. The data cover both the overall Danish construction industry and a specific region, North Jutland, which has a relatively high...... specialisation of construction workers. Latent class and regression analyses reveal that firms that make extensive use of partnering, together with internal product and process evaluation and knowledge diffusion (labelled 'knowledge-anchoring mechanisms'), are more likely to participate in innovative activities...

  1. The disclosure of concealable stigmas: Analysis anchored in trust

    Directory of Open Access Journals (Sweden)

    Ben Capell

    2016-12-01

    Full Text Available Prior research on the disclosure of concealable stigmas at work has mostly overlooked the moderating and mediating role of employees’ trust in their supervisor and organization at large. The absence of trust from this field of study limits organizational efforts to foster inclusion at work. Thus, this paper presents a framework for examining the multiple linkages between employees’ trust in their direct supervisors and their organization, and the disclosure decision. Trust is proposed to be embedded in intra and extra organizational context, both in terms of the legal framework and the HR policies and practices. On the basis of synthesis of the literature, the article extends previous research and reviews of diversity by providing systematic review and recommendations that can help promote diversity management efforts and ultimately contribute to employees’ well-being as well as positive organizational outcomes.

  2. Dithiocarbamate Anchoring in Molecular Wire Junctions: A First Principles Study

    OpenAIRE

    Li, Zhenyu; Kosov, D. S.

    2007-01-01

    Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self assembly on gold surface opens the possibility for use of dithiocarbamate linkers to anchor molecular wires to gold electrodes. In this paper, we explore this hypothesis computationally. We computed the electron transport properties of 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based on the density ...

  3. Endoplasmic reticulum anchored heme-oxygenase 1 faces the cytosol

    OpenAIRE

    Gottlieb, Yehonatan; Truman, Marianna; Cohen, Lyora A.; Leichtmann-Bardoogo, Yael; Meyron-Holtz, Esther G.

    2012-01-01

    Heme-oxygenase 1 is an endoplasmic reticulum-anchored enzyme that breaks down heme into iron, carbon monoxide and biliverdin. Heme is a hydrophobic co-factor in many proteins, including hemoglobin. Free heme is highly cytotoxic and, therefore, both heme synthesis and breakdown are tightly regulated. During turnover of heme proteins, heme is released in the phago-lysosomal compartment or the cytosol. The subcellular location of the heme-oxygenase 1 active site has not been clarified. Using con...

  4. Indoor Pedestrian Positioning Tracking Algorithm with Sparse Anchor Nodes

    OpenAIRE

    Zhou Yong; Cai Zehui; Chen Pengpeng

    2013-01-01

    In order to solve the indoor pedestrian positioning and tracking problems under the condition of sparse anchor nodes, this paper presents a new tracking scheme which predicts the staff position under the condition of indoor location fingerprints based on particle filter. In the proposed algorithm, the indoor topology is adopted to constrain and correct the results. Simulation results show that the proposed algorithm can significantly improve the accuracy of indoor pedestrian positioning and t...

  5. PredGPI: a GPI-anchor predictor

    Directory of Open Access Journals (Sweden)

    Casadio Rita

    2008-09-01

    Full Text Available Abstract Background Several eukaryotic proteins associated to the extracellular leaflet of the plasma membrane carry a Glycosylphosphatidylinositol (GPI anchor, which is linked to the C-terminal residue after a proteolytic cleavage occurring at the so called ω-site. Computational methods were developed to discriminate proteins that undergo this post-translational modification starting from their aminoacidic sequences. However more accurate methods are needed for a reliable annotation of whole proteomes. Results Here we present PredGPI, a prediction method that, by coupling a Hidden Markov Model (HMM and a Support Vector Machine (SVM, is able to efficiently predict both the presence of the GPI-anchor and the position of the ω-site. PredGPI is trained on a non-redundant dataset of experimentally characterized GPI-anchored proteins whose annotation was carefully checked in the literature. Conclusion PredGPI outperforms all the other previously described methods and is able to correctly replicate the results of previously published high-throughput experiments. PredGPI reaches a lower rate of false positive predictions with respect to other available methods and it is therefore a costless, rapid and accurate method for screening whole proteomes.

  6. Experimental study and mechanism analysis of the anti-pulling behavior of glass fiber reinforced polymer anti-float anchor%玻璃纤维增强聚合物抗浮锚杆抗拔性能试验研究与机制分析

    Institute of Scientific and Technical Information of China (English)

    张明义; 寇海磊; 白晓宇; 张宗强

    2014-01-01

    As a kind of vertical anchoring technique, the anti-float anchor has been widely used in China, whose performance has begun to receive more attentions from researchers. However, steels may be eroded easily by groundwater or chemical solutions, which will cause the reductions of mechanical strength and service life, especially in subway engineering the steel anti-float anchor is forbidden. Glass fiber reinforced polymer (GFRP) anti-float anchor is a new kind of material which is composed of resin matrix and glass fiber. Compared with steel anchor, the GFRP anti-float anchor has higher strength, corrosion-resistance and light weight behavior. The field tests show the feasibility of GFRP anti-float anchor through embedded bare fiber optics sensor technique. According to the test results, the GFRP anti-float anchor stress-strain behaviors, load transfer mechanism and failure mechanism are considered. The test indicates that GFRP anti-float anchor is basically about shear failure and pullout capacity of anchors with28 mm are 250 kN, which can be satisfied with engineering demands. The axial forces of anchors fall gradually with depth, and it will not bear load beyond certain length. Results show that the effect distance of axial forces is about 3.7 m when the length of bond part is in range of 3.95~6.95 m in moderately weathered granite,which indicates that GFRP anti-float anchors also exist critical anchorage depth. The shear stress on interface of anchor is not evenly distributed, which peak value is being driven down, and so as to the zero value. The research results can provide evidence for application of GFRP anti-float anchor.%抗浮锚杆作为一种竖向锚固技术在我国许多地区广泛应用,锚杆作为抗浮结构的核心其性能受到极大关注。但因钢材易腐蚀,传统金属锚杆的耐久性受到质疑,特别是地铁等地下工程存在杂散电流,限制了金属抗浮锚杆的应用。玻璃纤维增强聚合物(GFRP)

  7. ANÁLISIS BAYESIANO DE ESTABILIDAD FENOTIPICA USANDO A PRIORI DE JEFFREYS BAYESIAN PHENOTYPIC STABILITY ANALYSIS USING JEFFREYS’S PRIOR

    Directory of Open Access Journals (Sweden)

    José Miguel Cotes Torres

    2006-06-01

    Full Text Available Uno de los métodos utilizados para evaluar estabilidad fenotípica es el propuesto por Shukla, el cual calcula la varianza de los genotipos dentro de la interacción genotipo por ambiente, para lo cual se hace uso de la estimación de los componentes de varianza dentro del análisis de varianza combinado. El acceso al cálculo de metodologías como REML e ML permitieron trabajar con datos que presentan algún grado de desbalance, sin embargo no solucionan de una manera adecuada el problema de la estimación de componentes de varianza negativos, los cuales son asumidos como cero y redistribuidos en los demás componentes positivos. El uso de la metodología bayesiana en la estimación de componentes de varianza resuelve satisfactoriamente este problema sin afectar los demás componentes. En este trabajo, se utilizaron datos de producción comercial de papa de 10 pruebas regionales realizadas en la región andina colombiana y se utilizó la metodología bayesiana en la solución del modelo mixto para la estimación de la varianza de Shukla con base en una distribución a priori no informativa de Jeffreys. Fueron obtenidas muestras de la distribución a posteriori conjunta mediante el algoritmo Independence Chain, con un tamaño de muestreo de 1,16x10(5 y un burnin de 500. Los resultados muestran que en la estimación REML de componentes de varianza tres genotipos presentan componentes de varianza estimados como cero. Las estimativas bayesianas son 89,35; 377,18 y 101,12; y los respectivos intervalos de credibilidad al 95% son: (2,13 - 371,70, (35,26 - 1363,67 y (2,33 - 434,53. Finalmente con estas estimativas no se afectó la estimación de los demás componentes de varianza.Shukla's variance is a very useful method for the analysis of phenotypic stability, computing the genotypic variance among the genotype by environment interaction, using variance component estimation of combined analysis of variance. New methodologies like REML or ML allow

  8. NOD2/CARD15 Gene Polymorphisms in Crohn's Disease: A Genotype-Phenotype Analysis in Danish and Portuguese Patients and Controls

    DEFF Research Database (Denmark)

    Vind, Ida; Vieira, A; Hougs, L; Tavares, L; Riis, L; Andersen, P S; Locht, H; Freitas, J; Monteiro, E; Christensen, Ib Jarle; Munkholm, P

    a healthy background population and to compare genotype-phenotype relations in the two countries. METHODS: 58 Danish patients and 29 Portuguese patients with CD were matched for age, sex and disease behaviour at time of diagnosis and compared with 200 healthy Danish and Portuguese controls....... Phenotypes were recorded at year of diagnosis, 3 years after diagnosis and at end of follow-up. Patients were genotyped for Arg702Trp, Gly908Arg and Leu1007InsC. RESULTS: 22% of the Danish patients vs. 9% of Danish controls compared to 21% of the Portuguese patients vs. 16% had at least one mutation....... Mutation rates in Danish patients were significantly different (p=0.02) compared with Danish controls, no difference (p=0.51) was found between Portuguese patients and controls. However, a possible relationship between CD and presence of genetic mutations was found when comparing the two countries (p=0...

  9. Phenotypic Switching in Fungi

    OpenAIRE

    Jain, Neena; Hasan, Fahmi; Fries, Bettina C.

    2008-01-01

    Over the past three decades new fungal diseases have emerged that now constitute a major threat, especially for patients with chronic diseases and/or underlying immune defi ciencies. Despite the epidemiologic data, the emergence of stable drug-resistant or hyper-virulent fungal strains in human disease has not been demonstrated as seen in emerging viral and bacterial infections. Fungi are eukaryotic microbes that capitalize on a sophisticated built-in ability to generate phenotypic variabilit...

  10. Analysis of Large Phenotypic Variability of EEC and SHFM4 Syndromes Caused by K193E Mutation of the TP63 Gene

    OpenAIRE

    Jianhua Wei; Yang Xue; Lian Wu; Jie Ma; Xiuli Yi; Junrui Zhang; Bin Lu; Chunying Li; Dashuang Shi; Songtao Shi; Xinghua Feng; Tao Cai

    2012-01-01

    EEC (ectrodactyly, ectodermal dysplasia, clefting; OMIM 604292) is an autosomal dominant developmental disorder resulting mainly from pathogenic mutations of the DNA-binding domain (DBD) of the TP63 gene. In this study, we showed that K193E mutation in nine affected individuals of a four-generation kindred with a large degree of phenotypic variability causes four different syndromes or TP63-related disorders: EEC, Ectrodactyly-ectodermal dysplasia (EE), isolated ectodermal dysplasia, and isol...

  11. Latent-class analysis of recurrence risks for complex phenotypes with selection and measurement error: a twin and family history study of autism.

    OpenAIRE

    Pickles, A; Bolton, P.; Macdonald, H.; Bailey, A; Le Couteur, A; Sim, C H; Rutter, M

    1995-01-01

    The use of the family history method to examine the pattern of recurrence risks for complex disorders such as autism is not straightforward. Problems such as uncertain phenotypic definition, unreliable measurement with increased error rates for more distant relatives, and selection due to reduced fertility all complicate the estimation of risk ratios. Using data from a recent family history study of autism, and a similar study of twins, this paper shows how a latent-class approach can be used...

  12. Proton transport properties of tin phosphate, chromotropic acid anchored onto tin phosphate and tin phenyl phosphonate

    Indian Academy of Sciences (India)

    Chithra Sumej; P P Sharmila; Nisha J Tharayil; S Suma

    2013-02-01

    Tin (IV) phosphates of the class of tetravalent metal acid (TMA) salts have been synthesized by sol–gel method. The functionalized materials of tin (IV) phosphate (SnP) like chromotropic acid anchored tin phosphate (SnPCA) and tin phenyl phosphonate (SnPP) were also synthesized. These materials have been characterized for elemental analysis (ICP–AES), thermal analysis, X-ray analysis and FTIR spectroscopy. Chemical resistivity of these materials has been accessed in acidic, basic and organic solvent media. The proton present in the structural hydroxyl groups indicates good potential for TMA salts to exhibit solid-state proton conduction. The transport properties of these materials have been explored by measuring specific proton conductance at different temperatures. Based on the specific conduction data and Arrhenius plots, a suitable mechanism has been proposed.

  13. Novel R pipeline for analyzing biolog phenotypic microarray data.

    OpenAIRE

    Minna Vehkala; Mikhail Shubin; Connor, Thomas R; Thomson, Nicholas R.; Jukka Corander

    2015-01-01

    Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells' respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, resp...

  14. P21-activated kinase 4 (PAK4) is required for metaphase spindle positioning and anchoring.

    Science.gov (United States)

    Bompard, G; Rabeharivelo, G; Cau, J; Abrieu, A; Delsert, C; Morin, N

    2013-02-14

    The oncogenic kinase PAK4 was recently found to be involved in the regulation of the G1 phase and the G2/M transition of the cell cycle. We have also identified that PAK4 regulates Ran GTPase activity during mitosis. Here, we show that after entering mitosis, PAK4-depleted cells maintain a prolonged metaphase-like state. In these cells, chromosome congression to the metaphase plate occurs with normal kinetics but is followed by an extended period during which membrane blebbing and spindle rotation are observed. These bipolar PAK4-depleted metaphase-like spindles have a defective astral microtubule (MT) network and are not centered in the cell but are in close contact with the cell cortex. As the metaphase-like state persists, centrosome fragmentation occurs, chromosomes scatter from the metaphase plate and move toward the spindle poles with an active spindle assembly checkpoint, a phenotype that is reminiscent of cohesion fatigue. PAK4 also regulates the acto-myosin cytoskeleton and we report that PAK4 depletion results in the induction of cortical membrane blebbing during prometaphase arrest. However, we show that membrane blebs, which are strongly enriched in phospho-cofilin, are not responsible for the poor anchoring of the spindle. As PAK4 depletion interferes with the localization of components of the dynein/dynactin complexes at the kinetochores and on the astral MTs, we propose that loss of PAK4 could induce a change in the activities of motor proteins. PMID:22450748

  15. The flame anchoring mechanism and associated flow structure in bluff-body stabilized lean premixed flames

    Science.gov (United States)

    Michaels, Dan; Shanbhogue, Santosh; Ghoniem, Ahmed

    2015-11-01

    We present numerical analysis of a lean premixed flame anchoring on a heat conducting bluff-body. Different mixtures of CH4/H2/air are analyzed in order to systematically vary the burning velocity, adiabatic flame temperature and extinction strain rate. The study was motivated by our experimental measurements in a step combustor which showed that both the recirculation zone length and stability map under acoustically coupled conditions for different fuels and thermodynamic conditions collapse using the extinction strain rate. The model fully resolves unsteady two-dimensional flow with detailed chemistry and species transport, and without artificial flame anchoring boundary conditions. The model includes a low Mach number operator-split projection algorithm, coupled with a block-structured adaptive mesh refinement and an immersed boundary method for the solid body. Calculations reveal that the recirculation zone length correlates with the flame extinction strain rate, consistent with the experimental evidence. It is found that in the vicinity of the bluff body the flame is highly stretched and its leading edge location is controlled by the reactants combustion characteristics under high strain. Moreover, the flame surface location relative to the shear layer influences the vorticity thus impacting the velocity field and the recirculation zone. The study sheds light on the experimentally observed collapse of the combustor dynamics using the reactants extinction strain rate.

  16. Covalent Anchoring of Chloroperoxidase and Glucose Oxidase on the Mesoporous Molecular Sieve SBA-15

    Directory of Open Access Journals (Sweden)

    Martin Hartmann

    2010-02-01

    Full Text Available Functionalization of porous solids plays an important role in many areas, including heterogeneous catalysis and enzyme immobilization. In this study, large-pore ordered mesoporous SBA-15 molecular sieves were synthesized with tetraethyl orthosilicate (TEOS in the presence of the non-ionic triblock co-polymer Pluronic P123 under acidic conditions. These materials were grafted with 3 aminopropyltrimethoxysilane (ATS, 3-glycidoxypropyltrimethoxysilane (GTS and with 3 aminopropyltrimethoxysilane and glutaraldehyde (GA-ATS in order to provide covalent anchoring points for enzymes. The samples were characterized by nitrogen adsorption, powder X-ray diffraction, solid-state NMR spectroscopy, elemental analysis, diffuse reflectance fourier transform infrared spectroscopy and diffuse reflectance UV/Vis spectroscopy. The obtained grafted materials were then used for the immobilization of chloroperoxidase (CPO and glucose oxidase (GOx and the resulting biocatalysts were tested in the oxidation of indole. It is found that enzymes anchored to the mesoporous host by the organic moieties can be stored for weeks without losing their activity. Furthermore, the covalently linked enzymes are shown to be less prone to leaching than the physically adsorbed enzymes, as tested in a fixed-bed reactor under continuous operation conditions.

  17. Stretching of a polymer chain anchored to a surface: the massive field theory approach

    Science.gov (United States)

    Usatenko, Zoryana

    2014-09-01

    Taking into account the well-known correspondence between the field theoretical φ4 O(n)-vector model in the limit n → 0 and the behaviour of long-flexible polymer chains, the investigation of stretching of an ideal and a real polymer chain with excluded volume interactions in a good solvent anchored to repulsive and inert surfaces is performed. The calculations of the average stretching force which arises when the free end of a polymer chain moves away from a repulsive or inert surface are performed up to one-loop order of the massive field theory approach in fixed space dimensions d = 3. The analysis of the obtained results indicates that the average stretching force for a real polymer chain anchored to a repulsive surface demonstrates different behaviour for the cases \\tilde{z}\\ll1 and \\tilde{z}\\gg1 , where \\tilde{z}=z^\\prime/Rz . Besides, the results obtained in the framework of the massive field theory approach are in good agreement with previous theoretical results for an ideal polymer chain and results of a density functional theory approach for the region of small applied forces when deformation of a polymer chain in the direction of the applied force is not bigger than the linear extension of a polymer chain in this direction. The better agreement between these two methods is observed in the case where the number of monomers increases and the polymer chain becomes longer.

  18. Evidence for the presence of a phosphatidylinositol anchor on the lipoarabinomannan and lipomannan of Mycobacterium tuberculosis.

    Science.gov (United States)

    Hunter, S W; Brennan, P J

    1990-06-01

    The recent availability (Hunter, S.W., Gaylord, H., and Brennan, P.J. (1986) J. Biol. Chem. 261, 12345-12351) of the well known arabinomannan of Mycobacterium leprae and Mycobacterium tuberculosis as the pure native lipoarabinomannan has resulted in its implication in key aspects of the immunopathogenesis of leprosy and tuberculosis. We had indicated that the lipid moiety of lipoarabinomannan is probably based on a diacylglycerol unit in that glycerol and the two fatty acids, hexadecanoate and 10-methyloctadecanoate, were identified. In addition, lipoarabinomannan was also shown to contain myo-inositol 1-phosphate. Evidence is now presented, based on selective radiolabeling and analysis of various cleavage fragments, that the inositol phosphate exists as both an alkalilable phosphodiester and as part of a phosphatidylinositol "membrane anchor." The mannan of M. tuberculosis was also isolated as the native lipomannan. It also apparently contains a phosphatidylinositol unit but is devoid of the alkali-labile inositol phosphate residues. These lipopolysaccharides are apparently multiglycosylated versions of the well known myocobacterial mannosyl phosphatidylinositols and are prokaryotic versions of the growing list of phosphatidylinositol-anchored macromolecules. Immunogold labeling demonstrates that lipoarabinomannan is a true antigenic capsular or extracellular product of M. tuberculosis. The presence of a phosphatidylinositol residue on lipoarabinomannan may explain its interaction with macrophage membranes and role in mycobacterial pathogenesis. PMID:2111816

  19. Novel telomere-anchored PCR approach for studying sexual stage telomeres in Aspergillus nidulans.

    Science.gov (United States)

    Wang, Nengding; Rizvydeen, Saajidha; Vahedi, Mithaq; Vargas Gonzalez, Daysi M; Allred, Amanda L; Perry, Dustin W; Mirabito, Peter M; Kirk, Karen E

    2014-01-01

    Telomere length varies between germline and somatic cells of the same organism, leading to the hypothesis that telomeres are lengthened during meiosis. However, little is known about the meiotic telomere length in many organisms. In the filamentous fungus Aspergillus nidulans, the telomere lengths in hyphae and asexual spores are invariant. No study using existing techniques has determined the telomere length of the sexual ascospores due to the relatively low abundance of pure meiotic cells in A. nidulans and the small quantity of DNA present. To address this, we developed a simple and sensitive PCR strategy to measure the telomere length of A. nidulans meiotic cells. This novel technique, termed "telomere-anchored PCR," measures the length of the telomere on chromosome II-L using a small fraction of the DNA required for the traditional terminal restriction fragment (TRF) Southern analysis. Using this approach, we determined that the A. nidulans ascospore telomere length is virtually identical to telomeres of other cell types from this organism, approximately 110 bp, indicating that a surprisingly strict telomere length regulation exists in the major cell types of A. nidulans. When the hyphal telomeres were measured in a telomerase reverse transcriptase (TERT) knockout strain, small decreases in length were readily detected. Thus, this technique can detect telomeres in relatively rare cell types and is particularly sensitive in measuring exceptionally short telomeres. This rapid and inexpensive telomere-anchored PCR method potentially can be utilized in other filamentous fungi and types of organisms. PMID:24927411

  20. Major surface antigen, P30, of Toxoplasma gondii is anchored by a glycolipid

    International Nuclear Information System (INIS)

    P30, the major surface antigen of the parasitic protozoan Toxoplasma gondii, can be specifically labeled with [3H]palmitic acid and with myo-[2-3H]inositol. The fatty acid label can be released by treatment of P30 with phosphatidylinositol-specific phospholipase C (PI-PLC). Such treatment exposes an immunological cross-reacting determinant first described on Trypanosoma brucei variant surface glycoprotein. PI-PLC cleavage of intact parasites metabolically labeled with [35S]methionine results in the release of intact P30 polypeptide in a form which migrates faster in polyacrylamide gel electrophoresis. These results argue that P30 is anchored by a glycolipid. Results from thin layer chromatography analysis of purified [3H] palmitate-labeled P30 treated with PI-PLC, together with susceptibility to mild alkali hydrolysis and to cleavage with phospholipase A2, suggest that the glycolipid anchor of T. gondii P30 includes a 1,2-diacylglycerol moiety

  1. Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults.

    Directory of Open Access Journals (Sweden)

    Fang Chen

    Full Text Available Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419, we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010, and estimated an additive heritability of 44.7% (se: 3.7% for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1 whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2 whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the

  2. Not all nutrition claims are perceived equal: anchoring effects and moderating mechanisms in food advertising.

    Science.gov (United States)

    Paek, Hye-Jin; Yoon, Hye Jin; Hove, Thomas

    2011-03-01

    Despite the increased use of health claims in food advertising, few studies have investigated how specific nutrition claims have differential effects depending on how they are presented. In this context, the current study tests the anchoring hypothesis. Anchoring refers to a common human tendency to evaluate information differently depending on the presence or absence of a numerical "anchor" or reference point. Two (pilot and main) experimental studies explore anchoring effects on audience response to food advertising both directly and moderated by cognitive, motivational, and message factors. The pilot study finds that food product ads employing nutrition claims with an anchor rather than without an anchor generate two results: First, participants perceive the product to have lower fat/lower calorie contents (anchoring hypothesis); second, they prefer the messages with an anchor over those without an anchor. The main study reports that when anchoring is successfully evoked, it produces favorable attitudes toward the ad, favorable attitudes toward the brand, and purchase intention-but only when moderated by health orientation, claim believability, and nutrition knowledge. Practical implications are provided with respect to regulatory guidelines and effective communication strategies for promoting low-fat and low-calorie products in food advertising. PMID:21308579

  3. NOD2/CARD15 mutations in Polish and Bosnian populations with and without Crohn's disease: prevalence and genotype-phenotype analysis

    Directory of Open Access Journals (Sweden)

    Nermin N Salkic

    2015-05-01

    Full Text Available Data on prevalence and phenotypic consequences of nucleotide-binding oligomerisation domain 2/caspase recruitment domains 15 (NOD2/CARD15 variants in Crohn's disease (CD population in Poland and Bosnia and Herzegovina (B&H are nonexistent. We aimed to determine the prevalence of NOD2/CARD15 mutations and their association with disease phenotype in Polish and Bosnian patients with CD and in healthy controls. We prospectively recruited 86 CD patients and 83 controls in Poland and 30 CD patients and 30 controls in B&H, 229 in total. We determined the prevalence of NOD2/CARD15 mutations and their association with the disease phenotype according to Montreal classification. Participants were genotyped for Leu1007fsinsC and Gly908Arg mutations. At least one CD-associated allele was found in 29/86 (33.7% of Polish CD patients and in 9/83 (10.8% of healthy controls (p<0.001. In both CD patients and controls in Bosnian sample, at least one NOD2 mutation was found in equal number of patients (3/30; 10% with all of the NOD2 mutation positive CD patients being homozygous, while controls being heterozygous. In Polish sample, perianal disease was less frequent in CD patients with any NOD2 mutation (1/21; 4.8% compared to those without (11/41; 26.8%; p=0.046. Higher percentage of patients with NOD2 mutations had history of CD related surgery when compared with those without mutations (66.7% vs. 43.3%; p=0.05. The risk for CD is increased in patients with NOD2 mutations (Poland and especially in the presence of homozygous NOD2 mutations (Poland and Bosnia. The presence of variant NOD2 alleles is associated with increased need for surgery and reduced occurrence of perianal disease.

  4. COPD: Definition and Phenotypes

    DEFF Research Database (Denmark)

    Vestbo, J.

    2014-01-01

    Chronic obstructive pulmonary disease (COPD) is currently defined as a common preventable and treatable disease that is characterized by persistent airflow limitation that is usually progressive and associated with an enhanced chronic inflammatory response in the airways and the lung to noxious...... particles or gases. Exacerbations and comorbidities contribute to the overall severity in individual patients. The evolution of this definition and the diagnostic criteria currently in use are discussed. COPD is increasingly divided in subgroups or phenotypes based on specific features and association with...

  5. Analysis of the Sequence and Phenotype of Drosophila Sex combs reduced Alleles Reveals Potential Functions of Conserved Protein Motifs of the Sex combs reduced Protein

    OpenAIRE

    Sivanantharajah, Lovesha; Percival-Smith, Anthony

    2009-01-01

    The Drosophila Hox gene, Sex combs reduced (Scr), is required for patterning the larval and adult, labial and prothoracic segments. Fifteen Scr alleles were sequenced and the phenotypes analyzed in detail. Six null alleles were nonsense mutations (Scr2, Scr4, Scr11, Scr13, Scr13A, and Scr16) and one was an intragenic deletion (Scr17). Five hypomorphic alleles were missense mutations (Scr1, Scr3, Scr5, Scr6, and Scr8) and one was a small protein deletion (Scr15). Protein sequence changes were ...

  6. Morphological distinctness despite large-scale phenotypic plasticity—analysis of wild and pond-bred juveniles of allopatric populations of Tropheus moorii

    Science.gov (United States)

    Kerschbaumer, Michaela; Postl, Lisbeth; Koch, Martin; Wiedl, Thomas; Sturmbauer, Christian

    2011-02-01

    Cichlids are an excellent model to study explosive speciation and adaptive radiation. Their evolutionary success has been attributed to their ability to undergo rapid morphological changes related to diet, and their particular breeding biology. Relatively minor changes in morphology allow for exploitation of novel food resources. The importance of phenotypic plasticity and genetically based differences for diversification was long recognized, but their relationship and relative magnitude remained unclear. We compared morphology of individuals of four wild populations of the Lake Tanganyika cichlid Tropheus moorii with their pond-raised F1 offspring. The magnitude of morphological change via phenotypic plasticity between wild and pond-bred F1 fish exceeds pairwise population differences by a factor of 2.4 (mean Mahalanobis distances). The genetic and environmental effects responsible for among population differentiation in the wild could still be recognized in the pond-bred F1 fish. All four pond populations showed the same trends in morphological change, mainly in mouth orientation, size and orientation of fins, and thickness of the caudal peduncle. As between population differentiation was lower in the wild than differentiation between pond-raised versus wild fish, we suggest the narrow ecological niche and intense interspecific competition in rock habitats is responsible for consistent shape similarity, even among long-term isolated populations.

  7. Anchoring a Lexicalized Tree-Adjoining Grammar for Discourse

    CERN Document Server

    Webber, Bryan R; Webber, Bonnie Lynn; Joshi, Aravind K.

    1998-01-01

    We here explore a ``fully'' lexicalized Tree-Adjoining Grammar for discourse that takes the basic elements of a (monologic) discourse to be not simply clauses, but larger structures that are anchored on variously realized discourse cues. This link with intra-sentential grammar suggests an account for different patterns of discourse cues, while the different structures and operations suggest three separate sources for elements of discourse meaning: (1) a compositional semantics tied to the basic trees and operations; (2) a presuppositional semantics carried by cue phrases that freely adjoin to trees; and (3) general inference, that draws additional, defeasible conclusions that flesh out what is conveyed compositionally.

  8. Direct imaging of rotating molecules anchored on graphene

    Science.gov (United States)

    Choe, Jeongheon; Lee, Yangjin; Fang, Lei; Lee, Gun-Do; Bao, Zhenan; Kim, Kwanpyo

    2016-07-01

    There has been significant research interest in controlling and imaging molecular dynamics, such as translational and rotational motions, especially at a single molecular level. Here we applied aberration-corrected transmission electron microscopy (ACTEM) to actuate and directly image the rotational motions of molecules anchored on a single-layer-graphene sheet. Nanometer-sized carbonaceous molecules anchored on graphene provide ideal systems for monitoring rotational motions via ACTEM. We observed the preferential registry of longer molecular axis along graphene zigzag or armchair lattice directions due to the stacking-dependent molecule-graphene energy landscape. The calculated cross section from elastic scattering theory was used to experimentally estimate the rotational energy barriers of molecules on graphene. The observed energy barrier was within the range of 1.5-12 meV per atom, which is in good agreement with previous calculation results. We also performed molecular dynamics simulations, which revealed that the edge atoms of the molecule form stably bonds to graphene defects and can serve as a pivot point for rotational dynamics. Our study demonstrates the versatility of ACTEM for the investigation of molecular dynamics and configuration-dependent energetics at a single molecular level.There has been significant research interest in controlling and imaging molecular dynamics, such as translational and rotational motions, especially at a single molecular level. Here we applied aberration-corrected transmission electron microscopy (ACTEM) to actuate and directly image the rotational motions of molecules anchored on a single-layer-graphene sheet. Nanometer-sized carbonaceous molecules anchored on graphene provide ideal systems for monitoring rotational motions via ACTEM. We observed the preferential registry of longer molecular axis along graphene zigzag or armchair lattice directions due to the stacking-dependent molecule-graphene energy landscape. The

  9. Analytical Model for Hook Anchor Pull-Out

    DEFF Research Database (Denmark)

    Brincker, Rune; Ulfkjær, Jens Peder; Adamsen, Peter; Langvad, Lotte; Toft, Rune

    A simple analytical model for the pull-out of a hook anchor is presented. The model is based on a simplified version of the fictitious crack model. It is assumed that the fracture process is the pull-off of a cone shaped concrete part, simplifying the problem by assuming pure rigid body motions...... allowing elastic deformations only in a layer between the pull-out cone and the concrete base. The derived model is in good agreement with experimental results, it predicts size effects and the model parameters found by calibration of the model on experimental data are in good agreement with what should be...

  10. Models for Anchoring and Acquiescence Bias in Consumption Data

    OpenAIRE

    van Soest, A.H.O.; Hurd, M.

    2004-01-01

    Item non-response in household survey data on economic variables such as income, assets or consumption is a well-known problem. Follow-up unfolding bracket questions have been used as a tool to collect partial information on respondents that do not answer an open-ended question. It is also known, however, that mistakes are made in answering such unfolding bracket questions. In this paper, we develop several limited dependent variable models to analyze two sources of mistakes, anchoring and ac...

  11. Adjusting phenotypes by noise control.

    Directory of Open Access Journals (Sweden)

    Kyung H Kim

    2012-01-01

    Full Text Available Genetically identical cells can show phenotypic variability. This is often caused by stochastic events that originate from randomness in biochemical processes involving in gene expression and other extrinsic cellular processes. From an engineering perspective, there have been efforts focused on theory and experiments to control noise levels by perturbing and replacing gene network components. However, systematic methods for noise control are lacking mainly due to the intractable mathematical structure of noise propagation through reaction networks. Here, we provide a numerical analysis method by quantifying the parametric sensitivity of noise characteristics at the level of the linear noise approximation. Our analysis is readily applicable to various types of noise control and to different types of system; for example, we can orthogonally control the mean and noise levels and can control system dynamics such as noisy oscillations. As an illustration we applied our method to HIV and yeast gene expression systems and metabolic networks. The oscillatory signal control was applied to p53 oscillations from DNA damage. Furthermore, we showed that the efficiency of orthogonal control can be enhanced by applying extrinsic noise and feedback. Our noise control analysis can be applied to any stochastic model belonging to continuous time Markovian systems such as biological and chemical reaction systems, and even computer and social networks. We anticipate the proposed analysis to be a useful tool for designing and controlling synthetic gene networks.

  12. Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes

    OpenAIRE

    Pantazatos, Spiro P.; Jianrong Li; Paul Pavlidis; Lussier, Yves A.

    2009-01-01

    An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledge-based phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT®). The approach was implemented using sample datasets from fMRIDC, GEO, The Whole Brain Atlas and Neuronames, and allowed for complex queries such as “List all disorders...

  13. Integration of Neuroimaging and Microarray Datasets  through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes

    OpenAIRE

    Pantazatos, Spiro P.; Jianrong Li; Paul Pavlidis; Lussier, Yves A.

    2009-01-01

    An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledge-based phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT®). The approach was implemented using sample datasets from fMRIDC, GEO, The Whole Brain Atlas and Neuronames, and allowed for complex queries such as “List all disorders...

  14. Study of two dimensional nematic liquid crystal reorientations and anchoring effects

    OpenAIRE

    S Shoarinejad; MA Shahzamanian

    2010-01-01

    In this paper, the director distribution is calculated for a nematic liquid crystal, in the cell with different surface anchoring conditions and external fields. The effects of finite and infinite surface anchoring on molecular orientations for one dimensional geometry are discussed. In these situations, the planar alignment is considered. Then, in a two dimensional geometry the planar and homotropic anchoring conditions are assumed for wall- interfaces of confined nematic, and the reorientat...

  15. Membrane curvature enables N-Ras lipid anchor sorting to liquid-ordered membrane phases

    DEFF Research Database (Denmark)

    Larsen, Jannik Bruun; Jensen, Martin Borch; Bhatia, Vikram Kjøller;

    2015-01-01

    Trafficking and sorting of membrane-anchored Ras GTPases are regulated by partitioning between distinct membrane domains. Here, in vitro experiments and microscopic molecular theory reveal membrane curvature as a new modulator of N-Ras lipid anchor and palmitoyl chain partitioning. Membrane...... curvature was essential for enrichment in raft-like liquid-ordered phases; enrichment was driven by relief of lateral pressure upon anchor insertion and most likely affects the localization of lipidated proteins in general....

  16. An internally positioned signal can direct attachment of a glycophospholipid membrane anchor

    OpenAIRE

    1991-01-01

    All known glycophosphatidylinositol (GPI)-anchored membrane proteins contain a COOH-terminal hydrophobic domain necessary for signalling anchor attachment. To examine the requirement that this signal be at the COOH terminus of the protein, we constructed a chimeric protein, DAFhGH, in which human growth hormone (hGH) was fused to the COOH terminus of decay accelerating factor (DAF) (a GPI-anchored protein), thereby placing the GPI signal in the middle of the chimeric protein. We show that the...

  17. A glycophospholipid membrane anchor acts as an apical targeting signal in polarized epithelial cells

    OpenAIRE

    1989-01-01

    Glycosyl-phosphatidylinositol- (GPI) anchored proteins contain a large extracellular protein domain that is linked to the membrane via a glycosylated form of phosphatidylinositol. We recently reported the polarized apical distribution of all endogenous GPI-anchored proteins in the MDCK cell line (Lisanti, M. P., M. Sargiacomo, L. Graeve, A. R. Saltiel, and E. Rodriguez-Boulan. 1988. Proc. Natl. Acad. Sci. USA. 85:9557-9561). To study the role of this mechanism of membrane anchoring in targeti...

  18. Model Test of Anchoring Effect on Zonal Disintegration in Deep Surrounding Rock Masses

    OpenAIRE

    Xu-Guang Chen; Qiang-Yong Zhang; Yuan Wang; De-Jun Liu; Ning Zhang

    2013-01-01

    The deep rock masses show a different mechanical behavior compared with the shallow rock masses. They are classified into alternating fractured and intact zones during the excavation, which is known as zonal disintegration. Such phenomenon is a great disaster and will induce the different excavation and anchoring methodology. In this study, a 3D geomechanics model test was conducted to research the anchoring effect of zonal disintegration. The model was constructed with anchoring in a half an...

  19. Nothing so certain as your anchors? A consumer bias that might lower prices

    OpenAIRE

    Bakó, Barna; Kálecz-Simon, András

    2014-01-01

    Anchoring is a well-known decision-making bias: original guesses for a certain question could act as anchors and could influence our final answers. Reference prices - in a similar fashion - can lead to a bias in consumer valuations, and thus consumer demand will be coherent but not one derived from a utility framework. In our paper we investigate the effect of the existence of anchoring on how oligopolistic firms might change their pricing strategy. More specifically, we analyze the effec...

  20. Construction and Expression of Bivalent Membrane-anchored DNA Vaccine Encoding Sj14FABP and Sj26GST Genes

    Institute of Scientific and Technical Information of China (English)

    GUO Ping; DAI Wuxing; LIU Shuojie; YANG Ping; CHENG Jizhong; LIANG Liang; CHEN Zhihao; GAO Hong

    2006-01-01

    In order to construct a eukaryotic co-expression plasmid containing membrane-anchored Sjcl4FABP and Sjc26GST genes and identify their expression in vitro, Sj14 and Sj26 genes were obtained by RT-PCR with total RNA of Schistosoma japonicum adult worms as the template and cloned into eukaryotic expression plasmid pVAC to construct recombinant plasmids pVAC-Sj14 and pVAC-Sj26. Then a 23 amino-acid signal peptide of human interleukin-2 (IL-2) upstream Sj14 or Sj26 gene and a membrane-anchored sequence containing 32 amino-acids of carboxyl-terminal of human placental alkaline phosphatase (PLAP) downstream were amplified by PCR as the template of plasmid pVAC-Sjl4 or pVAC-Sj26 only to get two gene fragments including Sjl4 gene and Sj26 gene. The two modified genes were altogether cloned into a eukaryotic co-expression plasmid pIRES,resulting in another new recombinant plasmid pIRES-Sj26-Sj 14. The expression of Sj14 and Sj26genes was detected by RT-PCR and indirect immunofluorescent assays (IFA) when the plasmid pIRES-Sj26-Sj 14 was transfected into eukaryotic Hela cells. Restriction enzyme analysis, PCR and sequencing results revealed that the recombinant plasmids pVAC-Sj14, pVAC-Sj26 and pIRES-Sj26-Sj14 were successfully constructed and the expression of modified Sj 14 and Sj26 genes could be detected by RT-PCR and IFA. A bivalent membrane-anchored DNA vaccine encoding Sj14 and Sj26 genes was acquired and expressed proteins were proved to be mostly anchored in cellular membranes.

  1. Post-installed concrete anchors in nuclear power plants: Performance and qualification

    International Nuclear Information System (INIS)

    Graphical abstract: - Highlights: • Review of qualification and design regulations for anchors in nuclear power plants. • First complete set of nuclear anchor load–displacement data and its evaluation ever. • Demonstration of robust test behavior of a qualified post-installed anchor product. - Abstract: In nuclear power plants (NPPs), post-installed anchors are widely used for structural and non-structural connections to concrete. In many countries, anchor products employed for safety relevant applications have to be approved by the authorities. For the high safety standards in force for NPPs, special requirements have to be met to allow for extreme design situations. This paper presents an experimental test program conducted to evaluate the performance of anchors according to the German Guideline for Anchorages in Nuclear Power Plants and Nuclear Technology Installations (DIBt KKW Leitfaden, 2010). After a brief introduction to anchor behavior and the regulative context, the results of tension and shear tests carried out on undercut anchors are discussed. Robust load capacities and relatively small displacements determined for demanding load and crack cycling tests demonstrated the suitability of anchors qualified according to a state-of-the-art qualification guideline

  2. The biggest stone anchors (Indo-Arab type) from Mithi Virdi, Bhavnagar, west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Gaur, A.S.; Sundaresh; Kumar, B.

    as Bhima Ka Khatiya ('Cot of Bhima'), was discovered near the village of Mithi Virdi. Here, five grapnel type of stone anchors were noticed lying in a field. The lower two holes of the grapnel anchors on either face of the section of stone block... been cut from conglomeratic sedimentary grit rock, which is dark brown in colour and small gravel can be noticed. The anchors have only lower two rectangular holes and the upper circular hole is absent in all the anchors. A brief description...

  3. Radiocarbon dates of the medieval period stone anchors from Dabhol, west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Gaur, A.S.; Sundaresh; Tripati, S.; Vora, K.H.

    dredging operation in Dabhol creek. the anchors are lying in front of the Cus- tom Office of Dabhol. One of the anchors had wooden fluke remains in the holes, which were removed and kept safely by an active social worker at Dabhol. These anchors.... The calibrated date of the first sam- ple ranged between 654 and 524 yrs BP, and the second sample ranged between 653 and 537 yrs BP (Table 2). Discussion The discovery of anchors from the Dab- hol creek is one of the significant find- ings to support...

  4. Dithiocarbamate anchoring in molecular wire junctions: a first principles study.

    Science.gov (United States)

    Li, Zhenyu; Kosov, Daniel S

    2006-05-25

    Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self-assembly on gold surface opens the possibility for use of dithiocarbamate linkers to anchor molecular wires to gold electrodes. In this paper, we explore this hypothesis computationally. We computed the electron transport properties of 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based on the density functional theory and nonequilibrium Green's functions. We demonstrated that the stronger molecule-electrode coupling associated with the conjugated dithiocarbamate linker broadens transmission resonances near the Fermi energy. The broadening effect along with the extension of the pi conjugation from the molecule to the gold electrodes lead to enhanced electrical conductance for BPBC molecule. The conductance enhancement factor is as large as 25 at applied voltage bias 1.0 V. Rectification behavior is predicted for BPC molecular wire junction, which has the asymmetric anchoring groups. PMID:16706444

  5. Adaptive anchored inversion for Gaussian random fields using nonlinear data

    International Nuclear Information System (INIS)

    In a broad and fundamental type of ‘inverse problems’ in science, one infers a spatially distributed physical attribute based on observations of processes that are controlled by the spatial attribute in question. The data-generating field processes, known as ‘forward processes’, are usually nonlinear with respect to the spatial attribute, and are often defined non-analytically by a numerical model. The data often contain a large number of elements with significant inter-correlation. We propose a general statistical method to tackle this problem. The method is centered on a parameterization device called ‘anchors’ and an iterative algorithm for deriving the distribution of anchors conditional on the observed data. The algorithm draws upon techniques of importance sampling and multivariate kernel density estimation with weighted samples. Anchors are selected automatically; the selection evolves in iterations in a way that is tailored to important features of the attribute field. The method and the algorithm are general with respect to the scientific nature and technical details of the forward processes. Conceptual and technical components render the method in contrast to standard approaches that are based on regularization or optimization. Some important features of the proposed method are demonstrated by examples from the earth sciences, including groundwater flow, rainfall-runoff and seismic tomography. (paper)

  6. Field Behavior of A High Anchored Reinforced Earth Wall

    Directory of Open Access Journals (Sweden)

    Faisal H. Ali

    2008-01-01

    Full Text Available Since the invention of Reinforced Earth by the French architect Hendri Vidal in 1966, numerous reinforced soil walls have been designed and constructed all over the world. In this study the focus was on a particular type of reinforced wall called Nehemiah wall which differed from the Vidal type in the sense that instead of steel strips, the reinforcing elements consisted of steel bars with anchor blocks attached at the free ends. A full scale high anchored reinforced earth wall was constructed and instrumented to capture the essential behavior of the wall. Two sections of the wall were monitored where at one of the sections polystyrene foam was inserted at the back face of the wall panel to allow for lateral deformation to take place which means that the facing was less flexible in the transverse direction. The lateral deformation, axial forces along the reinforcing bars and settlement were monitored and measured for both cases and the results were compared and discussed.

  7. Direct imaging of rotating molecules anchored on graphene.

    Science.gov (United States)

    Choe, Jeongheon; Lee, Yangjin; Fang, Lei; Lee, Gun-Do; Bao, Zhenan; Kim, Kwanpyo

    2016-07-21

    There has been significant research interest in controlling and imaging molecular dynamics, such as translational and rotational motions, especially at a single molecular level. Here we applied aberration-corrected transmission electron microscopy (ACTEM) to actuate and directly image the rotational motions of molecules anchored on a single-layer-graphene sheet. Nanometer-sized carbonaceous molecules anchored on graphene provide ideal systems for monitoring rotational motions via ACTEM. We observed the preferential registry of longer molecular axis along graphene zigzag or armchair lattice directions due to the stacking-dependent molecule-graphene energy landscape. The calculated cross section from elastic scattering theory was used to experimentally estimate the rotational energy barriers of molecules on graphene. The observed energy barrier was within the range of 1.5-12 meV per atom, which is in good agreement with previous calculation results. We also performed molecular dynamics simulations, which revealed that the edge atoms of the molecule form stably bonds to graphene defects and can serve as a pivot point for rotational dynamics. Our study demonstrates the versatility of ACTEM for the investigation of molecular dynamics and configuration-dependent energetics at a single molecular level. PMID:27333828

  8. Phenotypic approaches to drought in cassava: review.

    Science.gov (United States)

    Okogbenin, Emmanuel; Setter, Tim L; Ferguson, Morag; Mutegi, Rose; Ceballos, Hernan; Olasanmi, Bunmi; Fregene, Martin

    2013-01-01

    Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12-18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding. PMID

  9. Phenotypic Approaches to Drought in Cassava: Review

    Directory of Open Access Journals (Sweden)

    Emmanuel eOkogbenin

    2013-05-01

    Full Text Available 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

  10. Phenotypic variation in cultivated populations of Azadirachta indica in Yunnan, China

    OpenAIRE

    PENG Xing-Min; WU Jiang-Chong; ZHENG Yi-Xing; Zhang, Yan-Ping; LI Gen-Qian

    2012-01-01

    Aims Our objectives were to investigate phenotypic variation of Azadirachta indica in cultivated populations and to describe the relationship between phenotypic variation of the cultivated populations and different distribution areas.Methods We investigated 14 phenotypic traits for 90 individuals in nine cultivated populations of A. indica from Yunnan Province of China and used variance analysis, nested analysis, correlation analysis, principal component analysis, UPGMA cluster analysis and m...

  11. Anchoring novel molecular biomarker responses to traditional responses in fish exposed to environmental contamination

    Energy Technology Data Exchange (ETDEWEB)

    Nogueira, Patricia [CESAM and Departamento de Biologia, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Department of Biology and Environmental Science, University of Sussex, Falmer, Brighton BN1 9QJ (United Kingdom); Pacheco, Mario [CESAM and Departamento de Biologia, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Lourdes Pereira, M. [CICECO and Departamento de Biologia, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Mendo, Sonia [CESAM and Departamento de Biologia, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Rotchell, Jeanette M., E-mail: J.Rotchell@sussex.ac.u [Department of Biology and Environmental Science, University of Sussex, Falmer, Brighton BN1 9QJ (United Kingdom)

    2010-05-15

    The responses of Dicentrarchus labrax and Liza aurata to aquatic pollution were assessed in a contaminated coastal lagoon, using both traditional and novel biomarkers combined. DNA damage, assessed by comet assay, was higher in both fish species from the contaminated sites, whereas levels of cytochrome P450 1A1 gene expression were not significantly altered. The liver histopathological analysis also revealed significant lesions in fish from contaminated sites. Alterations in ras and xpf genes were analysed and additional pollutant-responsive genes were identified. While no alterations were found in ras gene, a downregulation of xpf gene was observed in D. labrax from a contaminated site. Suppression subtractive hybridization applied to D. labrax collected at a contaminated site, revealed altered expression in genes involved in energy metabolism, immune system activity and antioxidant response. The approach and results reported herein demonstrate the utility of anchoring traditional biomarker responses alongside novel biomarker responses. - Novel molecular biomarkers of aquatic environmental contamination in fish.

  12. Weak Anchoring and Surface Elasticity Effects in Electroosmotic Flow of Nematic Liquid Crystals Through Narrow Confinements

    CERN Document Server

    Poddar, Antarip; Chakraborty, Suman

    2016-01-01

    Advent of nematic liquid crystals flows have attracted renewed attention in view of microfluidic transport phenomena. Among various transport processes, electroosmosis stands as one of the efficient flow actuation method through narrow confinement. In the present study, we explore the electrically actuated flow of a nematic fluid with ionic inclusions taking into account the influences from surface induced elastic and electrical double layer phenomena. Influence of surface effects on the flow characteristics is known to get augmented in micro-confined environment and must be properly addressed. Towards this, we devise the coupled flow governing equations from fundamental free energy analysis considering the contributions from first and second-order elastic, dielectric, flexoelectric, ionic and entropic energies. We have further considered weak anchoring surface conditions with second order elasticity which helps us to more accurately capture the director deformations along the boundaries. The present study fo...

  13. GEE-WIS Anchored Problem Solving Using Real-Time Authentic Water Quality Data

    Science.gov (United States)

    Young, M.; Wlodarczyk, M. S.; Branco, B.; Torgersen, T.

    2002-05-01

    GEE-WIS scientific problem solving consists of observing, hypothesizing, synthesis, argument building and reasoning, in the context of analysis, representation, modeling and sense-making of real-time authentic water quality data. Geoscience Environmental Education - Web-accessible Instrumented Systems, or GEE-WIS, an NSF Geoscience Education grant, has established a set of companion websites that stream real-time data from two campus retention ponds for research and use in secondary and undergraduate water quality lessons. We have targeted scientific problem solving skills because of the nature of the GEE-WIS environment, but further because they are central to state and federal efforts to establish science education curriculum standards and are at the core of performance-based testing. We have used a design experiment process to create and test two Anchored Instruction scenario problems. Customization such as that done through a design process, is acknowledged to be a fundamental component of educational research from an ecological psychology perspective. Our efforts have shared core design elements with other NSF water quality projects. Our method involves the analysis of student written scenario responses for level of scientific problem solving using a qualitative scoring rubric designed from participation in a related NSF project, SCALE (Synergy Communities: Aggregating Learning about Education). Student solutions of GEE-WIS anchor problems from Fall 2001 and Spring 2002 will be summarized. Implications are drawn for those interested in making secondary and high education geoscience more realistic and more motivating for students through the use of real-time authentic data via Internet.

  14. C-Anchor for Strengthening the Connection between Adhesively Bonded Laminates and Concrete Substrates

    Directory of Open Access Journals (Sweden)

    Ghani Razaqpur

    2015-11-01

    Full Text Available A new carbon fiber reinforced polymer (CFRP anchor is developed and tested to delay debonding in reinforced concrete (RC beams externally strengthened with FRP laminate/sheet. The C-shape anchor is made from a commercially available CFRP grid. The anchors legs are 95 mm long while the spacing between the legs is adjustable, depending on FRP laminate and beam widths. Nine full scale RC beams, 3.0 m long, 250 mm wide and 400 mm deep, were strengthened with CFRP laminate/sheet, with and without the C-anchor. The main test parameters were the type and amount of FRP laminate and the presence/absence of the anchor. Test results showed that beams with the anchor had generally 5%–10% higher debonding and failure load, and they reached higher deflection at failure than the companion beams without anchors. Although complete separation of the FRP laminate from the concrete was not observed in any of the beams with anchors, there was noticeable slip at failure at one end of the laminate. A significant outcome of the study is that anchors are effective in limiting the extent of debonding along the laminate, thus contributing to the flexural stiffness of the beam by reducing the extent of cracking and limiting the crack width along the beam. Finally, the anchor allowed the FRP to reach or exceed its theoretically allowable strain computed based on the American Concrete Institute (ACI Committee 440 recommendation while in none of the beams without anchors, the FRP reached its theoretically allowable strain.

  15. Pseudomonas Aeruginosa Resistance Phenotypes and Phenotypic Highlighting Methods

    Science.gov (United States)

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

    2014-01-01

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

  16. Impingement syndrome of the shoulder following double row suture anchor technique for arthroscopic rotator cuff repair: a case report

    Directory of Open Access Journals (Sweden)

    Rambani Rohit

    2009-06-01

    Full Text Available Abstract Introduction Arthroscopic repair of the rotator cuff is a demanding surgery. Accurate placement of anchors is key to success. Case presentation A 38-year-old woman received arthroscopic repair of her rotator cuff using a double row suture anchor technique. Postoperatively, she developed impingement syndrome which resulted from vertical displacement of a suture anchor once the shoulder was mobilised. The anchor was removed eight weeks following initial surgery and the patient had an uneventful recovery. Conclusion Impingement syndrome following arthroscopic repair of the rotator cuffs using double row suture anchor has not been widely reported. This is the first such case where anchoring has resulted in impingement syndrome.

  17. Multi-dimensional discovery of biomarker and phenotype complexes

    Directory of Open Access Journals (Sweden)

    Huang Kun

    2010-10-01

    Full Text Available Abstract Background Given the rapid growth of translational research and personalized healthcare paradigms, the ability to relate and reason upon networks of bio-molecular and phenotypic variables at various levels of granularity in order to diagnose, stage and plan treatments for disease states is highly desirable. Numerous techniques exist that can be used to develop networks of co-expressed or otherwise related genes and clinical features. Such techniques can also be used to create formalized knowledge collections based upon the information incumbent to ontologies and domain literature. However, reports of integrative approaches that bridge such networks to create systems-level models of disease or wellness are notably lacking in the contemporary literature. Results In response to the preceding gap in knowledge and practice, we report upon a prototypical series of experiments that utilize multi-modal approaches to network induction. These experiments are intended to elicit meaningful and significant biomarker-phenotype complexes spanning multiple levels of granularity. This work has been performed in the experimental context of a large-scale clinical and basic science data repository maintained by the National Cancer Institute (NCI funded Chronic Lymphocytic Leukemia Research Consortium. Conclusions Our results indicate that it is computationally tractable to link orthogonal networks of genes, clinical features, and conceptual knowledge to create multi-dimensional models of interrelated biomarkers and phenotypes. Further, our results indicate that such systems-level models contain interrelated bio-molecular and clinical markers capable of supporting hypothesis discovery and testing. Based on such findings, we propose a conceptual model intended to inform the cross-linkage of the results of such methods. This model has as its aim the identification of novel and knowledge-anchored biomarker-phenotype complexes.

  18. Mouse embryonic fibroblasts exhibit extensive developmental and phenotypic diversity

    Science.gov (United States)

    Singhal, Prabhat K.; Sassi, Slim; Lan, Lan; Au, Patrick; Halvorsen, Stefan C.; Fukumura, Dai; Jain, Rakesh K.; Seed, Brian

    2016-01-01

    Analysis of embryonic fibroblasts from GFP reporter mice indicates that the fibroblast cell type harbors a large collection of developmentally and phenotypically heterogeneous subtypes. Some of these cells exhibit multipotency, whereas others do not. Multiparameter flow cytometry analysis shows that a large number of distinct populations of fibroblast-like cells can be found in cultures initiated from different embryonic organs, and cells sorted according to their surface phenotype typically retain their characteristics on continued propagation in culture. Similarly, surface phenotypes of individual cloned fibroblast-like cells exhibit significant variation. The fibroblast cell class appears to contain a very large number of denumerable subtypes. PMID:26699463

  19. Phenotypic extremes in rare variant study designs.

    Science.gov (United States)

    Peloso, Gina M; Rader, Daniel J; Gabriel, Stacey; Kathiresan, Sekar; Daly, Mark J; Neale, Benjamin M

    2016-06-01

    Currently, next-generation sequencing studies aim to identify rare and low-frequency variation that may contribute to disease. For a given effect size, as the allele frequency decreases, the power to detect genes or variants of interest also decreases. Although many methods have been proposed for the analysis of such data, study design and analytic issues still persist in data interpretation. In this study we present sequencing data for ABCA1 that has known rare variants associated with high-density lipoprotein cholesterol (HDL-C). We contrast empirical findings from two study designs: a phenotypic extreme sample and a population-based random sample. We found differing strengths of association with HDL-C across the two study designs (P=0.0006 with n=701 phenotypic extremes vs P=0.03 with n=1600 randomly sampled individuals). To explore this apparent difference in evidence for association, we performed a simulation study focused on the impact of phenotypic selection on power. We demonstrate that the power gain for an extreme phenotypic selection study design is much greater in rare variant studies than for studies of common variants. Our study confirms that studying phenotypic extremes is critical in rare variant studies because it boosts power in two ways: the typical increases from extreme sampling and increasing the proportion of relevant functional variants ascertained and thereby tested for association. Furthermore, we show that when combining statistical evidence through meta-analysis from an extreme-selected sample and a second separate population-based random sample, power is lower when a traditional sample size weighting is used compared with weighting by the noncentrality parameter. PMID:26350511

  20. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M;

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection...