Temporal expression-based analysis of metabolism.

Directory of Open Access Journals (Sweden)

Sara B Collins

Full Text Available Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress in this regard has been made by integrating high-throughput gene expression data into genome-scale stoichiometric models of metabolism. Here, we extend previous approaches to perform a Temporal Expression-based Analysis of Metabolism (TEAM. We apply TEAM to understanding the complex metabolic dynamics of the respiratorily versatile bacterium Shewanella oneidensis grown under aerobic, lactate-limited conditions. TEAM predicts temporal metabolic flux distributions using time-series gene expression data. Increased predictive power is achieved by supplementing these data with a large reference compendium of gene expression, which allows us to take into account the unique character of the distribution of expression of each individual gene. We further propose a straightforward method for studying the sensitivity of TEAM to changes in its fundamental free threshold parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed. By comparing the qualitative characteristics of these zones to additional experimental data, we are able to constrain the range of θ to a small, well-defined interval. In parallel, the sensitivity analysis reveals the inherently difficult nature of dynamic metabolic flux modeling: small errors early in the simulation propagate to relatively large changes later in the simulation. We expect that handling such "history-dependent" sensitivities will be a major challenge in the future development of dynamic metabolic-modeling techniques.

Expression induction of P450 genes by imidacloprid in Nilaparvata lugens: A genome-scale analysis.

Science.gov (United States)

Zhang, Jianhua; Zhang, Yixi; Wang, Yunchao; Yang, Yuanxue; Cang, Xinzhu; Liu, Zewen

2016-09-01

The overexpression of P450 monooxygenase genes is a main mechanism for the resistance to imidacloprid, a representative neonicotinoid insecticide, in Nilaparvata lugens (brown planthopper, BPH). However, only two P450 genes (CYP6AY1 and CYP6ER1), among fifty-four P450 genes identified from BPH genome database, have been reported to play important roles in imidacloprid resistance until now. In this study, after the confirmation of important roles of P450s in imidacloprid resistance by the synergism analysis, the expression induction by imidacloprid was determined for all P450 genes. In the susceptible (Sus) strain, eight P450 genes in Clade4, eight in Clade3 and two in Clade2 were up-regulated by imidacloprid, among which three genes (CYP6CS1, CYP6CW1 and CYP6ER1, all in Clade3) were increased to above 4.0-fold and eight genes to above 2.0-fold. In contrast, no P450 genes were induced in Mito clade. Eight genes induced to above 2.0-fold were selected to determine their expression and induced levels in Huzhou population, in which piperonyl butoxide showed the biggest effects on imidacloprid toxicity among eight field populations. The expression levels of seven P450 genes were higher in Huzhou population than that in Sus strain, with the biggest differences for CYP6CS1 (9.8-fold), CYP6ER1 (7.7-fold) and CYP6AY1 (5.1-fold). The induction levels for all tested genes were bigger in Sus strain than that in Huzhou population except CYP425B1. Screening the induction of P450 genes by imidacloprid in the genome-scale will provide an overall view on the possible metabolic factors in the resistance to neonicotinoid insecticides. The further work, such as the functional study of recombinant proteins, will be performed to validate the roles of these P450s in imidacloprid resistance. Copyright © 2015 Elsevier B.V. All rights reserved.

Interactive analysis of systems biology molecular expression data

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Prabhakar Sunil

2008-02-01

Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

Large-scale analysis of protein expression changes in human keratinocytes immortalized by human papilloma virus type 16 E6 and E7 oncogenes

Directory of Open Access Journals (Sweden)

Arnouk Hilal

2009-08-01

Full Text Available Abstract Background Infection with high-risk type human papilloma viruses (HPVs is associated with cervical carcinomas and with a subset of head and neck squamous cell carcinomas. Viral E6 and E7 oncogenes cooperate to achieve cell immortalization by a mechanism that is not yet fully understood. Here, human keratinocytes were immortalized by long-term expression of HPV type 16 E6 or E7 oncoproteins, or both. Proteomic profiling was used to compare expression levels for 741 discrete protein features. Results Six replicate measurements were performed for each group using two-dimensional difference gel electrophoresis (2D-DIGE. The median within-group coefficient of variation was 19–21%. Significance of between-group differences was tested based on Significance Analysis of Microarray and fold change. Expression of 170 (23% of the protein features changed significantly in immortalized cells compared to primary keratinocytes. Most of these changes were qualitatively similar in cells immortalized by E6, E7, or E6/7 expression, indicating convergence on a common phenotype, but fifteen proteins (~2% were outliers in this regulatory pattern. Ten demonstrated opposite regulation in E6- and E7-expressing cells, including the cell cycle regulator p16INK4a; the carbohydrate binding protein Galectin-7; two differentially migrating forms of the intermediate filament protein Cytokeratin-7; HSPA1A (Hsp70-1; and five unidentified proteins. Five others had a pattern of expression that suggested cooperativity between the co-expressed oncoproteins. Two of these were identified as forms of the small heat shock protein HSPB1 (Hsp27. Conclusion This large-scale analysis provides a framework for understanding the cooperation between E6 and E7 oncoproteins in HPV-driven carcinogenesis.

Large-Scale Analysis of Network Bistability for Human Cancers

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Shiraishi, Tetsuya; Matsuyama, Shinako; Kitano, Hiroaki

2010-01-01

Protein–protein interaction and gene regulatory networks are likely to be locked in a state corresponding to a disease by the behavior of one or more bistable circuits exhibiting switch-like behavior. Sets of genes could be over-expressed or repressed when anomalies due to disease appear, and the circuits responsible for this over- or under-expression might persist for as long as the disease state continues. This paper shows how a large-scale analysis of network bistability for various human cancers can identify genes that can potentially serve as drug targets or diagnosis biomarkers. PMID:20628618

Serial Expression Analysis: a web tool for the analysis of serial gene expression data

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Nueda, Maria José; Carbonell, José; Medina, Ignacio; Dopazo, Joaquín; Conesa, Ana

2010-01-01

Serial transcriptomics experiments investigate the dynamics of gene expression changes associated with a quantitative variable such as time or dosage. The statistical analysis of these data implies the study of global and gene-specific expression trends, the identification of significant serial changes, the comparison of expression profiles and the assessment of transcriptional changes in terms of cellular processes. We have created the SEA (Serial Expression Analysis) suite to provide a complete web-based resource for the analysis of serial transcriptomics data. SEA offers five different algorithms based on univariate, multivariate and functional profiling strategies framed within a user-friendly interface and a project-oriented architecture to facilitate the analysis of serial gene expression data sets from different perspectives. SEA is available at sea.bioinfo.cipf.es. PMID:20525784

An innovative expression model of human health risk based on the quantitative analysis of soil metals sources contribution in different spatial scales.

Science.gov (United States)

Zhang, Yimei; Li, Shuai; Wang, Fei; Chen, Zhuang; Chen, Jie; Wang, Liqun

2018-09-01

Toxicity of heavy metals from industrialization poses critical concern, and analysis of sources associated with potential human health risks is of unique significance. Assessing human health risk of pollution sources (factored health risk) concurrently in the whole and the sub region can provide more instructive information to protect specific potential victims. In this research, we establish a new expression model of human health risk based on quantitative analysis of sources contribution in different spatial scales. The larger scale grids and their spatial codes are used to initially identify the level of pollution risk, the type of pollution source and the sensitive population at high risk. The smaller scale grids and their spatial codes are used to identify the contribution of various sources of pollution to each sub region (larger grid) and to assess the health risks posed by each source for each sub region. The results of case study show that, for children (sensitive populations, taking school and residential area as major region of activity), the major pollution source is from the abandoned lead-acid battery plant (ALP), traffic emission and agricultural activity. The new models and results of this research present effective spatial information and useful model for quantifying the hazards of source categories and human health a t complex industrial system in the future. Copyright © 2018 Elsevier Ltd. All rights reserved.

Analysis of musical expression in audio signals

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Dixon, Simon

2003-01-01

In western art music, composers communicate their work to performers via a standard notation which specificies the musical pitches and relative timings of notes. This notation may also include some higher level information such as variations in the dynamics, tempo and timing. Famous performers are characterised by their expressive interpretation, the ability to convey structural and emotive information within the given framework. The majority of work on audio content analysis focusses on retrieving score-level information; this paper reports on the extraction of parameters describing the performance, a task which requires a much higher degree of accuracy. Two systems are presented: BeatRoot, an off-line beat tracking system which finds the times of musical beats and tracks changes in tempo throughout a performance, and the Performance Worm, a system which provides a real-time visualisation of the two most important expressive dimensions, tempo and dynamics. Both of these systems are being used to process data for a large-scale study of musical expression in classical and romantic piano performance, which uses artificial intelligence (machine learning) techniques to discover fundamental patterns or principles governing expressive performance.

Precise Analysis of String Expressions

DEFF Research Database (Denmark)

Christensen, Aske Simon; Møller, Anders; Schwartzbach, Michael Ignatieff

2003-01-01

We perform static analysis of Java programs to answer a simple question: which values may occur as results of string expressions? The answers are summarized for each expression by a regular language that is guaranteed to contain all possible values. We present several applications of this analysis...... are automatically produced. We present extensive benchmarks demonstrating that the analysis is efficient and produces results of useful precision......., including statically checking the syntax of dynamically generated expressions, such as SQL queries. Our analysis constructs flow graphs from class files and generates a context-free grammar with a nonterminal for each string expression. The language of this grammar is then widened into a regular language...

German taxi drivers' experiences and expressions of driving anger: Are the driving anger scale and the driving anger expression inventory valid measures?

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Brandenburg, Stefan; Oehl, Michael; Seigies, Kristin

2017-11-17

The objective of this article was 2-fold: firstly, we wanted to examine whether the original Driving Anger Scale (DAS) and the original Driving Anger Expression Inventory (DAX) apply to German professional taxi drivers because these scales have previously been given to professional and particularly to nonprofessional drivers in different countries. Secondly, we wanted to examine possible differences in driving anger experience and expression between professional German taxi drivers and nonprofessional German drivers. We applied German versions of the DAS, the DAX, and the State-Trait Anger Expression Inventory (STAXI) to a sample of 138 professional German taxi drivers. We then compared their ratings to the ratings of a sample of 1,136 nonprofessional German drivers (Oehl and Brandenburg n.d. ). Regarding our first objective, confirmatory factor analysis shows that the model fit of the DAS is better for nonprofessional drivers than for professional drivers. The DAX applies neither to professional nor to nonprofessional German drivers properly. Consequently, we suggest modified shorter versions of both scales for professional drivers. The STAXI applies to both professional and nonprofessional drivers. With respect to our second objective, we show that professional drivers experience significantly less driving anger than nonprofessional drivers, but they express more driving anger. We conclude that the STAXI can be applied to professional German taxi drivers. In contrast, for the DAS and the DAX we found particular shorter versions for professional taxi drivers. Especially for the DAX, most statements were too strong for German drivers to agree to. They do not show behaviors related to driving anger expression as they are described in the DAX. These problems with the original American DAX items are in line with several other studies in different countries. Future investigations should examine whether (professional) drivers from further countries express their anger

Scaling of gene expression data allowing the comparison of different gene expression platforms

NARCIS (Netherlands)

van Ruissen, Fred; Schaaf, Gerben J.; Kool, Marcel; Baas, Frank; Ruijter, Jan M.

2008-01-01

Serial analysis of gene expression (SAGE) and microarrays have found a widespread application, but much ambiguity exists regarding the amalgamation of the data resulting from these technologies. Cross-platform utilization of gene expression data from the SAGE and microarray technology could reduce

Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens.

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Jiang, Zhenhong; He, Fei; Zhang, Ziding

2017-07-01

Through large-scale transcriptional data analyses, we highlighted the importance of plant metabolism in plant immunity and identified 26 metabolic pathways that were frequently influenced by the infection of 14 different pathogens. Reprogramming of plant metabolism is a common phenomenon in plant defense responses. Currently, a large number of transcriptional profiles of infected tissues in Arabidopsis (Arabidopsis thaliana) have been deposited in public databases, which provides a great opportunity to understand the expression patterns of metabolic pathways during plant defense responses at the systems level. Here, we performed a large-scale transcriptome analysis based on 135 previously published expression samples, including 14 different pathogens, to explore the expression pattern of Arabidopsis metabolic pathways. Overall, metabolic genes are significantly changed in expression during plant defense responses. Upregulated metabolic genes are enriched on defense responses, and downregulated genes are enriched on photosynthesis, fatty acid and lipid metabolic processes. Gene set enrichment analysis (GSEA) identifies 26 frequently differentially expressed metabolic pathways (FreDE_Paths) that are differentially expressed in more than 60% of infected samples. These pathways are involved in the generation of energy, fatty acid and lipid metabolism as well as secondary metabolite biosynthesis. Clustering analysis based on the expression levels of these 26 metabolic pathways clearly distinguishes infected and control samples, further suggesting the importance of these metabolic pathways in plant defense responses. By comparing with FreDE_Paths from abiotic stresses, we find that the expression patterns of 26 FreDE_Paths from biotic stresses are more consistent across different infected samples. By investigating the expression correlation between transcriptional factors (TFs) and FreDE_Paths, we identify several notable relationships. Collectively, the current study

Meta Analysis of Gene Expression Data within and Across Species.

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Fierro, Ana C; Vandenbussche, Filip; Engelen, Kristof; Van de Peer, Yves; Marchal, Kathleen

2008-12-01

Since the second half of the 1990s, a large number of genome-wide analyses have been described that study gene expression at the transcript level. To this end, two major strategies have been adopted, a first one relying on hybridization techniques such as microarrays, and a second one based on sequencing techniques such as serial analysis of gene expression (SAGE), cDNA-AFLP, and analysis based on expressed sequence tags (ESTs). Despite both types of profiling experiments becoming routine techniques in many research groups, their application remains costly and laborious. As a result, the number of conditions profiled in individual studies is still relatively small and usually varies from only two to few hundreds of samples for the largest experiments. More and more, scientific journals require the deposit of these high throughput experiments in public databases upon publication. Mining the information present in these databases offers molecular biologists the possibility to view their own small-scale analysis in the light of what is already available. However, so far, the richness of the public information remains largely unexploited. Several obstacles such as the correct association between ESTs and microarray probes with the corresponding gene transcript, the incompleteness and inconsistency in the annotation of experimental conditions, and the lack of standardized experimental protocols to generate gene expression data, all impede the successful mining of these data. Here, we review the potential and difficulties of combining publicly available expression data from respectively EST analyses and microarray experiments. With examples from literature, we show how meta-analysis of expression profiling experiments can be used to study expression behavior in a single organism or between organisms, across a wide range of experimental conditions. We also provide an overview of the methods and tools that can aid molecular biologists in exploiting these public data.

Multi-scale Analysis of Topographic Surface Roughness in the Midland Valley, Scotland

OpenAIRE

Grohmann, Carlos

2017-01-01

Surface roughness is an important geomorphological variable which has been used in the earth and planetary sciences to infer material properties, current/past processes and the time elapsed since formation. No single definition exists, however within the context of geomorphometry we use surface roughness as a expression of the variability of a topographic surface at a given scale, where the scale of analysis is determined by the size of the landforms or geomorphic features of interest. Six te...

Gene expression analysis of flax seed development

Science.gov (United States)

2011-01-01

Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise

Gene expression analysis of flax seed development

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Sharpe Andrew

2011-04-01

Full Text Available Abstract Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages seed coats (globular and torpedo stages and endosperm (pooled globular to torpedo stages and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST (GenBank accessions LIBEST_026995 to LIBEST_027011 were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152 had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid

A rank-based algorithm of differential expression analysis for small cell line data with statistical control.

Science.gov (United States)

Li, Xiangyu; Cai, Hao; Wang, Xianlong; Ao, Lu; Guo, You; He, Jun; Gu, Yunyan; Qi, Lishuang; Guan, Qingzhou; Lin, Xu; Guo, Zheng

2017-10-13

To detect differentially expressed genes (DEGs) in small-scale cell line experiments, usually with only two or three technical replicates for each state, the commonly used statistical methods such as significance analysis of microarrays (SAM), limma and RankProd (RP) lack statistical power, while the fold change method lacks any statistical control. In this study, we demonstrated that the within-sample relative expression orderings (REOs) of gene pairs were highly stable among technical replicates of a cell line but often widely disrupted after certain treatments such like gene knockdown, gene transfection and drug treatment. Based on this finding, we customized the RankComp algorithm, previously designed for individualized differential expression analysis through REO comparison, to identify DEGs with certain statistical control for small-scale cell line data. In both simulated and real data, the new algorithm, named CellComp, exhibited high precision with much higher sensitivity than the original RankComp, SAM, limma and RP methods. Therefore, CellComp provides an efficient tool for analyzing small-scale cell line data. © The Author 2017. Published by Oxford University Press.

Confirmatory factor analysis of the Drive for Muscularity Scale-S (DMS-S) and Male Body Attitudes Scale-S (MBAS-S) among male university students in Buenos Aires.

Science.gov (United States)

Compte, Emilio J; Sepúlveda, Ana R; de Pellegrin, Yolanda; Blanco, Miriam

2015-06-01

Several studies have demonstrated that men express body dissatisfaction differently than women. Although specific instruments that address body dissatisfaction in men have been developed, only a few have been validated in Latin-American male populations. The aim of this study was to reassess the factor structure of the Spanish versions of the Drive for Muscularity Scale (DMS-S) and the Male Body Attitudes Scale (MBAS-S) in an Argentinian sample. A cross-sectional study was conducted among 423 male students to examine: the factorial structure (confirmatory factor analysis), the internal consistency reliability, and the concurrent, convergent and discriminant validity of both scales. Results replicated the two factor structures for the DMS-S and MBAS-S. Both scales showed excellent levels of internal consistency, and various measures of construct validity indicated that the DMS-S and MBAS-S were acceptable and valid instruments to assess body dissatisfaction in Argentinian males. Copyright © 2015 Elsevier Ltd. All rights reserved.

Crater ejecta scaling laws: fundamental forms based on dimensional analysis

International Nuclear Information System (INIS)

Housen, K.R.; Schmidt, R.M.; Holsapple, K.A.

1983-01-01

A model of crater ejecta is constructed using dimensional analysis and a recently developed theory of energy and momentum coupling in cratering events. General relations are derived that provide a rationale for scaling laboratory measurements of ejecta to larger events. Specific expressions are presented for ejection velocities and ejecta blanket profiles in two limiting regimes of crater formation: the so-called gravity and strength regimes. In the gravity regime, ejectra velocities at geometrically similar launch points within craters vary as the square root of the product of crater radius and gravity. This relation implies geometric similarity of ejecta blankets. That is, the thickness of an ejecta blanket as a function of distance from the crater center is the same for all sizes of craters if the thickness and range are expressed in terms of crater radii. In the strength regime, ejecta velocities are independent of crater size. Consequently, ejecta blankets are not geometrically similar in this regime. For points away from the crater rim the expressions for ejecta velocities and thickness take the form of power laws. The exponents in these power laws are functions of an exponent, α, that appears in crater radius scaling relations. Thus experimental studies of the dependence of crater radius on impact conditions determine scaling relations for ejecta. Predicted ejection velocities and ejecta-blanket profiles, based on measured values of α, are compared to existing measurements of velocities and debris profiles

Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression

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Cohn Zachary A

2007-06-01

Full Text Available Abstract Background Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate into chondrocytes to shape the early skeleton. Subsequently, the cartilage anlagen differentiate to form the growth plates, which are responsible for linear bone growth, and the articular chondrocytes, which facilitate joint function. However, despite the multiplicity of roles of cartilage during human fetal life, surprisingly little is known about its transcriptome. To address this, a whole genome microarray expression profile was generated using RNA isolated from 18–22 week human distal femur fetal cartilage and compared with a database of control normal human tissues aggregated at UCLA, termed Celsius. Results 161 cartilage-selective genes were identified, defined as genes significantly expressed in cartilage with low expression and little variation across a panel of 34 non-cartilage tissues. Among these 161 genes were cartilage-specific genes such as cartilage collagen genes and 25 genes which have been associated with skeletal phenotypes in humans and/or mice. Many of the other cartilage-selective genes do not have established roles in cartilage or are novel, unannotated genes. Quantitative RT-PCR confirmed the unique pattern of gene expression observed by microarray analysis. Conclusion Defining the gene expression pattern for cartilage has identified new genes that may contribute to human skeletogenesis as well as provided further candidate genes for skeletal dysplasias. The data suggest that fetal cartilage is a complex and transcriptionally active tissue and demonstrate that the set of genes selectively expressed in the tissue has been greatly underestimated.

Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

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Schlegel Brigitte

2004-03-01

Full Text Available Abstract Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.

Optimal consistency in microRNA expression analysis using reference-gene-based normalization.

Science.gov (United States)

Wang, Xi; Gardiner, Erin J; Cairns, Murray J

2015-05-01

Normalization of high-throughput molecular expression profiles secures differential expression analysis between samples of different phenotypes or biological conditions, and facilitates comparison between experimental batches. While the same general principles apply to microRNA (miRNA) normalization, there is mounting evidence that global shifts in their expression patterns occur in specific circumstances, which pose a challenge for normalizing miRNA expression data. As an alternative to global normalization, which has the propensity to flatten large trends, normalization against constitutively expressed reference genes presents an advantage through their relative independence. Here we investigated the performance of reference-gene-based (RGB) normalization for differential miRNA expression analysis of microarray expression data, and compared the results with other normalization methods, including: quantile, variance stabilization, robust spline, simple scaling, rank invariant, and Loess regression. The comparative analyses were executed using miRNA expression in tissue samples derived from subjects with schizophrenia and non-psychiatric controls. We proposed a consistency criterion for evaluating methods by examining the overlapping of differentially expressed miRNAs detected using different partitions of the whole data. Based on this criterion, we found that RGB normalization generally outperformed global normalization methods. Thus we recommend the application of RGB normalization for miRNA expression data sets, and believe that this will yield a more consistent and useful readout of differentially expressed miRNAs, particularly in biological conditions characterized by large shifts in miRNA expression.

Dual Temporal Scale Convolutional Neural Network for Micro-Expression Recognition

Directory of Open Access Journals (Sweden)

Min Peng

2017-10-01

Full Text Available Facial micro-expression is a brief involuntary facial movement and can reveal the genuine emotion that people try to conceal. Traditional methods of spontaneous micro-expression recognition rely excessively on sophisticated hand-crafted feature design and the recognition rate is not high enough for its practical application. In this paper, we proposed a Dual Temporal Scale Convolutional Neural Network (DTSCNN for spontaneous micro-expressions recognition. The DTSCNN is a two-stream network. Different of stream of DTSCNN is used to adapt to different frame rate of micro-expression video clips. Each stream of DSTCNN consists of independent shallow network for avoiding the overfitting problem. Meanwhile, we fed the networks with optical-flow sequences to ensure that the shallow networks can further acquire higher-level features. Experimental results on spontaneous micro-expression databases (CASME I/II showed that our method can achieve a recognition rate almost 10% higher than what some state-of-the-art method can achieve.

Dual Temporal Scale Convolutional Neural Network for Micro-Expression Recognition.

Science.gov (United States)

Peng, Min; Wang, Chongyang; Chen, Tong; Liu, Guangyuan; Fu, Xiaolan

2017-01-01

Facial micro-expression is a brief involuntary facial movement and can reveal the genuine emotion that people try to conceal. Traditional methods of spontaneous micro-expression recognition rely excessively on sophisticated hand-crafted feature design and the recognition rate is not high enough for its practical application. In this paper, we proposed a Dual Temporal Scale Convolutional Neural Network (DTSCNN) for spontaneous micro-expressions recognition. The DTSCNN is a two-stream network. Different of stream of DTSCNN is used to adapt to different frame rate of micro-expression video clips. Each stream of DSTCNN consists of independent shallow network for avoiding the overfitting problem. Meanwhile, we fed the networks with optical-flow sequences to ensure that the shallow networks can further acquire higher-level features. Experimental results on spontaneous micro-expression databases (CASME I/II) showed that our method can achieve a recognition rate almost 10% higher than what some state-of-the-art method can achieve.

Dual Temporal Scale Convolutional Neural Network for Micro-Expression Recognition

Science.gov (United States)

Peng, Min; Wang, Chongyang; Chen, Tong; Liu, Guangyuan; Fu, Xiaolan

2017-01-01

Facial micro-expression is a brief involuntary facial movement and can reveal the genuine emotion that people try to conceal. Traditional methods of spontaneous micro-expression recognition rely excessively on sophisticated hand-crafted feature design and the recognition rate is not high enough for its practical application. In this paper, we proposed a Dual Temporal Scale Convolutional Neural Network (DTSCNN) for spontaneous micro-expressions recognition. The DTSCNN is a two-stream network. Different of stream of DTSCNN is used to adapt to different frame rate of micro-expression video clips. Each stream of DSTCNN consists of independent shallow network for avoiding the overfitting problem. Meanwhile, we fed the networks with optical-flow sequences to ensure that the shallow networks can further acquire higher-level features. Experimental results on spontaneous micro-expression databases (CASME I/II) showed that our method can achieve a recognition rate almost 10% higher than what some state-of-the-art method can achieve. PMID:29081753

Dimensions of assertiveness: factors underlying the college self-expression scale.

Science.gov (United States)

Kipper, D A; Jaffe, Y

1978-02-01

A total of 447 Israeli students, both males and females, from four educational institutions were administered the College Self-expression Scale, a measure of assertiveness. The obtained responses were factor analyzed using the principal axis solution and the varimax rotation method. The results showed four main factors which included 43 of the 50 items of the original scale. These factors were identified as the willingness to take risks in interpersonal interactions, the ability to communicate feelings, setting rules and rectifying injustices, and the presence or absence of a tendency to invoke a self-punitive attitude. The findings were interpreted as adding support to the validity of the scale as a measure of assertiveness.

In Silico Expression Analysis.

Science.gov (United States)

Bolívar, Julio; Hehl, Reinhard; Bülow, Lorenz

2016-01-01

Information on the specificity of cis-sequences enables the design of functional synthetic plant promoters that are responsive to specific stresses. Potential cis-sequences may be experimentally tested, however, correlation of genomic sequence with gene expression data enables an in silico expression analysis approach to bioinformatically assess the stress specificity of candidate cis-sequences prior to experimental verification. The present chapter demonstrates an example for the in silico validation of a potential cis-regulatory sequence responsive to cold stress. The described online tool can be applied for the bioinformatic assessment of cis-sequences responsive to most abiotic and biotic stresses of plants. Furthermore, a method is presented based on a reverted in silico expression analysis approach that predicts highly specific potentially functional cis-regulatory elements for a given stress.

Comparative modular analysis of gene expression in vertebrate organs

Directory of Open Access Journals (Sweden)

Piasecka Barbara

2012-03-01

Full Text Available Abstract Background The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity. Results Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human. Conclusions Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.

Comparative modular analysis of gene expression in vertebrate organs.

Science.gov (United States)

Piasecka, Barbara; Kutalik, Zoltán; Roux, Julien; Bergmann, Sven; Robinson-Rechavi, Marc

2012-03-29

The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity. Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human. Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.

Mokken scale analysis : Between the Guttman scale and parametric item response theory

NARCIS (Netherlands)

van Schuur, Wijbrandt H.

2003-01-01

This article introduces a model of ordinal unidimensional measurement known as Mokken scale analysis. Mokken scaling is based on principles of Item Response Theory (IRT) that originated in the Guttman scale. I compare the Mokken model with both Classical Test Theory (reliability or factor analysis)

Gene expression plasticity across hosts of an invasive scale insect species

DEFF Research Database (Denmark)

Christodoulides, Nicholas; Van Dam, Alex; Peterson, Daniel A.

2017-01-01

For plant-eating insects, we still have only a nascent understanding of the genetic basis of host-use promiscuity. Here, to improve that situation, we investigated host-induced gene expression plasticity in the invasive lobate lac scale insect, Paratachardina pseudolobata (Hemiptera: Keriidae). We...

H2@Scale Analysis

Energy Technology Data Exchange (ETDEWEB)

Ruth, Mark

2017-07-12

'H2@Scale' is a concept based on the opportunity for hydrogen to act as an intermediate between energy sources and uses. Hydrogen has the potential to be used like the primary intermediate in use today, electricity, because it too is fungible. This presentation summarizes the H2@Scale analysis efforts performed during the first third of 2017. Results of technical potential uses and supply options are summarized and show that the technical potential demand for hydrogen is 60 million metric tons per year and that the U.S. has sufficient domestic resources to meet that demand. A high level infrastructure analysis is also presented that shows an 85% increase in energy on the grid if all hydrogen is produced from grid electricity. However, a preliminary spatial assessment shows that supply is sufficient in most counties across the U.S. The presentation also shows plans for analysis of the economic potential for the H2@Scale concept. Those plans involve developing supply and demand curves for potential hydrogen generation options and as compared to other options for use of that hydrogen.

Multi-Scale Entropy Analysis as a Method for Time-Series Analysis of Climate Data

Directory of Open Access Journals (Sweden)

Heiko Balzter

2015-03-01

Full Text Available Evidence is mounting that the temporal dynamics of the climate system are changing at the same time as the average global temperature is increasing due to multiple climate forcings. A large number of extreme weather events such as prolonged cold spells, heatwaves, droughts and floods have been recorded around the world in the past 10 years. Such changes in the temporal scaling behaviour of climate time-series data can be difficult to detect. While there are easy and direct ways of analysing climate data by calculating the means and variances for different levels of temporal aggregation, these methods can miss more subtle changes in their dynamics. This paper describes multi-scale entropy (MSE analysis as a tool to study climate time-series data and to identify temporal scales of variability and their change over time in climate time-series. MSE estimates the sample entropy of the time-series after coarse-graining at different temporal scales. An application of MSE to Central European, variance-adjusted, mean monthly air temperature anomalies (CRUTEM4v is provided. The results show that the temporal scales of the current climate (1960–2014 are different from the long-term average (1850–1960. For temporal scale factors longer than 12 months, the sample entropy increased markedly compared to the long-term record. Such an increase can be explained by systems theory with greater complexity in the regional temperature data. From 1961 the patterns of monthly air temperatures are less regular at time-scales greater than 12 months than in the earlier time period. This finding suggests that, at these inter-annual time scales, the temperature variability has become less predictable than in the past. It is possible that climate system feedbacks are expressed in altered temporal scales of the European temperature time-series data. A comparison with the variance and Shannon entropy shows that MSE analysis can provide additional information on the

Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants.

Science.gov (United States)

Kudo, Toru; Sasaki, Yohei; Terashima, Shin; Matsuda-Imai, Noriko; Takano, Tomoyuki; Saito, Misa; Kanno, Maasa; Ozaki, Soichi; Suwabe, Keita; Suzuki, Go; Watanabe, Masao; Matsuoka, Makoto; Takayama, Seiji; Yano, Kentaro

2016-10-13

In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various

Recognition of facial expressions by cortical multi-scale line and edge coding

OpenAIRE

Sousa, R.; Rodrigues, J. M. F.; du Buf, J. M. H.

2010-01-01

Face-to-face communications between humans involve emotions, which often are unconsciously conveyed by facial expressions and body gestures. Intelligent human-machine interfaces, for example in cognitive robotics, need to recognize emotions. This paper addresses facial expressions and their neural correlates on the basis of a model of the visual cortex: the multi-scale line and edge coding. The recognition model links the cortical representation with Paul Ekman's Action Units which are relate...

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies.

Science.gov (United States)

Zhao, Shanrong; Prenger, Kurt; Smith, Lance

2013-01-01

RNA-Seq is becoming a promising replacement to microarrays in transcriptome profiling and differential gene expression study. Technical improvements have decreased sequencing costs and, as a result, the size and number of RNA-Seq datasets have increased rapidly. However, the increasing volume of data from large-scale RNA-Seq studies poses a practical challenge for data analysis in a local environment. To meet this challenge, we developed Stormbow, a cloud-based software package, to process large volumes of RNA-Seq data in parallel. The performance of Stormbow has been tested by practically applying it to analyse 178 RNA-Seq samples in the cloud. In our test, it took 6 to 8 hours to process an RNA-Seq sample with 100 million reads, and the average cost was $3.50 per sample. Utilizing Amazon Web Services as the infrastructure for Stormbow allows us to easily scale up to handle large datasets with on-demand computational resources. Stormbow is a scalable, cost effective, and open-source based tool for large-scale RNA-Seq data analysis. Stormbow can be freely downloaded and can be used out of box to process Illumina RNA-Seq datasets.

Screening and large-scale expression of membrane proteins in mammalian cells for structural studies.

Science.gov (United States)

Goehring, April; Lee, Chia-Hsueh; Wang, Kevin H; Michel, Jennifer Carlisle; Claxton, Derek P; Baconguis, Isabelle; Althoff, Thorsten; Fischer, Suzanne; Garcia, K Christopher; Gouaux, Eric

2014-11-01

Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in overexpression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient production of baculovirus and robust expression of the target protein. In this protocol, we show how to use small-scale transient transfection and fluorescence-detection size-exclusion chromatography (FSEC) experiments using a GFP-His8-tagged candidate protein to screen for monodispersity and expression level. Once promising candidates are identified, we describe how to generate baculovirus, transduce HEK293S GnTI(-) (N-acetylglucosaminyltransferase I-negative) cells in suspension culture and overexpress the candidate protein. We have used these methods to prepare pure samples of chicken acid-sensing ion channel 1a (cASIC1) and Caenorhabditis elegans glutamate-gated chloride channel (GluCl) for X-ray crystallography, demonstrating how to rapidly and efficiently screen hundreds of constructs and accomplish large-scale expression in 4-6 weeks.

Parallelizing Gene Expression Programming Algorithm in Enabling Large-Scale Classification

Directory of Open Access Journals (Sweden)

Lixiong Xu

2017-01-01

Full Text Available As one of the most effective function mining algorithms, Gene Expression Programming (GEP algorithm has been widely used in classification, pattern recognition, prediction, and other research fields. Based on the self-evolution, GEP is able to mine an optimal function for dealing with further complicated tasks. However, in big data researches, GEP encounters low efficiency issue due to its long time mining processes. To improve the efficiency of GEP in big data researches especially for processing large-scale classification tasks, this paper presents a parallelized GEP algorithm using MapReduce computing model. The experimental results show that the presented algorithm is scalable and efficient for processing large-scale classification tasks.

Anger Expression Types and Interpersonal Problems in Nurses.

Science.gov (United States)

Han, Aekyung; Won, Jongsoon; Kim, Oksoo; Lee, Sang E

2015-06-01

The purpose of this study was to investigate the anger expression types in nurses and to analyze the differences between the anger expression types and interpersonal problems. The data were collected from 149 nurses working in general hospitals with 300 beds or more in Seoul or Gyeonggi province, Korea. For anger expression type, the anger expression scale from the Korean State-Trait Anger Expression Inventory was used. For interpersonal problems, the short form of the Korean Inventory of Interpersonal Problems Circumplex Scales was used. Data were analyzed using descriptive statistics, cluster analysis, multivariate analysis of variance, and Duncan's multiple comparisons test. Three anger expression types in nurses were found: low-anger expression, anger-in, and anger-in/control type. From the results of multivariate analysis of variance, there were significant differences between anger expression types and interpersonal problems (Wilks lambda F = 3.52, p interpersonal problems by Duncan's post hoc test (p interpersonal problems. Copyright © 2015. Published by Elsevier B.V.

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

DEFF Research Database (Denmark)

Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.

2017-01-01

orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME......Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...... models have 70,000 constraints and variables and will grow larger). We have developed a quadrupleprecision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging...

Spiritual Competency Scale: Further Analysis

Science.gov (United States)

Dailey, Stephanie F.; Robertson, Linda A.; Gill, Carman S.

2015-01-01

This article describes a follow-up analysis of the Spiritual Competency Scale, which initially validated ASERVIC's (Association for Spiritual, Ethical and Religious Values in Counseling) spiritual competencies. The study examined whether the factor structure of the Spiritual Competency Scale would be supported by participants (i.e., ASERVIC…

Analysis of Facial Expression by Taste Stimulation

Science.gov (United States)

Tobitani, Kensuke; Kato, Kunihito; Yamamoto, Kazuhiko

In this study, we focused on the basic taste stimulation for the analysis of real facial expressions. We considered that the expressions caused by taste stimulation were unaffected by individuality or emotion, that is, such expressions were involuntary. We analyzed the movement of facial muscles by taste stimulation and compared real expressions with artificial expressions. From the result, we identified an obvious difference between real and artificial expressions. Thus, our method would be a new approach for facial expression recognition.

mESAdb: microRNA expression and sequence analysis database.

Science.gov (United States)

Kaya, Koray D; Karakülah, Gökhan; Yakicier, Cengiz M; Acar, Aybar C; Konu, Ozlen

2011-01-01

microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.

Unified Scaling Law for flux pinning in practical superconductors: III. Minimum datasets, core parameters, and application of the Extrapolative Scaling Expression

Science.gov (United States)

Ekin, Jack W.; Cheggour, Najib; Goodrich, Loren; Splett, Jolene

2017-03-01

In Part 2 of these articles, an extensive analysis of pinning-force curves and raw scaling data was used to derive the Extrapolative Scaling Expression (ESE). This is a parameterization of the Unified Scaling Law (USL) that has the extrapolation capability of fundamental unified scaling, coupled with the application ease of a simple fitting equation. Here in Part 3, the accuracy of the ESE relation to interpolate and extrapolate limited critical-current data to obtain complete I c(B,T,ɛ) datasets is evaluated and compared with present fitting equations. Accuracy is analyzed in terms of root mean square (RMS) error and fractional deviation statistics. Highlights from 92 test cases are condensed and summarized, covering most fitting protocols and proposed parameterizations of the USL. The results show that ESE reliably extrapolates critical currents at fields B, temperatures T, and strains ɛ that are remarkably different from the fitted minimum dataset. Depending on whether the conductor is moderate-J c or high-J c, effective RMS extrapolation errors for ESE are in the range 2-5 A at 12 T, which approaches the I c measurement error (1-2%). The minimum dataset for extrapolating full I c(B,T,ɛ) characteristics is also determined from raw scaling data. It consists of one set of I c(B,ɛ) data at a fixed temperature (e.g., liquid helium temperature), and one set of I c(B,T) data at a fixed strain (e.g., zero applied strain). Error analysis of extrapolations from the minimum dataset with different fitting equations shows that ESE reduces the percentage extrapolation errors at individual data points at high fields, temperatures, and compressive strains down to 1/10th to 1/40th the size of those for extrapolations with present fitting equations. Depending on the conductor, percentage fitting errors for interpolations are also reduced to as little as 1/15th the size. The extrapolation accuracy of the ESE relation offers the prospect of straightforward implementation of

Comparison between Camberwell Family Interview and Expressed Emotion Scale in Determining Emotions of Caregivers of Schizophrenic Patients

Science.gov (United States)

ÇETİNKAYA DUMAN, Zekiye; KUŞCU, M. Kemal; ÖZGÜN, Serkan

2013-01-01

Introduction The aim of the study was to compare the Camberwell Family Interview (CFI) and the Expressed Emotion Scale (EES) in determining the level of expressed emotion in caregivers of patients with schizophrenia. Method The study sample included caregivers of 22 schizophrenic patients followed in two psychiatric clinics. The level of expressed emotion in the caregivers was assessed by the CFI and the EES. CFI was applied to caregivers of the inpatients and the procedure was audio recorded. These records were later used for the ratings. EES was completed by the caregivers. Total EES scores were used to determine the level of expressed emotion in the caregivers. Results Forty point nine percent and 50% of the caregivers had high level of expressed emotion based on the analysis of the data obtained from the CFI and EES. Fifty-nine percent and 50% of the caregivers had low level of expressed emotion based on the data obtained from the CFI and EES. The proportion of the caregivers with high level of expressed emotion as measured by the CFI and the EES were not statistically significantly different within the sample (χ2= 0.727). Conclusion The CFI and the EES were similar in determining the level of expressed emotion in caregivers of schizophrenic patients. It can be suggested that the EES, a user friendly tool, may be preferred to determine the level of expressed emotion in caregivers of patients with schizophrenia. However, further studies with larger samples are needed to obtain more reliable results. PMID:28360561

Automatic emotional expression analysis from eye area

Science.gov (United States)

Akkoç, Betül; Arslan, Ahmet

2015-02-01

Eyes play an important role in expressing emotions in nonverbal communication. In the present study, emotional expression classification was performed based on the features that were automatically extracted from the eye area. Fırst, the face area and the eye area were automatically extracted from the captured image. Afterwards, the parameters to be used for the analysis through discrete wavelet transformation were obtained from the eye area. Using these parameters, emotional expression analysis was performed through artificial intelligence techniques. As the result of the experimental studies, 6 universal emotions consisting of expressions of happiness, sadness, surprise, disgust, anger and fear were classified at a success rate of 84% using artificial neural networks.

Analysis of gene expression in normal and neoplastic human testis: new roles of RNA

DEFF Research Database (Denmark)

Novotny, G W; Nielsen, J E; Sonne, Si Brask

2007-01-01

Large-scale methods for analysing gene expression, such as microarrays, have yielded a wealth of information about gene expression at the mRNA level. However, expression of alternative transcripts, together with the presence of a wide range of largely undescribed RNA transcripts combined with reg......Large-scale methods for analysing gene expression, such as microarrays, have yielded a wealth of information about gene expression at the mRNA level. However, expression of alternative transcripts, together with the presence of a wide range of largely undescribed RNA transcripts combined...

MALDI-TOF mass spectrometry for quantitative gene expression analysis of acid responses in Staphylococcus aureus.

Science.gov (United States)

Rode, Tone Mari; Berget, Ingunn; Langsrud, Solveig; Møretrø, Trond; Holck, Askild

2009-07-01

Microorganisms are constantly exposed to new and altered growth conditions, and respond by changing gene expression patterns. Several methods for studying gene expression exist. During the last decade, the analysis of microarrays has been one of the most common approaches applied for large scale gene expression studies. A relatively new method for gene expression analysis is MassARRAY, which combines real competitive-PCR and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. In contrast to microarray methods, MassARRAY technology is suitable for analysing a larger number of samples, though for a smaller set of genes. In this study we compare the results from MassARRAY with microarrays on gene expression responses of Staphylococcus aureus exposed to acid stress at pH 4.5. RNA isolated from the same stress experiments was analysed using both the MassARRAY and the microarray methods. The MassARRAY and microarray methods showed good correlation. Both MassARRAY and microarray estimated somewhat lower fold changes compared with quantitative real-time PCR (qRT-PCR). The results confirmed the up-regulation of the urease genes in acidic environments, and also indicated the importance of metal ion regulation. This study shows that the MassARRAY technology is suitable for gene expression analysis in prokaryotes, and has advantages when a set of genes is being analysed for an organism exposed to many different environmental conditions.

Serial analysis of gene expression (SAGE)

NARCIS (Netherlands)

van Ruissen, Fred; Baas, Frank

2007-01-01

In 1995, serial analysis of gene expression (SAGE) was developed as a versatile tool for gene expression studies. SAGE technology does not require pre-existing knowledge of the genome that is being examined and therefore SAGE can be applied to many different model systems. In this chapter, the SAGE

Large-scale gene expression reveals different adaptations of Hyalopterus persikonus to winter and summer host plants.

Science.gov (United States)

Cui, Na; Yang, Peng-Cheng; Guo, Kun; Kang, Le; Cui, Feng

2017-06-01

Host alternation, an obligatory seasonal shifting between host plants of distant genetic relationship, has had significant consequences for the diversification and success of the superfamily of aphids. However, the underlying molecular mechanism remains unclear. In this study, the molecular mechanism of host alternation was explored through a large-scale gene expression analysis of the mealy aphid Hyalopterus persikonus on winter and summer host plants. More than four times as many unigenes of the mealy aphid were significantly upregulated on summer host Phragmites australis than on winter host Rosaceae plants. In order to identify gene candidates related to host alternation, the differentially expressed unigenes of H. persikonus were compared to salivary gland expressed genes and secretome of Acyrthosiphon pisum. Genes involved in ribosome and oxidative phosphorylation and with molecular functions of heme-copper terminal oxidase activity, hydrolase activity and ribosome binding were potentially upregulated in salivary glands of H. persikonus on the summer host. Putative secretory proteins, such as detoxification enzymes (carboxylesterases and cytochrome P450s), antioxidant enzymes (peroxidase and superoxide dismutase), glutathione peroxidase, glucose dehydrogenase, angiotensin-converting enzyme, cadherin, and calreticulin, were highly expressed in H. persikonus on the summer host, while a SCP GAPR-1-like family protein and a salivary sheath protein were highly expressed in the aphids on winter hosts. These results shed light on phenotypic plasticity in host utilization and seasonal adaptation of aphids. © 2016 Institute of Zoology, Chinese Academy of Sciences.

Scale characters analysis for gully structure in the watersheds of loess landforms based on digital elevation models

Science.gov (United States)

Zhu, Hongchun; Zhao, Yipeng; Liu, Haiying

2018-04-01

Scale is the basic attribute for expressing and describing spatial entity and phenomena. It offers theoretical significance in the study of gully structure information, variable characteristics of watershed morphology, and development evolution at different scales. This research selected five different areas in China's Loess Plateau as the experimental region and used DEM data at different scales as the experimental data. First, the change rule of the characteristic parameters of the data at different scales was analyzed. The watershed structure information did not change along with a change in the data scale. This condition was proven by selecting indices of gully bifurcation ratio and fractal dimension as characteristic parameters of watershed structure information. Then, the change rule of the characteristic parameters of gully structure with different analysis scales was analyzed by setting the scale sequence of analysis at the extraction gully. The gully structure of the watershed changed with variations in the analysis scale, and the change rule was obvious when the gully level changed. Finally, the change rule of the characteristic parameters of the gully structure at different areas was analyzed. The gully fractal dimension showed a significant numerical difference in different areas, whereas the variation of the gully branch ratio was small. The change rule indicated that the development degree of the gully obviously varied in different regions, but the morphological structure was basically similar.

Scale characters analysis for gully structure in the watersheds of loess landforms based on digital elevation models

Science.gov (United States)

Zhu, Hongchun; Zhao, Yipeng; Liu, Haiying

2018-06-01

Scale is the basic attribute for expressing and describing spatial entity and phenomena. It offers theoretical significance in the study of gully structure information, variable characteristics of watershed morphology, and development evolution at different scales. This research selected five different areas in China's Loess Plateau as the experimental region and used DEM data at different scales as the experimental data. First, the change rule of the characteristic parameters of the data at different scales was analyzed. The watershed structure information did not change along with a change in the data scale. This condition was proven by selecting indices of gully bifurcation ratio and fractal dimension as characteristic parameters of watershed structure information. Then, the change rule of the characteristic parameters of gully structure with different analysis scales was analyzed by setting the scale sequence of analysis at the extraction gully. The gully structure of the watershed changed with variations in the analysis scale, and the change rule was obvious when the gully level changed. Finally, the change rule of the characteristic parameters of the gully structure at different areas was analyzed. The gully fractal dimension showed a significant numerical difference in different areas, whereas the variation of the gully branch ratio was small. The change rule indicated that the development degree of the gully obviously varied in different regions, but the morphological structure was basically similar.

The effects of ultrasonic scaling duration and replication on caspase-3 expression of Sprague Dawley rat's pulp cells

Directory of Open Access Journals (Sweden)

Archadian Nuryanti

2015-03-01

Full Text Available Background: Ultrasonic scaling has been used commonly for stain and calculus removal in dental clinic for over 60years. Previous researches even had proved that ultrasonic scaling may give effects on the surface of tooth root. Ultrasonic wave exposure for 20 seconds or more can increase caspase-3 activity as an indicator of increased apoptotic cells associated with tissue damage. Purpose: This research was aimed to investigate the effects of ultrasonic scaling duration and replication on caspace-3 expression in dental pulp cells. Methods: The samples of this research were 54 male Sprague Dawley rats aged 2 months old divided into 2 groups, each of which consisted of 27 mice. The first group was induced with stain, while the second group was not. Each group was divided into 3 subgroups for ultrasonic scaling 1, 3, and 5 times. Each subgroup was divided into 3 sub-subgroups for duration procedure of 15, 30 and 60 seconds respectively. During scaling process, those rats were anesthetized using 0.1 ml of ketamine and 0.1 ml of xylol added to 2 ml of distilled water injected intramuscularly into their right thigh as much as 0.4 ml. Scaling was done on buccal surface of right first maxillary molar from cervical to occlusal. The teeth were decalcified and embedded in paraffin, then their sagittal plane was cut for thickness of 3µm and painted with immunohystochemistry for detecting caspace-3 expression of cell within dental pulp. Results: The results showed that the duration and replication of ultrasonic scaling procedures affected on the expression of caspace-3 cells as analyzed with Univariate Analisis of Variance test (p<0.05. Conclusion: It can be concluded that duration and replication of ultrasonic scaling procedure on teeth with and without stain enhauced the expression of  caspace-3 in dental pulp cells.

Scaling analysis for a Savannah River reactor scaled model integral system

International Nuclear Information System (INIS)

Boucher, T.J.; Larson, T.K.; McCreery, G.E.; Anderson, J.L.

1990-11-01

801The Savannah River Laboratory has requested that the Idaho National Engineering Laboratory perform an analysis to help define, examine, and assess potential concepts for the design of a scaled integral hydraulics test facility representative of the current Savannah River Plant reactor design. In this report the thermal-hydraulic phenomena of importance (based on the knowledge and experience of the authors and the results of the joint INEL/TPG/SRL phenomena identification and ranking effort) to reactor safety during the design basis loss-of-coolant accident were examined and identified. Established scaling methodologies were used to develop potential concepts for integral hydraulic testing facilities. Analysis is conducted to examine the scaling of various phenomena in each of the selected concepts. Results generally support that a one-fourth (1/4) linear scale visual facility capable of operating at pressures up to 350 kPa (51 psia) and temperatures up to 330 K (134 degree F) will scale most hydraulic phenomena reasonably well. However, additional research will be necessary to determine the most appropriate method of simulating several of the reactor components, since the scaling methodology allows for several approaches which may only be assessed via appropriate research. 34 refs., 20 figs., 14 tabs

Recognizing spontaneous facial expressions of emotion in a small-scale society of Papua New Guinea.

Science.gov (United States)

Crivelli, Carlos; Russell, James A; Jarillo, Sergio; Fernández-Dols, José-Miguel

2017-03-01

We report 2 studies on how residents of Papua New Guinea interpret facial expressions produced spontaneously by other residents of Papua New Guinea. Members of a small-scale indigenous society, Trobrianders (Milne Bay Province; N = 32, 14 to 17 years) were shown 5 facial expressions spontaneously produced by members of another small-scale indigenous society, Fore (Eastern Highlands Province) that Ekman had photographed, labeled, and published in The Face of Man (1980), each as an expression of a basic emotion: happiness, sadness, anger, surprise, and disgust. Trobrianders were asked to use any word they wanted to describe how each person shown felt and to provide valence and arousal ratings. Other Trobrianders (N = 24, 12 to 14 years) were shown the same photographs but asked to choose their response from a short list. In both studies, agreement with Ekman's predicted labels was low: 0% to 16% and 13% to 38% of observers, respectively. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

H2@Scale Resource and Market Analysis

Energy Technology Data Exchange (ETDEWEB)

Ruth, Mark

2017-05-04

The 'H2@Scale' concept is based on the potential for wide-scale utilization of hydrogen as an energy intermediate where the hydrogen is produced from low cost energy resources and it is used in both the transportation and industrial sectors. H2@Scale has the potential to address grid resiliency, energy security, and cross-sectoral emissions reductions. This presentation summarizes the status of an ongoing analysis effort to quantify the benefits of H2@Scale. It includes initial results regarding market potential, resource potential, and impacts of when electrolytic hydrogen is produced with renewable electricity to meet the potential market demands. It also proposes additional analysis efforts to better quantify each of the factors.

SIGNATURE: A workbench for gene expression signature analysis

Directory of Open Access Journals (Sweden)

Chang Jeffrey T

2011-11-01

Full Text Available Abstract Background The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise. Results We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access. Conclusions SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays

Directory of Open Access Journals (Sweden)

Lu Chao

2004-07-01

Full Text Available Abstract Background Normalization is an important step for microarray data analysis to minimize biological and technical variations. Choosing a suitable approach can be critical. The default method in GeneChip expression microarray uses a constant factor, the scaling factor (SF, for every gene on an array. The SF is obtained from a trimmed average signal of the array after excluding the 2% of the probe sets with the highest and the lowest values. Results Among the 76 U34A GeneChip experiments, the total signals on each array showed 25.8% variations in terms of the coefficient of variation, although all microarrays were hybridized with the same amount of biotin-labeled cRNA. The 2% of the probe sets with the highest signals that were normally excluded from SF calculation accounted for 34% to 54% of the total signals (40.7% ± 4.4%, mean ± sd. In comparison with normalization factors obtained from the median signal or from the mean of the log transformed signal, SF showed the greatest variation. The normalization factors obtained from log transformed signals showed least variation. Conclusions Eliminating 40% of the signal data during SF calculation failed to show any benefit. Normalization factors obtained with log transformed signals performed the best. Thus, it is suggested to use the mean of the logarithm transformed data for normalization, rather than the arithmetic mean of signals in GeneChip gene expression microarrays.

DAG expression: high-throughput gene expression analysis of real-time PCR data using standard curves for relative quantification.

Directory of Open Access Journals (Sweden)

María Ballester

Full Text Available BACKGROUND: Real-time quantitative PCR (qPCR is still the gold-standard technique for gene-expression quantification. Recent technological advances of this method allow for the high-throughput gene-expression analysis, without the limitations of sample space and reagent used. However, non-commercial and user-friendly software for the management and analysis of these data is not available. RESULTS: The recently developed commercial microarrays allow for the drawing of standard curves of multiple assays using the same n-fold diluted samples. Data Analysis Gene (DAG Expression software has been developed to perform high-throughput gene-expression data analysis using standard curves for relative quantification and one or multiple reference genes for sample normalization. We discuss the application of DAG Expression in the analysis of data from an experiment performed with Fluidigm technology, in which 48 genes and 115 samples were measured. Furthermore, the quality of our analysis was tested and compared with other available methods. CONCLUSIONS: DAG Expression is a freely available software that permits the automated analysis and visualization of high-throughput qPCR. A detailed manual and a demo-experiment are provided within the DAG Expression software at http://www.dagexpression.com/dage.zip.

Fatigue Analysis of Large-scale Wind turbine

Directory of Open Access Journals (Sweden)

Zhu Yongli

2017-01-01

Full Text Available The paper does research on top flange fatigue damage of large-scale wind turbine generator. It establishes finite element model of top flange connection system with finite element analysis software MSC. Marc/Mentat, analyzes its fatigue strain, implements load simulation of flange fatigue working condition with Bladed software, acquires flange fatigue load spectrum with rain-flow counting method, finally, it realizes fatigue analysis of top flange with fatigue analysis software MSC. Fatigue and Palmgren-Miner linear cumulative damage theory. The analysis result indicates that its result provides new thinking for flange fatigue analysis of large-scale wind turbine generator, and possesses some practical engineering value.

Dynamic association rules for gene expression data analysis.

Science.gov (United States)

Chen, Shu-Chuan; Tsai, Tsung-Hsien; Chung, Cheng-Han; Li, Wen-Hsiung

2015-10-14

The purpose of gene expression analysis is to look for the association between regulation of gene expression levels and phenotypic variations. This association based on gene expression profile has been used to determine whether the induction/repression of genes correspond to phenotypic variations including cell regulations, clinical diagnoses and drug development. Statistical analyses on microarray data have been developed to resolve gene selection issue. However, these methods do not inform us of causality between genes and phenotypes. In this paper, we propose the dynamic association rule algorithm (DAR algorithm) which helps ones to efficiently select a subset of significant genes for subsequent analysis. The DAR algorithm is based on association rules from market basket analysis in marketing. We first propose a statistical way, based on constructing a one-sided confidence interval and hypothesis testing, to determine if an association rule is meaningful. Based on the proposed statistical method, we then developed the DAR algorithm for gene expression data analysis. The method was applied to analyze four microarray datasets and one Next Generation Sequencing (NGS) dataset: the Mice Apo A1 dataset, the whole genome expression dataset of mouse embryonic stem cells, expression profiling of the bone marrow of Leukemia patients, Microarray Quality Control (MAQC) data set and the RNA-seq dataset of a mouse genomic imprinting study. A comparison of the proposed method with the t-test on the expression profiling of the bone marrow of Leukemia patients was conducted. We developed a statistical way, based on the concept of confidence interval, to determine the minimum support and minimum confidence for mining association relationships among items. With the minimum support and minimum confidence, one can find significant rules in one single step. The DAR algorithm was then developed for gene expression data analysis. Four gene expression datasets showed that the proposed

Large-Scale Analysis of Art Proportions

DEFF Research Database (Denmark)

Jensen, Karl Kristoffer

2014-01-01

While literature often tries to impute mathematical constants into art, this large-scale study (11 databases of paintings and photos, around 200.000 items) shows a different truth. The analysis, consisting of the width/height proportions, shows a value of rarely if ever one (square) and with majo......While literature often tries to impute mathematical constants into art, this large-scale study (11 databases of paintings and photos, around 200.000 items) shows a different truth. The analysis, consisting of the width/height proportions, shows a value of rarely if ever one (square...

Analysis of supply chain, scale factor, and optimum plant capacity for the production of ethanol from corn stover

International Nuclear Information System (INIS)

Leboreiro, Jose; Hilaly, Ahmad K.

2013-01-01

A detailed model is used to perform a thorough analysis on ethanol production from corn stover via the dilute acid process. The biomass supply chain cost model accounts for all steps needed to source corn stover including collection, transportation, and storage. The manufacturing cost model is based on work done at NREL; attainable conversions of key process parameters are used to calculate production cost. The choice of capital investment scaling function and scaling parameter has a significant impact on the optimum plant capacity. For the widely used exponential function, the scaling factors are functions of plant capacity. The pre-exponential factor decreases with increasing plant capacity while the exponential factor increases as the plant capacity increases. The use of scaling parameters calculated for small plant capacities leads to falsely large optimum plants; data from a wide range of plant capacities is required to produce accurate results. A mathematical expression to scale capital investment for fermentation-based biorefineries is proposed which accounts for the linear scaling behavior of bio-reactors (such as saccharification vessels and fermentors) as well as the exponential nature of all other plant equipment. Ignoring the linear scaling behavior of bio-reactors leads to artificially large optimum plant capacities. The minimum production cost is found to be in the range of 789–830 $ m −3 which is significantly higher than previously reported. Optimum plant capacities are in the range of 5750–9850 Mg d −1 . The optimum plant capacity and production cost are highly sensitive to farmer participation in biomass harvest for low participation rates. -- Highlights: •A detailed model is used to perform a technoeconomic analysis for the production of ethanol from corn stover. •The capital investment scaling factors were found to be a function of plant capacity. •Bio-reactors (such as saccharification vessels and fermentors) in large size

Multidimensional scaling technique for analysis of magnetic storms ...

Indian Academy of Sciences (India)

R.Narasimhan(krishtel emaging) 1461 1996 Oct 15 13:05:22

Multidimensional Scaling (MDS) comprises a set of models and associated methods for construct- ing a geometrical representation of proximity and dominance relationship between elements in one or more sets of entities. MDS can be applied to data that express two types of relationships: proxim- ity relations and ...

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

DEFF Research Database (Denmark)

Hansen, Kasper Lage; Hansen, Niclas Tue; Karlberg, Erik, Olof, Linnart

2008-01-01

to be overexpressed in the normal tissues where defects cause pathology. In contrast, cancer genes and complexes were not overexpressed in the tissues from which the tumors emanate. We specifically identified a complex involved in XY sex reversal that is testis-specific and down-regulated in ovaries. We also......Heritable diseases are caused by germ-line mutations that, despite tissuewide presence, often lead to tissue-specific pathology. Here, we make a systematic analysis of the link between tissue-specific gene expression and pathological manifestations in many human diseases and cancers. Diseases were...

Effective field theory analysis on μ problem in low-scale gauge mediation

International Nuclear Information System (INIS)

Zheng Sibo

2012-01-01

Supersymmetric models based on the scenario of gauge mediation often suffer from the well-known μ problem. In this paper, we reconsider this problem in low-scale gauge mediation in terms of effective field theory analysis. In this paradigm, all high energy input soft mass can be expressed via loop expansions. If the corrections coming from messenger thresholds are small, as we assume in this letter, then all RG evaluations can be taken as linearly approximation for low-scale supersymmetric breaking. Due to these observations, the parameter space can be systematically classified and studied after constraints coming from electro-weak symmetry breaking are imposed. We find that some old proposals in the literature are reproduced, and two new classes are uncovered. We refer to a microscopic model, where the specific relations among coefficients in one of the new classes are well motivated. Also, we discuss some primary phenomenologies.

Groundwater flow analysis on local scale. Setting boundary conditions for groundwater flow analysis on site scale model in step 1

International Nuclear Information System (INIS)

Ohyama, Takuya; Saegusa, Hiromitsu; Onoe, Hironori

2005-05-01

Japan Nuclear Cycle Development Institute has been conducting a wide range of geoscientific research in order to build a foundation for multidisciplinary studies of the deep geological environment as a basis of research and development for geological disposal of nuclear wastes. Ongoing geoscientific research programs include the Regional Hydrogeological Study (RHS) project and Mizunami Underground Research Laboratory (MIU) project in the Tono region, Gifu Prefecture. The main goal of these projects is to establish comprehensive techniques for investigation, analysis, and assessment of the deep geological environment at several spatial scales. The RHS project is a local scale study for understanding the groundwater flow system from the recharge area to the discharge area. The surface-based Investigation Phase of the MIU project is a site scale study for understanding the groundwater flow system immediately surrounding the MIU construction site. The MIU project is being conducted using a multiphase, iterative approach. In this study, the hydrogeological modeling and groundwater flow analysis of the local scale were carried out in order to set boundary conditions of the site scale model based on the data obtained from surface-based investigations in Step 1 in site scale of the MIU project. As a result of the study, head distribution to set boundary conditions for groundwater flow analysis on the site scale model could be obtained. (author)

Accuracy analysis of the CTBTO nuclear test detection scale and Improvement

Energy Technology Data Exchange (ETDEWEB)

Ryu, Young Kwang [Seoul National Univ., Seoul (Korea, Republic of)

2014-10-15

CTBTO (Comprehensive nuclear Test Ban Treaty Organization) is charge of nuclear test monitoring for nuclear non-proliferation. CTBTO has 170 seismic stations in operation in 76 countries in order to detect the artificial earthquake that was caused by an underground nuclear test. Korea use formula that is based on the equations that are used by the IMS (International Monitoring System) of CTBTO for analysis of explosive scale, and reflect the nature of the terrain, such as rock. But the expression for calculating the exact scale explosive is still un-established state. And generally CTBTO doesn't care about artificial explosive that is being received low-yield in accordance with the criteria of nuclear detection. But, at the time that North Korea conduct a nuclear test, it should not be overlooked that the scale of the earthquake detection criteria below. Because DPRK is trying to conceal their nuclear development capability, there are possibility of low-yield nuclear test or possibility of install a buffer to hide actual explosive scale. These radionuclide observations were consistent with a DPRK low-yield nuclear test on May 2010, even though no seismic signals from such a test have been detected. But there were a few times of low-yield (magnitude 1.39-1.93) occurred around DPRK nuclear test site at that time.

A comparative study of three different gene expression analysis methods.

Science.gov (United States)

Choe, Jae Young; Han, Hyung Soo; Lee, Seon Duk; Lee, Hanna; Lee, Dong Eun; Ahn, Jae Yun; Ryoo, Hyun Wook; Seo, Kang Suk; Kim, Jong Kun

2017-12-04

TNF-α regulates immune cells and acts as an endogenous pyrogen. Reverse transcription polymerase chain reaction (RT-PCR) is one of the most commonly used methods for gene expression analysis. Among the alternatives to PCR, loop-mediated isothermal amplification (LAMP) shows good potential in terms of specificity and sensitivity. However, few studies have compared RT-PCR and LAMP for human gene expression analysis. Therefore, in the present study, we compared one-step RT-PCR, two-step RT-LAMP and one-step RT-LAMP for human gene expression analysis. We compared three gene expression analysis methods using the human TNF-α gene as a biomarker from peripheral blood cells. Total RNA from the three selected febrile patients were subjected to the three different methods of gene expression analysis. In the comparison of three gene expression analysis methods, the detection limit of both one-step RT-PCR and one-step RT-LAMP were the same, while that of two-step RT-LAMP was inferior. One-step RT-LAMP takes less time, and the experimental result is easy to determine. One-step RT-LAMP is a potentially useful and complementary tool that is fast and reasonably sensitive. In addition, one-step RT-LAMP could be useful in environments lacking specialized equipment or expertise.

From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data.

Science.gov (United States)

Vella, Danila; Zoppis, Italo; Mauri, Giancarlo; Mauri, Pierluigi; Di Silvestre, Dario

2017-12-01

The reductionist approach of dissecting biological systems into their constituents has been successful in the first stage of the molecular biology to elucidate the chemical basis of several biological processes. This knowledge helped biologists to understand the complexity of the biological systems evidencing that most biological functions do not arise from individual molecules; thus, realizing that the emergent properties of the biological systems cannot be explained or be predicted by investigating individual molecules without taking into consideration their relations. Thanks to the improvement of the current -omics technologies and the increasing understanding of the molecular relationships, even more studies are evaluating the biological systems through approaches based on graph theory. Genomic and proteomic data are often combined with protein-protein interaction (PPI) networks whose structure is routinely analyzed by algorithms and tools to characterize hubs/bottlenecks and topological, functional, and disease modules. On the other hand, co-expression networks represent a complementary procedure that give the opportunity to evaluate at system level including organisms that lack information on PPIs. Based on these premises, we introduce the reader to the PPI and to the co-expression networks, including aspects of reconstruction and analysis. In particular, the new idea to evaluate large-scale proteomic data by means of co-expression networks will be discussed presenting some examples of application. Their use to infer biological knowledge will be shown, and a special attention will be devoted to the topological and module analysis.

The Arabidopsis co-expression tool (act): a WWW-based tool and database for microarray-based gene expression analysis

DEFF Research Database (Denmark)

Jen, C. H.; Manfield, I. W.; Michalopoulos, D. W.

2006-01-01

be examined using the novel clique finder tool to determine the sets of genes most likely to be regulated in a similar manner. In combination, these tools offer three levels of analysis: creation of correlation lists of co-expressed genes, refinement of these lists using two-dimensional scatter plots......We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (act) , based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The co-expression analysis tool allows users to identify genes whose expression...

Inferring gene expression dynamics via functional regression analysis

Directory of Open Access Journals (Sweden)

Leng Xiaoyan

2008-01-01

Full Text Available Abstract Background Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene expression associated with different developmental stages to each other to study patterns of long-term developmental gene regulation. We use tools from functional data analysis to study dynamic changes by relating temporal gene expression profiles of different developmental stages to each other. Results We demonstrate that functional regression methodology can pinpoint relationships that exist between temporary gene expression profiles for different life cycle phases and incorporates dimension reduction as needed for these high-dimensional data. By applying these tools, gene expression profiles for pupa and adult phases are found to be strongly related to the profiles of the same genes obtained during the embryo phase. Moreover, one can distinguish between gene groups that exhibit relationships with positive and others with negative associations between later life and embryonal expression profiles. Specifically, we find a positive relationship in expression for muscle development related genes, and a negative relationship for strictly maternal genes for Drosophila, using temporal gene expression profiles. Conclusion Our findings point to specific reactivation patterns of gene expression during the Drosophila life cycle which differ in characteristic ways between various gene groups. Functional regression emerges as a useful tool for relating gene expression patterns from different developmental stages, and avoids the problems with large numbers of parameters and multiple testing that affect alternative approaches.

Gene expression profiling of resting and activated vascular smooth muscle cells by serial analysis of gene expression and clustering analysis

NARCIS (Netherlands)

Beauchamp, Nicholas J.; van Achterberg, Tanja A. E.; Engelse, Marten A.; Pannekoek, Hans; de Vries, Carlie J. M.

2003-01-01

Migration and proliferation of vascular smooth muscle cells (SMCs) are key events in atherosclerosis. However, little is known about alterations in gene expression upon transition of the quiescent, contractile SMC to the proliferative SMC. We performed serial analysis of gene expression (SAGE) of

Does expressive timing in music performance scale proportionally with tempo?

NARCIS (Netherlands)

Desain, P.; Honing, H.

1994-01-01

Evidence is presented that expressive timing in music is not relationally invariant with global tempo. Our results stem from an analysis of repeated performances of Beethoven's variations on a Paisiello theme. Recordings were made of two pianists playing the pieces at three tempi. In contrast with

Gene Expression Browser: Large-Scale and Cross-Experiment Microarray Data Management, Search & Visualization

Science.gov (United States)

The amount of microarray gene expression data in public repositories has been increasing exponentially for the last couple of decades. High-throughput microarray data integration and analysis has become a critical step in exploring the large amount of expression data for biological discovery. Howeve...

Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients

Directory of Open Access Journals (Sweden)

DeYoung Joseph

2009-08-01

Full Text Available Abstract Background Amyotrophic Lateral Sclerosis (ALS is a lethal disorder characterized by progressive degeneration of motor neurons in the brain and spinal cord. Diagnosis is mainly based on clinical symptoms, and there is currently no therapy to stop the disease or slow its progression. Since access to spinal cord tissue is not possible at disease onset, we investigated changes in gene expression profiles in whole blood of ALS patients. Results Our transcriptional study showed dramatic changes in blood of ALS patients; 2,300 probes (9.4% showed significant differential expression in a discovery dataset consisting of 30 ALS patients and 30 healthy controls. Weighted gene co-expression network analysis (WGCNA was used to find disease-related networks (modules and disease related hub genes. Two large co-expression modules were found to be associated with ALS. Our findings were replicated in a second (30 patients and 30 controls and third dataset (63 patients and 63 controls, thereby demonstrating a highly significant and consistent association of two large co-expression modules with ALS disease status. Ingenuity Pathway Analysis of the ALS related module genes implicates enrichment of functional categories related to genetic disorders, neurodegeneration of the nervous system and inflammatory disease. The ALS related modules contain a number of candidate genes possibly involved in pathogenesis of ALS. Conclusion This first large-scale blood gene expression study in ALS observed distinct patterns between cases and controls which may provide opportunities for biomarker development as well as new insights into the molecular mechanisms of the disease.

Scaling analysis of meteorite shower mass distributions

DEFF Research Database (Denmark)

Oddershede, Lene; Meibom, A.; Bohr, Jakob

1998-01-01

Meteorite showers are the remains of extraterrestrial objects which are captivated by the gravitational field of the Earth. We have analyzed the mass distribution of fragments from 16 meteorite showers for scaling. The distributions exhibit distinct scaling behavior over several orders of magnetude......; the observed scaling exponents vary from shower to shower. Half of the analyzed showers show a single scaling region while the orther half show multiple scaling regimes. Such an analysis can provide knowledge about the fragmentation process and about the original meteoroid. We also suggest to compare...... the observed scaling exponents to exponents observed in laboratory experiments and discuss the possibility that one can derive insight into the original shapes of the meteoroids....

Large scale expression changes of genes related to neuronal signaling and developmental processes found in lateral septum of postpartum outbred mice.

Directory of Open Access Journals (Sweden)

Brian E Eisinger

Full Text Available Coordinated gene expression changes across the CNS are required to produce the mammalian maternal phenotype. Lateral septum (LS is a brain region critically involved with aspects of maternal care, and we recently examined gene expression of whole septum (LS and medial septum in selectively bred maternal mice. Here, we expand on the prior study by 1 conducting microarray analysis solely on LS in virgin and postpartum mice, 2 using outbred mice, and 3 evaluating the role of sensory input on gene expression changes. Large scale changes in genes related to neuronal signaling were identified, including four GABAA receptor subunits. Subunits α4 and δ were downregulated in maternal LS, likely reflecting a reduction in the extrasynaptic, neurosteroid-sensitive α4/δ containing receptor subtype. Conversely, subunits ε and θ were increased in maternal LS. Fifteen K+ channel related genes showed altered expression, as did dopamine receptors Drd1a and Drd2 (both downregulated, hypocretin receptor 1 (Hcrtr1, kappa opioid receptor 1 (Oprk1, and transient receptor potential channel 4 (Trpc4. Expression of a large number of genes linked to developmental processes or cell differentiation were also altered in postpartum LS, including chemokine (C-X-C motif ligand 12 (Cxcl12, fatty acid binding protein 7 (Fabp7, plasma membrane proteolipid (Pllp, and suppressor of cytokine signaling 2 (Socs2. Additional genes that are linked to anxiety, such as glutathione reductase (Gsr, exhibited altered expression. Pathway analysis also identified changes in genes related to cyclic nucleotide metabolism, chromatin structure, and the Ras gene family. The sensory presence of pups was found to contribute to the altered expression of a subset of genes across all categories. This study suggests that both large changes in neuronal signaling and the possible terminal differentiation of neuronal and/or glial cells play important roles in producing the maternal state.

Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis

Directory of Open Access Journals (Sweden)

Arias Covadonga

2007-06-01

Full Text Available Abstract Background The ciliate protozoan Ichthyophthirius multifiliis (Ich is an important parasite of freshwater fish that causes 'white spot disease' leading to significant losses. A genomic resource for large-scale studies of this parasite has been lacking. To study gene expression involved in Ich pathogenesis and virulence, our goal was to generate expressed sequence tags (ESTs for the development of a powerful microarray platform for the analysis of global gene expression in this species. Here, we initiated a project to sequence and analyze over 10,000 ESTs. Results We sequenced 10,368 EST clones using a normalized cDNA library made from pooled samples of the trophont, tomont, and theront life-cycle stages, and generated 9,769 sequences (94.2% success rate. Post-sequencing processing led to 8,432 high quality sequences. Clustering analysis of these ESTs allowed identification of 4,706 unique sequences containing 976 contigs and 3,730 singletons. These unique sequences represent over two million base pairs (~10% of Plasmodium falciparum genome, a phylogenetically related protozoan. BLASTX searches produced 2,518 significant (E-value -5 hits and further Gene Ontology (GO analysis annotated 1,008 of these genes. The ESTs were analyzed comparatively against the genomes of the related protozoa Tetrahymena thermophila and P. falciparum, allowing putative identification of additional genes. All the EST sequences were deposited by dbEST in GenBank (GenBank: EG957858–EG966289. Gene discovery and annotations are presented and discussed. Conclusion This set of ESTs represents a significant proportion of the Ich transcriptome, and provides a material basis for the development of microarrays useful for gene expression studies concerning Ich development, pathogenesis, and virulence.

Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family.

Science.gov (United States)

Guo, Chunlei; Guo, Rongrong; Xu, Xiaozhao; Gao, Min; Li, Xiaoqin; Song, Junyang; Zheng, Yi; Wang, Xiping

2014-04-01

WRKY proteins comprise a large family of transcription factors that play important roles in plant defence regulatory networks, including responses to various biotic and abiotic stresses. To date, no large-scale study of WRKY genes has been undertaken in grape (Vitis vinifera L.). In this study, a total of 59 putative grape WRKY genes (VvWRKY) were identified and renamed on the basis of their respective chromosome distribution. A multiple sequence alignment analysis using all predicted grape WRKY genes coding sequences, together with those from Arabidopsis thaliana and tomato (Solanum lycopersicum), indicated that the 59 VvWRKY genes can be classified into three main groups (I-III). An evaluation of the duplication events suggested that several WRKY genes arose before the divergence of the grape and Arabidopsis lineages. Moreover, expression profiles derived from semiquantitative PCR and real-time quantitative PCR analyses showed distinct expression patterns in various tissues and in response to different treatments. Four VvWRKY genes showed a significantly higher expression in roots or leaves, 55 responded to varying degrees to at least one abiotic stress treatment, and the expression of 38 were altered following powdery mildew (Erysiphe necator) infection. Most VvWRKY genes were downregulated in response to abscisic acid or salicylic acid treatments, while the expression of a subset was upregulated by methyl jasmonate or ethylene treatments.

Genome-scale analysis of positional clustering of mouse testis-specific genes

Directory of Open Access Journals (Sweden)

Lee Bernett TK

2005-01-01

Full Text Available Abstract Background Genes are not randomly distributed on a chromosome as they were thought even after removal of tandem repeats. The positional clustering of co-expressed genes is known in prokaryotes and recently reported in several eukaryotic organisms such as Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens. In order to further investigate the mode of tissue-specific gene clustering in higher eukaryotes, we have performed a genome-scale analysis of positional clustering of the mouse testis-specific genes. Results Our computational analysis shows that a large proportion of testis-specific genes are clustered in groups of 2 to 5 genes in the mouse genome. The number of clusters is much higher than expected by chance even after removal of tandem repeats. Conclusion Our result suggests that testis-specific genes tend to cluster on the mouse chromosomes. This provides another piece of evidence for the hypothesis that clusters of tissue-specific genes do exist.

Comparison of reverse transcription-quantitative polymerase chain reaction methods and platforms for single cell gene expression analysis.

Science.gov (United States)

Fox, Bridget C; Devonshire, Alison S; Baradez, Marc-Olivier; Marshall, Damian; Foy, Carole A

2012-08-15

Single cell gene expression analysis can provide insights into development and disease progression by profiling individual cellular responses as opposed to reporting the global average of a population. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the "gold standard" for the quantification of gene expression levels; however, the technical performance of kits and platforms aimed at single cell analysis has not been fully defined in terms of sensitivity and assay comparability. We compared three kits using purification columns (PicoPure) or direct lysis (CellsDirect and Cells-to-CT) combined with a one- or two-step RT-qPCR approach using dilutions of cells and RNA standards to the single cell level. Single cell-level messenger RNA (mRNA) analysis was possible using all three methods, although the precision, linearity, and effect of lysis buffer and cell background differed depending on the approach used. The impact of using a microfluidic qPCR platform versus a standard instrument was investigated for potential variability introduced by preamplification of template or scaling down of the qPCR to nanoliter volumes using laser-dissected single cell samples. The two approaches were found to be comparable. These studies show that accurate gene expression analysis is achievable at the single cell level and highlight the importance of well-validated experimental procedures for low-level mRNA analysis. Copyright © 2012 Elsevier Inc. All rights reserved.

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.

Directory of Open Access Journals (Sweden)

Bordeaux John M

2011-05-01

Full Text Available Abstract Background Global transcriptional analysis of loblolly pine (Pinus taeda L. is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine. Results Microarrays were used to interrogate root cDNA populations obtained from 12 genotype × treatment combinations (four genotypes, three watering regimes. Comparison of drought-stressed roots with roots from the control treatment identified 2445 genes displaying at least a 1.5-fold expression difference (false discovery rate = 0.01. Genes commonly associated with drought response in pine and other plant species, as well as a number of abiotic and biotic stress-related genes, were up-regulated in drought-stressed roots. Only 76 genes were identified as differentially expressed in drought-recovered roots, indicating that the transcript population can return to the pre-drought state within 48 hours. Gene correlation analysis predicts a scale-free network topology and identifies eleven co-expression modules that ranged in size from 34 to 938 members. Network topological parameters identified a number of central nodes (hubs including those with significant homology (E-values ≤ 2 × 10-30 to 9-cis-epoxycarotenoid dioxygenase, zeatin O-glucosyltransferase, and ABA-responsive protein. Identified hubs also include genes that have been associated previously with osmotic stress, phytohormones, enzymes that detoxify reactive oxygen species, and several genes of unknown function. Conclusion PtGen2 was used to evaluate transcriptome responses in loblolly pine and was leveraged to identify 2445 differentially expressed genes responding to severe drought stress in

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

Science.gov (United States)

2011-01-01

Background Global transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine. Results Microarrays were used to interrogate root cDNA populations obtained from 12 genotype × treatment combinations (four genotypes, three watering regimes). Comparison of drought-stressed roots with roots from the control treatment identified 2445 genes displaying at least a 1.5-fold expression difference (false discovery rate = 0.01). Genes commonly associated with drought response in pine and other plant species, as well as a number of abiotic and biotic stress-related genes, were up-regulated in drought-stressed roots. Only 76 genes were identified as differentially expressed in drought-recovered roots, indicating that the transcript population can return to the pre-drought state within 48 hours. Gene correlation analysis predicts a scale-free network topology and identifies eleven co-expression modules that ranged in size from 34 to 938 members. Network topological parameters identified a number of central nodes (hubs) including those with significant homology (E-values ≤ 2 × 10-30) to 9-cis-epoxycarotenoid dioxygenase, zeatin O-glucosyltransferase, and ABA-responsive protein. Identified hubs also include genes that have been associated previously with osmotic stress, phytohormones, enzymes that detoxify reactive oxygen species, and several genes of unknown function. Conclusion PtGen2 was used to evaluate transcriptome responses in loblolly pine and was leveraged to identify 2445 differentially expressed genes responding to severe drought stress in roots. Many of the

Multi scale analysis of ITER pre-compression rings

Energy Technology Data Exchange (ETDEWEB)

Park, Ben, E-mail: ben.park@sener.es [SENER Ingeniería y Sistemas S.A., Barcelona (Spain); Foussat, Arnaud [ITER Organization, St. Paul-Lez-Durance (France); Rajainmaki, Hannu [Fusion for Energy, Barcelona (Spain); Knaster, Juan [IFMIF, Aomori (Japan)

2013-10-15

Highlights: • A multi-scale analysis approach employing various scales of ABAQUS FEM models have been used to calculate the response and performance of the rings. • We have studied the effects of various defects on the performance of the rings under the operating temperatures and loading that will be applied to the PCRs. • The multi scale analysis results are presented here. -- Abstract: The Pre-compression Rings of ITER (PCRs) represent one of the largest and most highly stressed composite structures ever designed for long term operation at 4 K. Six rings, each 5 m in diameter and 337 mm × 288 mm in cross-section, will be manufactured from S2 fiber-glass/epoxy composite and installed three at the top and three at the bottom of the eighteen D shaped toroidal field (TF) coils to apply a total centripetal pre-load of 70 MN per TF coil. The composite rings will be fabricated with a high content (65% by volume) of S2 fiber-glass in an epoxy resin matrix. During the manufacture emphasis will be placed on obtaining a structure with a very low void content and minimal presence of critical defects, such as delaminations. This paper presents a unified framework for the multi-scale analysis of the composite structure of the PCRs. A multi-scale analysis approach employing various scales of ABAQUS FEM models and other analysis tools have been used to calculate the response and performance of the rings over the design life of the structure. We have studied the effects of various defects on the performance of the rings under the operating temperatures and loading that will be applied to the PCRs. The results are presented here.

Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L.

Science.gov (United States)

Wang, Haibo; Zou, Zhurong; Wang, Shasha; Gong, Ming

2013-01-01

Jatropha curcas L., also called the Physic nut, is an oil-rich shrub with multiple uses, including biodiesel production, and is currently exploited as a renewable energy resource in many countries. Nevertheless, because of its origin from the tropical MidAmerican zone, J. curcas confers an inherent but undesirable characteristic (low cold resistance) that may seriously restrict its large-scale popularization. This adaptive flaw can be genetically improved by elucidating the mechanisms underlying plant tolerance to cold temperatures. The newly developed Illumina Hiseq™ 2000 RNA-seq and Digital Gene Expression (DGE) are deep high-throughput approaches for gene expression analysis at the transcriptome level, using which we carefully investigated the gene expression profiles in response to cold stress to gain insight into the molecular mechanisms of cold response in J. curcas. In total, 45,251 unigenes were obtained by assembly of clean data generated by RNA-seq analysis of the J. curcas transcriptome. A total of 33,363 and 912 complete or partial coding sequences (CDSs) were determined by protein database alignments and ESTScan prediction, respectively. Among these unigenes, more than 41.52% were involved in approximately 128 known metabolic or signaling pathways, and 4,185 were possibly associated with cold resistance. DGE analysis was used to assess the changes in gene expression when exposed to cold condition (12°C) for 12, 24, and 48 h. The results showed that 3,178 genes were significantly upregulated and 1,244 were downregulated under cold stress. These genes were then functionally annotated based on the transcriptome data from RNA-seq analysis. This study provides a global view of transcriptome response and gene expression profiling of J. curcas in response to cold stress. The results can help improve our current understanding of the mechanisms underlying plant cold resistance and favor the screening of crucial genes for genetically enhancing cold resistance

Analysis of Market Opportunities for Chinese Private Express Delivery Industry

Science.gov (United States)

Jiang, Changbing; Bai, Lijun; Tong, Xiaoqing

China's express delivery market has become the arena in which each express enterprise struggles to chase due to the huge potential demand and high profitable prospects. So certain qualitative and quantitative forecast for the future changes of China's express delivery market will help enterprises understand various types of market conditions and social changes in demand and adjust business activities to enhance their competitiveness timely. The development of China's express delivery industry is first introduced in this chapter. Then the theoretical basis of the regression model is overviewed. We also predict the demand trends of China's express delivery market by using Pearson correlation analysis and regression analysis from qualitative and quantitative aspects, respectively. Finally, we draw some conclusions and recommendations for China's express delivery industry.

Corroded scale analysis from water distribution pipes

Directory of Open Access Journals (Sweden)

Rajaković-Ognjanović Vladana N.

2011-01-01

Full Text Available The subject of this study was the steel pipes that are part of Belgrade's drinking water supply network. In order to investigate the mutual effects of corrosion and water quality, the corrosion scales on the pipes were analyzed. The idea was to improve control of corrosion processes and prevent impact of corrosion on water quality degradation. The instrumental methods for corrosion scales characterization used were: scanning electron microscopy (SEM, for the investigation of corrosion scales of the analyzed samples surfaces, X-ray diffraction (XRD, for the analysis of the presence of solid forms inside scales, scanning electron microscopy (SEM, for the microstructural analysis of the corroded scales, and BET adsorption isotherm for the surface area determination. Depending on the composition of water next to the pipe surface, corrosion of iron results in the formation of different compounds and solid phases. The composition and structure of the iron scales in the drinking water distribution pipes depends on the type of the metal and the composition of the aqueous phase. Their formation is probably governed by several factors that include water quality parameters such as pH, alkalinity, buffer intensity, natural organic matter (NOM concentration, and dissolved oxygen (DO concentration. Factors such as water flow patterns, seasonal fluctuations in temperature, and microbiological activity as well as water treatment practices such as application of corrosion inhibitors can also influence corrosion scale formation and growth. Therefore, the corrosion scales found in iron and steel pipes are expected to have unique features for each site. Compounds that are found in iron corrosion scales often include goethite, lepidocrocite, magnetite, hematite, ferrous oxide, siderite, ferrous hydroxide, ferric hydroxide, ferrihydrite, calcium carbonate and green rusts. Iron scales have characteristic features that include: corroded floor, porous core that contains

A Confirmatory Factor Analysis of Reilly's Role Overload Scale

Science.gov (United States)

Thiagarajan, Palaniappan; Chakrabarty, Subhra; Taylor, Ronald D.

2006-01-01

In 1982, Reilly developed a 13-item scale to measure role overload. This scale has been widely used, but most studies did not assess the unidimensionality of the scale. Given the significance of unidimensionality in scale development, the current study reports a confirmatory factor analysis of the 13-item scale in two samples. Based on the…

Multi-scale Analysis of High Resolution Topography: Feature Extraction and Identification of Landscape Characteristic Scales

Science.gov (United States)

Passalacqua, P.; Sangireddy, H.; Stark, C. P.

2015-12-01

With the advent of digital terrain data, detailed information on terrain characteristics and on scale and location of geomorphic features is available over extended areas. Our ability to observe landscapes and quantify topographic patterns has greatly improved, including the estimation of fluxes of mass and energy across landscapes. Challenges still remain in the analysis of high resolution topography data; the presence of features such as roads, for example, challenges classic methods for feature extraction and large data volumes require computationally efficient extraction and analysis methods. Moreover, opportunities exist to define new robust metrics of landscape characterization for landscape comparison and model validation. In this presentation we cover recent research in multi-scale and objective analysis of high resolution topography data. We show how the analysis of the probability density function of topographic attributes such as slope, curvature, and topographic index contains useful information for feature localization and extraction. The analysis of how the distributions change across scales, quantified by the behavior of modal values and interquartile range, allows the identification of landscape characteristic scales, such as terrain roughness. The methods are introduced on synthetic signals in one and two dimensions and then applied to a variety of landscapes of different characteristics. Validation of the methods includes the analysis of modeled landscapes where the noise distribution is known and features of interest easily measured.

New enhancements to SCALE for criticality safety analysis

International Nuclear Information System (INIS)

Hollenbach, D.F.; Bowman, S.M.; Petrie, L.M.; Parks, C.V.

1995-01-01

As the speed, available memory, and reliability of computer hardware increases and the cost decreases, the complexity and usability of computer software will increase, taking advantage of the new hardware capabilities. Computer programs today must be more flexible and user friendly than those of the past. Within available resources, the SCALE staff at Oak Ridge National Laboratory (ORNL) is committed to upgrading its computer codes to keep pace with the current level of technology. This paper examines recent additions and enhancements to the criticality safety analysis sections of the SCALE code package. These recent additions and enhancements made to SCALE can be divided into nine categories: (1) new analytical computer codes, (2) new cross-section libraries, (3) new criticality search sequences, (4) enhanced graphical capabilities, (5) additional KENO enhancements, (6) enhanced resonance processing capabilities, (7) enhanced material information processing capabilities, (8) portability of the SCALE code package, and (9) other minor enhancements, modifications, and corrections to SCALE. Each of these additions and enhancements to the criticality safety analysis capabilities of the SCALE code system are discussed below

Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis.

Science.gov (United States)

Asamizu, Erika; Nakamura, Yasukazu; Sato, Shusei; Tabata, Satoshi

2004-02-01

To perform a comprehensive analysis of genes expressed in a model legume, Lotus japonicus, a total of 74472 3'-end expressed sequence tags (EST) were generated from cDNA libraries produced from six different organs. Clustering of sequences was performed with an identity criterion of 95% for 50 bases, and a total of 20457 non-redundant sequences, 8503 contigs and 11954 singletons were generated. EST sequence coverage was analyzed by using the annotated L. japonicus genomic sequence and 1093 of the 1889 predicted protein-encoding genes (57.9%) were hit by the EST sequence(s). Gene content was compared to several plant species. Among the 8503 contigs, 471 were identified as sequences conserved only in leguminous species and these included several disease resistance-related genes. This suggested that in legumes, these genes may have evolved specifically to resist pathogen attack. The rate of gene sequence divergence was assessed by comparing similarity level and functional category based on the Gene Ontology (GO) annotation of Arabidopsis genes. This revealed that genes encoding ribosomal proteins, as well as those related to translation, photosynthesis, and cellular structure were more abundantly represented in the highly conserved class, and that genes encoding transcription factors and receptor protein kinases were abundantly represented in the less conserved class. To make the sequence information and the cDNA clones available to the research community, a Web database with useful services was created at http://www.kazusa.or.jp/en/plant/lotus/EST/.

A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer's disease progression.

Science.gov (United States)

Ray, Sumanta; Hossain, Sk Md Mosaddek; Khatun, Lutfunnesa; Mukhopadhyay, Anirban

2017-12-20

Alzheimer's disease (AD) is a chronic neuro-degenerative disruption of the brain which involves in large scale transcriptomic variation. The disease does not impact every regions of the brain at the same time, instead it progresses slowly involving somewhat sequential interaction with different regions. Analysis of the expression patterns of the genes in different regions of the brain influenced in AD surely contribute for a enhanced comprehension of AD pathogenesis and shed light on the early characterization of the disease. Here, we have proposed a framework to identify perturbation and preservation characteristics of gene expression patterns across six distinct regions of the brain ("EC", "HIP", "PC", "MTG", "SFG", and "VCX") affected in AD. Co-expression modules were discovered considering a couple of regions at once. These are then analyzed to know the preservation and perturbation characteristics. Different module preservation statistics and a rank aggregation mechanism have been adopted to detect the changes of expression patterns across brain regions. Gene ontology (GO) and pathway based analysis were also carried out to know the biological meaning of preserved and perturbed modules. In this article, we have extensively studied the preservation patterns of co-expressed modules in six distinct brain regions affected in AD. Some modules are emerged as the most preserved while some others are detected as perturbed between a pair of brain regions. Further investigation on the topological properties of preserved and non-preserved modules reveals a substantial association amongst "betweenness centrality" and "degree" of the involved genes. Our findings may render a deeper realization of the preservation characteristics of gene expression patterns in discrete brain regions affected by AD.

Iterated Process Analysis over Lattice-Valued Regular Expressions

DEFF Research Database (Denmark)

Midtgaard, Jan; Nielson, Flemming; Nielson, Hanne Riis

2016-01-01

We present an iterated approach to statically analyze programs of two processes communicating by message passing. Our analysis operates over a domain of lattice-valued regular expressions, and computes increasingly better approximations of each process's communication behavior. Overall the work e...... extends traditional semantics-based program analysis techniques to automatically reason about message passing in a manner that can simultaneously analyze both values of variables as well as message order, message content, and their interdependencies.......We present an iterated approach to statically analyze programs of two processes communicating by message passing. Our analysis operates over a domain of lattice-valued regular expressions, and computes increasingly better approximations of each process's communication behavior. Overall the work...

Scaling analysis for the OSU AP600 test facility (APEX)

International Nuclear Information System (INIS)

Reyes, J.N.

1998-01-01

In this paper, the authors summarize the key aspects of a state-of-the-art scaling analysis (Reyes et al. (1995)) performed to establish the facility design and test conditions for the advanced plant experiment (APEX) at Oregon State University (OSU). This scaling analysis represents the first, and most comprehensive, application of the hierarchical two-tiered scaling (H2TS) methodology (Zuber (1991)) in the design of an integral system test facility. The APEX test facility, designed and constructed on the basis of this scaling analysis, is the most accurate geometric representation of a Westinghouse AP600 nuclear steam supply system. The OSU APEX test facility has served to develop an essential component of the integral system database used to assess the AP600 thermal hydraulic safety analysis computer codes. (orig.)

Multiplexed expression and screening for recombinant protein production in mammalian cells

Directory of Open Access Journals (Sweden)

McCafferty John

2006-12-01

Full Text Available Abstract Background A variety of approaches to understanding protein structure and function require production of recombinant protein. Mammalian based expression systems have advantages over bacterial systems for certain classes of protein but can be slower and more laborious. Thus the availability of a simple system for production and rapid screening of constructs or conditions for mammalian expression would be of great benefit. To this end we have coupled an efficient recombinant protein production system based on transient transfection in HEK-293 EBNA1 (HEK-293E suspension cells with a dot blot method allowing pre-screening of proteins expressed in cells in a high throughput manner. Results A nested PCR approach was used to clone 21 extracellular domains of mouse receptors as CD4 fusions within a mammalian GATEWAY expression vector system. Following transient transfection, HEK-293E cells grown in 2 ml cultures in 24-deep well blocks showed similar growth kinetics, viability and recombinant protein expression profiles, to those grown in 50 ml shake flask cultures as judged by western blotting. Following optimisation, fluorescent dot blot analysis of transfection supernatants was shown to be a rapid method for analysing protein expression yielding similar results as western blot analysis. Addition of urea enhanced the binding of glycoproteins to a nitrocellulose membrane. A good correlation was observed between the results of a plate based small scale transient transfection dot blot pre-screen and successful purification of proteins expressed at the 50 ml scale. Conclusion The combination of small scale multi-well plate culture and dot blotting described here will allow the multiplex analysis of different mammalian expression experiments enabling a faster identification of high yield expression constructs or conditions prior to large scale protein production. The methods for parallel GATEWAY cloning and expression of multiple constructs in cell

Large-scale gene function analysis with the PANTHER classification system.

Science.gov (United States)

Mi, Huaiyu; Muruganujan, Anushya; Casagrande, John T; Thomas, Paul D

2013-08-01

The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.

The identification of functional motifs in temporal gene expression analysis

Directory of Open Access Journals (Sweden)

Michael G. Surette

2005-01-01

Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

Large scale gene expression profiles of regenerating inner ear sensory epithelia.

Directory of Open Access Journals (Sweden)

R David Hawkins

2007-06-01

Full Text Available Loss of inner ear sensory hair cells (HC is a leading cause of human hearing loss and balance disorders. Unlike mammals, many lower vertebrates can regenerate these cells. We used cross-species microarrays to examine this process in the avian inner ear. Specifically, changes in expression of over 1700 transcription factor (TF genes were investigated in hair cells of auditory and vestibular organs following treatment with two different damaging agents and regeneration in vitro. Multiple components of seven distinct known signaling pathways were clearly identifiable: TGFbeta, PAX, NOTCH, WNT, NFKappaB, INSULIN/IGF1 and AP1. Numerous components of apoptotic and cell cycle control pathways were differentially expressed, including p27(KIP and TFs that regulate its expression. A comparison of expression trends across tissues and treatments revealed identical patterns of expression that occurred at identical times during regenerative proliferation. Network analysis of the patterns of gene expression in this large dataset also revealed the additional presence of many components (and possible network interactions of estrogen receptor signaling, circadian rhythm genes and parts of the polycomb complex (among others. Equal numbers of differentially expressed genes were identified that have not yet been placed into any known pathway. Specific time points and tissues also exhibited interesting differences: For example, 45 zinc finger genes were specifically up-regulated at later stages of cochlear regeneration. These results are the first of their kind and should provide the starting point for more detailed investigations of the role of these many pathways in HC recovery, and for a description of their possible interactions.

Spectral map-analysis: a method to analyze gene expression data

OpenAIRE

Bijnens, Luc J.M.; Lewi, Paul J.; Göhlmann, Hinrich W.; Molenberghs, Geert; Wouters, Luc

2004-01-01

bioinformatics; biplot; correspondence factor analysis; data mining; data visualization; gene expression data; microarray data; multivariate exploratory data analysis; principal component analysis; Spectral map analysis

Testing the psychometric properties of a Chinese version of the level of expressed emotion scale.

Science.gov (United States)

Chien, Wai Tong; Chan, Zenobia Chung-Yee; Chan, Sally Wai-Chi

2014-01-01

This study tested the psychometric properties of a Chinese version of the level of expressed emotion scale in Hong Kong Chinese patients with severe mental illness and their family caregivers. First, the semantic equivalence with the original English version and test-retest reliability at 2-week interval of the Chinese version was examined. After that, the reproducibility, construct validity, and internal consistency of the Chinese version were tested. The Chinese version indicated good semantic equivalence with the English version (kappa values = 0.76-0.95 and ICC = 0.81-0.92), test-retest reliability (r = 0.89-0.95, P Chinese version had substantial loadings on one of the four factors identified (intrusiveness/hostility, attitude towards patient, tolerance, and emotional involvement), accounting for 71.8% of the total variance of expressed emotion. In confirmatory factor analysis, the identified four-factor model showed the best fit based on all fit indices (χ (2)/df = 1.93, P = 0.75; AGFI = 0.96; TLI = 1.02; RMSEA = 0.031; WRMR = 0.78) to the collected data. The four-factor Chinese version also indicated a good concurrent validity with significant correlations with family functioning (r = -0.54) and family burden (r = 0.49) and a satisfactory reproducibility over six months (intraclass correlation coefficient of 0.90). The mean scores of the overall and subscale of the Chinese version in patients with unipolar disorder were higher than in other illness groups (schizophrenia, psychotic disorders, and bipolar disorder; P Chinese version demonstrates sound psychometric properties to measure families' expressed emotion in Chinese patients with severe mental illness, which are found varied across countries.

An extensive (co-expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana

Directory of Open Access Journals (Sweden)

Provart Nicholas J

2008-04-01

Full Text Available Abstract Background Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism. Results We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here. Conclusion The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling.

Capturing heterogeneity in gene expression studies by surrogate variable analysis.

Directory of Open Access Journals (Sweden)

Jeffrey T Leek

2007-09-01

Full Text Available It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s of interest, there will tend to be sources of signal due to factors that are unknown, unmeasured, or too complicated to capture through simple models. We show that failing to incorporate these sources of heterogeneity into an analysis can have widespread and detrimental effects on the study. Not only can this reduce power or induce unwanted dependence across genes, but it can also introduce sources of spurious signal to many genes. This phenomenon is true even for well-designed, randomized studies. We introduce "surrogate variable analysis" (SVA to overcome the problems caused by heterogeneity in expression studies. SVA can be applied in conjunction with standard analysis techniques to accurately capture the relationship between expression and any modeled variables of interest. We apply SVA to disease class, time course, and genetics of gene expression studies. We show that SVA increases the biological accuracy and reproducibility of analyses in genome-wide expression studies.

CFD Analysis of Scale Effects on Conventional and Tip-Modified Propellers

DEFF Research Database (Denmark)

Shin, Keun Woo; Andersen, Poul

2017-01-01

Full-scale propeller performance is traditionally predictedby scaling model-scale test results, but the traditionalscaling methods do not take into account hydrodynamicdistinctions of tip-modified propellers in full-scaleperformance. An open-water CFD analysis is made onscale effects of tip...... the transition model shows that laminar and transitionalflow modeling is crucial in model-scale computations.Grid-independent solutions at model and full scale areachieved by grid verification studies. The CFD analysis of scale effects shows that theefficiency gain of the tip-modified propeller is increasedat...

Modeling gene expression measurement error: a quasi-likelihood approach

Directory of Open Access Journals (Sweden)

Strimmer Korbinian

2003-03-01

Full Text Available Abstract Background Using suitable error models for gene expression measurements is essential in the statistical analysis of microarray data. However, the true probabilistic model underlying gene expression intensity readings is generally not known. Instead, in currently used approaches some simple parametric model is assumed (usually a transformed normal distribution or the empirical distribution is estimated. However, both these strategies may not be optimal for gene expression data, as the non-parametric approach ignores known structural information whereas the fully parametric models run the risk of misspecification. A further related problem is the choice of a suitable scale for the model (e.g. observed vs. log-scale. Results Here a simple semi-parametric model for gene expression measurement error is presented. In this approach inference is based an approximate likelihood function (the extended quasi-likelihood. Only partial knowledge about the unknown true distribution is required to construct this function. In case of gene expression this information is available in the form of the postulated (e.g. quadratic variance structure of the data. As the quasi-likelihood behaves (almost like a proper likelihood, it allows for the estimation of calibration and variance parameters, and it is also straightforward to obtain corresponding approximate confidence intervals. Unlike most other frameworks, it also allows analysis on any preferred scale, i.e. both on the original linear scale as well as on a transformed scale. It can also be employed in regression approaches to model systematic (e.g. array or dye effects. Conclusions The quasi-likelihood framework provides a simple and versatile approach to analyze gene expression data that does not make any strong distributional assumptions about the underlying error model. For several simulated as well as real data sets it provides a better fit to the data than competing models. In an example it also

Short-term arginine deprivation results in large-scale modulation of hepatic gene expression in both normal and tumor cells: microarray bioinformatic analysis

Directory of Open Access Journals (Sweden)

Sabo Edmond

2006-09-01

Full Text Available Abstract Background We have reported arginine-sensitive regulation of LAT1 amino acid transporter (SLC 7A5 in normal rodent hepatic cells with loss of arginine sensitivity and high level constitutive expression in tumor cells. We hypothesized that liver cell gene expression is highly sensitive to alterations in the amino acid microenvironment and that tumor cells may differ substantially in gene sets sensitive to amino acid availability. To assess the potential number and classes of hepatic genes sensitive to arginine availability at the RNA level and compare these between normal and tumor cells, we used an Affymetrix microarray approach, a paired in vitro model of normal rat hepatic cells and a tumorigenic derivative with triplicate independent replicates. Cells were exposed to arginine-deficient or control conditions for 18 hours in medium formulated to maintain differentiated function. Results Initial two-way analysis with a p-value of 0.05 identified 1419 genes in normal cells versus 2175 in tumor cells whose expression was altered in arginine-deficient conditions relative to controls, representing 9–14% of the rat genome. More stringent bioinformatic analysis with 9-way comparisons and a minimum of 2-fold variation narrowed this set to 56 arginine-responsive genes in normal liver cells and 162 in tumor cells. Approximately half the arginine-responsive genes in normal cells overlap with those in tumor cells. Of these, the majority was increased in expression and included multiple growth, survival, and stress-related genes. GADD45, TA1/LAT1, and caspases 11 and 12 were among this group. Previously known amino acid regulated genes were among the pool in both cell types. Available cDNA probes allowed independent validation of microarray data for multiple genes. Among genes downregulated under arginine-deficient conditions were multiple genes involved in cholesterol and fatty acid metabolism. Expression of low-density lipoprotein receptor was

Gene expression data clustering and it’s application in differential analysis of leukemia

Directory of Open Access Journals (Sweden)

M. Vahedi

2008-02-01

Full Text Available Introduction: DNA microarray technique is one of the most important categories in bioinformatics,which allows the possibility of monitoring thousands of expressed genes has been resulted in creatinggiant data bases of gene expression data, recently. Statistical analysis of such databases includednormalization, clustering, classification and etc.Materials and Methods: Golub et al (1999 collected data bases of leukemia based on the method ofoligonucleotide. The data is on the internet. In this paper, we analyzed gene expression data. It wasclustered by several methods including multi-dimensional scaling, hierarchical and non-hierarchicalclustering. Data set included 20 Acute Lymphoblastic Leukemia (ALL patients and 14 Acute MyeloidLeukemia (AML patients. The results of tow methods of clustering were compared with regard to realgrouping (ALL & AML. R software was used for data analysis.Results: Specificity and sensitivity of divisive hierarchical clustering in diagnosing of ALL patientswere 75% and 92%, respectively. Specificity and sensitivity of partitioning around medoids indiagnosing of ALL patients were 90% and 93%, respectively. These results showed a wellaccomplishment of both methods of clustering. It is considerable that, due to clustering methodsresults, one of the samples was placed in ALL groups, which was in AML group in clinical test.Conclusion: With regard to concordance of the results with real grouping of data, therefore we canuse these methods in the cases where we don't have accurate information of real grouping of data.Moreover, Results of clustering might distinct subgroups of data in such a way that would be necessaryfor concordance with clinical outcomes, laboratory results and so on.

Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L.

Directory of Open Access Journals (Sweden)

Haibo Wang

Full Text Available BACKGROUND: Jatropha curcas L., also called the Physic nut, is an oil-rich shrub with multiple uses, including biodiesel production, and is currently exploited as a renewable energy resource in many countries. Nevertheless, because of its origin from the tropical MidAmerican zone, J. curcas confers an inherent but undesirable characteristic (low cold resistance that may seriously restrict its large-scale popularization. This adaptive flaw can be genetically improved by elucidating the mechanisms underlying plant tolerance to cold temperatures. The newly developed Illumina Hiseq™ 2000 RNA-seq and Digital Gene Expression (DGE are deep high-throughput approaches for gene expression analysis at the transcriptome level, using which we carefully investigated the gene expression profiles in response to cold stress to gain insight into the molecular mechanisms of cold response in J. curcas. RESULTS: In total, 45,251 unigenes were obtained by assembly of clean data generated by RNA-seq analysis of the J. curcas transcriptome. A total of 33,363 and 912 complete or partial coding sequences (CDSs were determined by protein database alignments and ESTScan prediction, respectively. Among these unigenes, more than 41.52% were involved in approximately 128 known metabolic or signaling pathways, and 4,185 were possibly associated with cold resistance. DGE analysis was used to assess the changes in gene expression when exposed to cold condition (12°C for 12, 24, and 48 h. The results showed that 3,178 genes were significantly upregulated and 1,244 were downregulated under cold stress. These genes were then functionally annotated based on the transcriptome data from RNA-seq analysis. CONCLUSIONS: This study provides a global view of transcriptome response and gene expression profiling of J. curcas in response to cold stress. The results can help improve our current understanding of the mechanisms underlying plant cold resistance and favor the screening of

Microarray analysis of the gene expression profile in triethylene ...

African Journals Online (AJOL)

Microarray analysis of the gene expression profile in triethylene glycol dimethacrylate-treated human dental pulp cells. ... Conclusions: Our results suggest that TEGDMA can change the many functions of hDPCs through large changes in gene expression levels and complex interactions with different signaling pathways.

Gene-expression analysis of cold-stress response in the sexually transmitted protist Trichomonas vaginalis.

Science.gov (United States)

Fang, Yi-Kai; Huang, Kuo-Yang; Huang, Po-Jung; Lin, Rose; Chao, Mei; Tang, Petrus

2015-12-01

Trichomonas vaginalis is the etiologic agent of trichomoniasis, the most common nonviral sexually transmitted disease in the world. This infection affects millions of individuals worldwide annually. Although direct sexual contact is the most common mode of transmission, increasing evidence indicates that T. vaginalis can survive in the external environment and can be transmitted by contaminated utensils. We found that the growth of T. vaginalis under cold conditions is greatly inhibited, but recovers after placing these stressed cells at the normal cultivation temperature of 37 °C. However, the mechanisms by which T. vaginalis regulates this adaptive process are unclear. An expressed sequence tag (EST) database generated from a complementary DNA library of T. vaginalis messenger RNAs expressed under cold-culture conditions (4 °C, TvC) was compared with a previously published normal-cultured EST library (37 °C, TvE) to assess the cold-stress responses of T. vaginalis. A total of 9780 clones were sequenced from the TvC library and were mapped to 2934 genes in the T. vaginalis genome. A total of 1254 genes were expressed in both the TvE and TvC libraries, and 1680 genes were only found in the TvC library. A functional analysis showed that cold temperature has effects on many cellular mechanisms, including increased H2O2 tolerance, activation of the ubiquitin-proteasome system, induction of iron-sulfur cluster assembly, and reduced energy metabolism and enzyme expression. The current study is the first large-scale transcriptomic analysis in cold-stressed T. vaginalis and the results enhance our understanding of this important protist. Copyright © 2014. Published by Elsevier B.V.

ADAGE signature analysis: differential expression analysis with data-defined gene sets.

Science.gov (United States)

Tan, Jie; Huyck, Matthew; Hu, Dongbo; Zelaya, René A; Hogan, Deborah A; Greene, Casey S

2017-11-22

Gene set enrichment analysis and overrepresentation analyses are commonly used methods to determine the biological processes affected by a differential expression experiment. This approach requires biologically relevant gene sets, which are currently curated manually, limiting their availability and accuracy in many organisms without extensively curated resources. New feature learning approaches can now be paired with existing data collections to directly extract functional gene sets from big data. Here we introduce a method to identify perturbed processes. In contrast with methods that use curated gene sets, this approach uses signatures extracted from public expression data. We first extract expression signatures from public data using ADAGE, a neural network-based feature extraction approach. We next identify signatures that are differentially active under a given treatment. Our results demonstrate that these signatures represent biological processes that are perturbed by the experiment. Because these signatures are directly learned from data without supervision, they can identify uncurated or novel biological processes. We implemented ADAGE signature analysis for the bacterial pathogen Pseudomonas aeruginosa. For the convenience of different user groups, we implemented both an R package (ADAGEpath) and a web server ( http://adage.greenelab.com ) to run these analyses. Both are open-source to allow easy expansion to other organisms or signature generation methods. We applied ADAGE signature analysis to an example dataset in which wild-type and ∆anr mutant cells were grown as biofilms on the Cystic Fibrosis genotype bronchial epithelial cells. We mapped active signatures in the dataset to KEGG pathways and compared with pathways identified using GSEA. The two approaches generally return consistent results; however, ADAGE signature analysis also identified a signature that revealed the molecularly supported link between the MexT regulon and Anr. We designed

Scheme-scale ambiguity in analysis of QCD observable

International Nuclear Information System (INIS)

Mirjalili, A.; Kniehl, B.A.

2010-01-01

The scheme-scale ambiguity that has plagued perturbative analysis in QCD remains on obstacle to making precise tests of the theory. Many attempts have been done to resolve the scale ambiguity. In this regard the BLM, EC, PMS and CORGI approaches are more distinct. We try to employ these methods to fix the scale ambiguity at NLO, NNLO and even in more higher order approximations. By optimizing the renormalization scale, there will be a possibility to predicate higher order terms. We present general results for predicted terms at any order, using different optimization methods. Some observable as specific examples will be used to indicate the validity of scale fixing to predicate the higher order terms. (authors)

Integrating cross-scale analysis in the spatial and temporal domains for classification of behavioral movement

Directory of Open Access Journals (Sweden)

Ali Soleymani

2014-06-01

Full Text Available Since various behavioral movement patterns are likely to be valid within different, unique ranges of spatial and temporal scales (e.g., instantaneous, diurnal, or seasonal with the corresponding spatial extents, a cross-scale approach is needed for accurate classification of behaviors expressed in movement. Here, we introduce a methodology for the characterization and classification of behavioral movement data that relies on computing and analyzing movement features jointly in both the spatial and temporal domains. The proposed methodology consists of three stages. In the first stage, focusing on the spatial domain, the underlying movement space is partitioned into several zonings that correspond to different spatial scales, and features related to movement are computed for each partitioning level. In the second stage, concentrating on the temporal domain, several movement parameters are computed from trajectories across a series of temporal windows of increasing sizes, yielding another set of input features for the classification. For both the spatial and the temporal domains, the ``reliable scale'' is determined by an automated procedure. This is the scale at which the best classification accuracy is achieved, using only spatial or temporal input features, respectively. The third stage takes the measures from the spatial and temporal domains of movement, computed at the corresponding reliable scales, as input features for behavioral classification. With a feature selection procedure, the most relevant features contributing to known behavioral states are extracted and used to learn a classification model. The potential of the proposed approach is demonstrated on a dataset of adult zebrafish (Danio rerio swimming movements in testing tanks, following exposure to different drug treatments. Our results show that behavioral classification accuracy greatly increases when firstly cross-scale analysis is used to determine the best analysis scale, and

Testing the Psychometric Properties of a Chinese Version of the Level of Expressed Emotion Scale

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Wai Tong Chien

2014-01-01

Full Text Available This study tested the psychometric properties of a Chinese version of the level of expressed emotion scale in Hong Kong Chinese patients with severe mental illness and their family caregivers. First, the semantic equivalence with the original English version and test-retest reliability at 2-week interval of the Chinese version was examined. After that, the reproducibility, construct validity, and internal consistency of the Chinese version were tested. The Chinese version indicated good semantic equivalence with the English version (kappa values = 0.76–0.95 and ICC = 0.81–0.92, test-retest reliability (r = 0.89–0.95, P<0.01, and internal consistency (Cronbach’s α = 0.86–0.92. Among 262 patients with severe mental illness and their caregivers, the 50-item Chinese version had substantial loadings on one of the four factors identified (intrusiveness/hostility, attitude towards patient, tolerance, and emotional involvement, accounting for 71.8% of the total variance of expressed emotion. In confirmatory factor analysis, the identified four-factor model showed the best fit based on all fit indices (χ2/df = 1.93, P=0.75; AGFI = 0.96; TLI = 1.02; RMSEA = 0.031; WRMR = 0.78 to the collected data. The four-factor Chinese version also indicated a good concurrent validity with significant correlations with family functioning (r = −0.54 and family burden (r = 0.49 and a satisfactory reproducibility over six months (intraclass correlation coefficient of 0.90. The mean scores of the overall and subscale of the Chinese version in patients with unipolar disorder were higher than in other illness groups (schizophrenia, psychotic disorders, and bipolar disorder; P<0.01. The Chinese version demonstrates sound psychometric properties to measure families’ expressed emotion in Chinese patients with severe mental illness, which are found varied across countries.

Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters.

Science.gov (United States)

Ottaviani, Gianluigi; Tsakalos, James L; Keppel, Gunnar; Mucina, Ladislav

2018-01-01

Complex processes related to biotic and abiotic forces can impose limitations to assembly and composition of plant communities. Quantifying the effects of these constraints on plant functional traits across environmental gradients, and among communities, remains challenging. We define ecological constraint ( C i ) as the combined, limiting effect of biotic interactions and environmental filtering on trait expression (i.e., the mean value and range of functional traits). Here, we propose a set of novel parameters to quantify this constraint by extending the trait-gradient analysis (TGA) methodology. The key parameter is ecological constraint, which is dimensionless and can be measured at various scales, for example, on population and community levels. It facilitates comparing the effects of ecological constraints on trait expressions across environmental gradients, as well as within and among communities. We illustrate the implementation of the proposed parameters using the bark thickness of 14 woody species along an aridity gradient on granite outcrops in southwestern Australia. We found a positive correlation between increasing environmental stress and strength of ecological constraint on bark thickness expression. Also, plants from more stressful habitats (shrublands on shallow soils and in sun-exposed locations) displayed higher ecological constraint for bark thickness than plants in more benign habitats (woodlands on deep soils and in sheltered locations). The relative ease of calculation and dimensionless nature of C i allow it to be readily implemented at various scales and make it widely applicable. It therefore has the potential to advance the mechanistic understanding of the ecological processes shaping trait expression. Some future applications of the new parameters could be investigating the patterns of ecological constraints (1) among communities from different regions, (2) on different traits across similar environmental gradients, and (3) for the same

Molecular characterization and expression analysis of fat mass and ...

Indian Academy of Sciences (India)

Keywords. fat mass and obesity-associated gene (FTO); rabbit; mRNA expression patterns; sequence analysis; Oryctolagus cuniculus. ... In this work, the molecular characterization and expression features of rabbit (Oryctolagus cuniculus) FTO cDNA were analysed. The rabbit FTO cDNA with a size of 2158 bp was cloned, ...

Status of large-scale analysis of post-translational modifications by mass spectrometry

DEFF Research Database (Denmark)

Olsen, Jesper V; Mann, Matthias

2013-01-01

Cellular function can be controlled through the gene expression program but often protein post translations modifications (PTMs) provide a more precisely and elegant mechanism. Key functional roles of specific modification events for instance during the cell cycle have been known for decades...... of protein modifications. For many PTMs, including phosphorylation, ubiquitination, glycosylation and acetylation, tens of thousands of sites can now be confidently identified and localized in the sequence of the protein. Quantitation of PTM levels between different cellular states is likewise established......, with label-free methods showing particular promise. It is also becoming possible to determine the absolute occupancy or stoichiometry of PTMS sites on a large scale. Powerful software for the bioinformatic analysis of thousands of PTM sites has been developed. However, a complete inventory of sites has...

Sensitivity Analysis of Oxide Scale Influence on General Carbon Steels during Hot Forging

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Bernd-Arno Behrens

2018-02-01

Full Text Available Increasing product requirements have made numerical simulation into a vital tool for the time- and cost-efficient process design. In order to accurately model hot forging processes with finite, element-based numerical methods, reliable models are required, which take the material behaviour, surface phenomena of die and workpiece, and machine kinematics into account. In hot forging processes, the surface properties are strongly affected by the growth of oxide scale, which influences the material flow, friction, and product quality of the finished component. The influence of different carbon contents on material behaviour is investigated by considering three different steel grades (C15, C45, and C60. For a general description of the material behaviour, an empirical approach is used to implement mathematical functions for expressing the relationship between flow stress and dominant influence variables like alloying elements, initial microstructure, and reheating mode. The deformation behaviour of oxide scale is separately modelled for each component with parameterized flow curves. The main focus of this work lies in the consideration of different materials as well as the calculation and assignment of their material properties in dependence on current process parameters by application of subroutines. The validated model is used to carry out the influence of various oxide scale parameters, like the scale thickness and the composition, on the hot forging process. Therefore, selected parameters have been varied within a numerical sensitivity analysis. The results show a strong influence of oxide scale on the friction behaviour as well as on the material flow during hot forging.

Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.

Energy Technology Data Exchange (ETDEWEB)

Reddy, Anireddy [Colorado State Univ., Fort Collins, CO (United States); Ben-Hur, Asa [Colorado State Univ., Fort Collins, CO (United States)

2017-11-22

Abiotic stresses including drought are major limiting factors of crop yields and cause significant crop losses. Acquisition of stress tolerance to abiotic stresses requires coordinated regulation of a multitude of biochemical and physiological changes, and most of these changes depend on alterations in gene expression. The goal of this work is to perform global analysis of differential regulation of gene expression and alternative splicing, and their relationship with chromatin landscape in drought sensitive and tolerant cultivars. our Iso-Seq study revealed transcriptome-wide full-length isoforms at an unprecedented scale with over 11000 novel splice isoforms. Additionally, we uncovered alternative polyadenylation sites of ~11000 expressed genes and many novel genes. Overall, Iso-Seq results greatly enhanced sorghum gene annotations that are not only useful in analyzing all our RNA-seq, ChIP-seq and ATAC-seq data but also serve as a great resource to the plant biology community. Our studies identified differentially expressed genes and splicing events that are correlated with the drought-resistant phenotype. An association between alternative splicing and chromatin accessibility was also revealed. Several computational tools developed here (TAPIS and iDiffIR) have been made freely available to the research community in analyzing alternative splicing and differential alternative splicing.

Comparison of scale analysis and numerical simulation for saturated zone convective mixing processes

International Nuclear Information System (INIS)

Oldenburg, C.M.

1998-01-01

Scale analysis can be used to predict a variety of quantities arising from natural systems where processes are described by partial differential equations. For example, scale analysis can be applied to estimate the effectiveness of convective missing on the dilution of contaminants in groundwater. Scale analysis involves substituting simple quotients for partial derivatives and identifying and equating the dominant terms in an order-of-magnitude sense. For free convection due to sidewall heating of saturated porous media, scale analysis shows that vertical convective velocity in the thermal boundary layer region is proportional to the Rayleigh number, horizontal convective velocity is proportional to the square root of the Rayleigh number, and thermal boundary layer thickness is proportional to the inverse square root of the Rayleigh number. These scale analysis estimates are corroborated by numerical simulations of an idealized system. A scale analysis estimate of mixing time for a tracer mixing by hydrodynamic dispersion in a convection cell also agrees well with numerical simulation for two different Rayleigh numbers. Scale analysis for the heating-from-below scenario produces estimates of maximum velocity one-half as large as the sidewall case. At small values of the Rayleigh number, this estimate is confirmed by numerical simulation. For larger Rayleigh numbers, simulation results suggest maximum velocities are similar to the sidewall heating scenario. In general, agreement between scale analysis estimates and numerical simulation results serves to validate the method of scale analysis. Application is to radioactive repositories

Computational methods for criticality safety analysis within the scale system

International Nuclear Information System (INIS)

Parks, C.V.; Petrie, L.M.; Landers, N.F.; Bucholz, J.A.

1986-01-01

The criticality safety analysis capabilities within the SCALE system are centered around the Monte Carlo codes KENO IV and KENO V.a, which are both included in SCALE as functional modules. The XSDRNPM-S module is also an important tool within SCALE for obtaining multiplication factors for one-dimensional system models. This paper reviews the features and modeling capabilities of these codes along with their implementation within the Criticality Safety Analysis Sequences (CSAS) of SCALE. The CSAS modules provide automated cross-section processing and user-friendly input that allow criticality safety analyses to be done in an efficient and accurate manner. 14 refs., 2 figs., 3 tabs

SCALE 5: Powerful new criticality safety analysis tools

International Nuclear Information System (INIS)

Bowman, Stephen M.; Hollenbach, Daniel F.; Dehart, Mark D.; Rearden, Bradley T.; Gauld, Ian C.; Goluoglu, Sedat

2003-01-01

Version 5 of the SCALE computer software system developed at Oak Ridge National Laboratory, scheduled for release in December 2003, contains several significant new modules and sequences for criticality safety analysis and marks the most important update to SCALE in more than a decade. This paper highlights the capabilities of these new modules and sequences, including continuous energy flux spectra for processing multigroup problem-dependent cross sections; one- and three-dimensional sensitivity and uncertainty analyses for criticality safety evaluations; two-dimensional flexible mesh discrete ordinates code; automated burnup-credit analysis sequence; and one-dimensional material distribution optimization for criticality safety. (author)

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

Directory of Open Access Journals (Sweden)

Boris P Hejblum

2015-06-01

Full Text Available Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial, and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

Rasch analysis of the Multiple Sclerosis Impact Scale (MSIS-29

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Misajon Rose

2009-06-01

Full Text Available Abstract Background Multiple Sclerosis (MS is a degenerative neurological disease that causes impairments, including spasticity, pain, fatigue, and bladder dysfunction, which negatively impact on quality of life. The Multiple Sclerosis Impact Scale (MSIS-29 is a disease-specific health-related quality of life (HRQoL instrument, developed using the patient's perspective on disease impact. It consists of two subscales assessing the physical (MSIS-29-PHYS and psychological (MSIS-29-PSYCH impact of MS. Although previous studies have found support for the psychometric properties of the MSIS-29 using traditional methods of scale evaluation, the scale has not been subjected to a detailed Rasch analysis. Therefore, the objective of this study was to use Rasch analysis to assess the internal validity of the scale, and its response format, item fit, targeting, internal consistency and dimensionality. Methods Ninety-two persons with definite MS residing in the community were recruited from a tertiary hospital database. Patients completed the MSIS-29 as part of a larger study. Rasch analysis was undertaken to assess the psychometric properties of the MSIS-29. Results Rasch analysis showed overall support for the psychometric properties of the two MSIS-29 subscales, however it was necessary to reduce the response format of the MSIS-29-PHYS to a 3-point response scale. Both subscales were unidimensional, had good internal consistency, and were free from item bias for sex and age. Dimensionality testing indicated it was not appropriate to combine the two subscales to form a total MSIS score. Conclusion In this first study to use Rasch analysis to fully assess the psychometric properties of the MSIS-29 support was found for the two subscales but not for the use of the total scale. Further use of Rasch analysis on the MSIS-29 in larger and broader samples is recommended to confirm these findings.

Rasch analysis of the Multiple Sclerosis Impact Scale (MSIS-29)

Science.gov (United States)

Ramp, Melina; Khan, Fary; Misajon, Rose Anne; Pallant, Julie F

2009-01-01

Background Multiple Sclerosis (MS) is a degenerative neurological disease that causes impairments, including spasticity, pain, fatigue, and bladder dysfunction, which negatively impact on quality of life. The Multiple Sclerosis Impact Scale (MSIS-29) is a disease-specific health-related quality of life (HRQoL) instrument, developed using the patient's perspective on disease impact. It consists of two subscales assessing the physical (MSIS-29-PHYS) and psychological (MSIS-29-PSYCH) impact of MS. Although previous studies have found support for the psychometric properties of the MSIS-29 using traditional methods of scale evaluation, the scale has not been subjected to a detailed Rasch analysis. Therefore, the objective of this study was to use Rasch analysis to assess the internal validity of the scale, and its response format, item fit, targeting, internal consistency and dimensionality. Methods Ninety-two persons with definite MS residing in the community were recruited from a tertiary hospital database. Patients completed the MSIS-29 as part of a larger study. Rasch analysis was undertaken to assess the psychometric properties of the MSIS-29. Results Rasch analysis showed overall support for the psychometric properties of the two MSIS-29 subscales, however it was necessary to reduce the response format of the MSIS-29-PHYS to a 3-point response scale. Both subscales were unidimensional, had good internal consistency, and were free from item bias for sex and age. Dimensionality testing indicated it was not appropriate to combine the two subscales to form a total MSIS score. Conclusion In this first study to use Rasch analysis to fully assess the psychometric properties of the MSIS-29 support was found for the two subscales but not for the use of the total scale. Further use of Rasch analysis on the MSIS-29 in larger and broader samples is recommended to confirm these findings. PMID:19545445

Time Scale Analysis of Interest Rate Spreads and Output Using Wavelets

Directory of Open Access Journals (Sweden)

Marco Gallegati

2013-04-01

Full Text Available This paper adds to the literature on the information content of different spreads for real activity by explicitly taking into account the time scale relationship between a variety of monetary and financial indicators (real interest rate, term and credit spreads and output growth. By means of wavelet-based exploratory data analysis we obtain richer results relative to the aggregate analysis by identifying the dominant scales of variation in the data and the scales and location at which structural breaks have occurred. Moreover, using the “double residuals” regression analysis on a scale-by-scale basis, we find that changes in the spread in several markets have different information content for output at different time frames. This is consistent with the idea that allowing for different time scales of variation in the data can provide a fruitful understanding of the complex dynamics of economic relationships between variables with non-stationary or transient components, certainly richer than those obtained using standard time domain methods.

Measuring the contribution of art therapy in multidisciplinary treatment of personality disorders: The construction of the Self‐expression and Emotion Regulation in Art Therapy Scale (SERATS)

Science.gov (United States)

van Hooren, Susan; van der Veld, William M.; Hutschemaekers, Giel

2017-01-01

Abstract Despite the use of art therapy in clinical practice, its appreciation and reported beneficial results, no instruments are available to measure specific effects of art therapy among patients with personality disorders cluster B/C in multidisciplinary treatment. In the present study, we described the development and psychometric evaluation of the Self‐expression and Emotion Regulation in Art Therapy Scale (SERATS). Structural validity (exploratory and confirmatory factor analysis), reliability, construct validity and sensitivity to change were examined using two independent databases (n = 335; n = 34) of patients diagnosed with personality disorders cluster B/C. This resulted in a nine‐item effect scale with a single factor with a high internal reliability and high test–retest reliability; it demonstrated discriminant validity and sensitivity to change. In conclusion, the SERATS is brief and content‐valid and offers objective and reliable information on self‐expression and emotion regulation in art therapy among patients with personality disorders cluster B/C. Although more research on construct validity is needed, the SERATS is a promising tool to be applied as an effect scale and as a monitoring tool during art therapy treatment. © 2017 The Authors Personality and Mental Health Published by John Wiley & Sons Ltd PMID:28730717

Development and evaluation of the Expressions of Moral Injury Scale-Military Version.

Science.gov (United States)

Currier, Joseph M; Farnsworth, Jacob K; Drescher, Kent D; McDermott, Ryon C; Sims, Brook M; Albright, David L

2018-05-01

There is consensus that military personnel can encounter a far more diverse set of challenges than researchers and clinicians have historically appreciated. Moral injury (MI) represents an emerging construct to capture behavioural, social, and spiritual suffering that may transcend and overlap with mental health diagnoses (e.g., post-traumatic stress disorder and major depressive disorder). The Expressions of Moral Injury Scale-Military Version (EMIS-M) was developed to provide a reliable and valid means for assessing the warning signs of a MI in military populations. Drawing on independent samples of veterans who had served in a war-zone environment, factor analytic results revealed 2 distinct factors related to MI expressions directed at both self (9 items) and others (8 items). These subscales generated excellent internal consistency and temporal stability over a 6-month period. When compared to measures of post-traumatic stress disorder, major depressive disorder, and other theoretically relevant constructs (e.g., forgiveness, social support, moral emotions, and combat exposure), EMIS-M scores demonstrated strong convergent, divergent, and incremental validity. In addition, although structural equation modelling findings supported a possible general MI factor in Study 2, the patterns of associations for self- and other-directed expressions yielded evidence for differential validity with varying forms of forgiveness and combat exposure. As such, the EMIS-M provides a face valid, psychometrically validated tool for assessing expressions of apparent MI subtypes in research and clinical settings. Looking ahead, the EMIS-M will hopefully advance the scientific understanding of MI while supporting innovation for clinicians to tailor evidence-based treatments and/or develop novel approaches for addressing MI in their work. Copyright © 2017 John Wiley & Sons, Ltd.

Transcriptome analysis of Schistosoma mansoni larval development using serial analysis of gene expression (SAGE).

Science.gov (United States)

Taft, A S; Vermeire, J J; Bernier, J; Birkeland, S R; Cipriano, M J; Papa, A R; McArthur, A G; Yoshino, T P

2009-04-01

Infection of the snail, Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke, Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of the S. mansoni miracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia and in vitro cultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of the B. glabrata embryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to the S. mansoni gene predictions (v4.0e) either by estimating theoretical 3' UTR lengths or using existing 3' EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

Sensitivity analysis for large-scale problems

Science.gov (United States)

Noor, Ahmed K.; Whitworth, Sandra L.

1987-01-01

The development of efficient techniques for calculating sensitivity derivatives is studied. The objective is to present a computational procedure for calculating sensitivity derivatives as part of performing structural reanalysis for large-scale problems. The scope is limited to framed type structures. Both linear static analysis and free-vibration eigenvalue problems are considered.

Genome-wide identification and expression analysis of SBP-like transcription factor genes in Moso Bamboo (Phyllostachys edulis).

Science.gov (United States)

Pan, Feng; Wang, Yue; Liu, Huanglong; Wu, Min; Chu, Wenyuan; Chen, Danmei; Xiang, Yan

2017-06-27

The SQUAMOSA promoter binding protein-like (SPL) proteins are plant-specific transcription factors (TFs) that function in a variety of developmental processes including growth, flower development, and signal transduction. SPL proteins are encoded by a gene family, and these genes have been characterized in two model grass species, Zea mays and Oryza sativa. The SPL gene family has not been well studied in moso bamboo (Phyllostachys edulis), a woody grass species. We identified 32 putative PeSPL genes in the P. edulis genome. Phylogenetic analysis arranged the PeSPL protein sequences in eight groups. Similarly, phylogenetic analysis of the SBP-like and SBP proteins from rice and maize clustered them into eight groups analogous to those from P. edulis. Furthermore, the deduced PeSPL proteins in each group contained very similar conserved sequence motifs. Our analyses indicate that the PeSPL genes experienced a large-scale duplication event ~15 million years ago (MYA), and that divergence between the PeSPL and OsSPL genes occurred 34 MYA. The stress-response expression profiles and tissue-specificity of the putative PeSPL gene promoter regions showed that SPL genes in moso bamboo have potential biological functions in stress resistance as well as in growth and development. We therefore examined PeSPL gene expression in response to different plant hormone and drought (polyethylene glycol-6000; PEG) treatments to mimic biotic and abiotic stresses. Expression of three (PeSPL10, -12, -17), six (PeSPL1, -10, -12, -17, -20, -31), and nine (PeSPL5, -8, -9, -14, -15, -19, -20, -31, -32) genes remained relatively stable after treating with salicylic acid (SA), gibberellic acid (GA), and PEG, respectively, while the expression patterns of other genes changed. In addition, analysis of tissue-specific expression of the moso bamboo SPL genes during development showed differences in their spatiotemporal expression patterns, and many were expressed at high levels in flowers and

Groundwater flow analysis on local scale. Setting boundary conditions of groundwater flow analysis on site scale model in the former part of the step 3

International Nuclear Information System (INIS)

Onoe, Hironori; Saegusa, Hiromitsu

2005-07-01

Japan Nuclear Cycle Development Institute has been conducting a wide range of geoscientific research in order to build a foundation for multidisciplinary studies of the deep geological environment as a basis of research and development for geological disposal of nuclear wastes. Ongoing geoscientific research programs include the Regional Hydrogeological Study (RHS) project and Mizunami Underground Research Laboratory (MIU) project in the Tono region, Gifu Prefecture. The main goal of these projects is to establish comprehensive techniques for investigation, analysis, and assessment of the deep geological environment at several spatial scales. The RHS project is a local scale study for understanding the groundwater flow system from the recharge area to the discharge area. The Surface-based Investigation Phase of the MIU project is a mainly site scale study for understanding the deep geological environment immediately surrounding the MIU construction site using a multiphase, iterative approach. In this study, the hydrogeological modeling and groundwater flow analysis on the Local scale were carried out in order to set boundary conditions of the site scale model based on the data obtained from surface-based investigations in the former part of the Step 3 in site scale of the MIU project. As a result of the study, the uncertainty of hydrogeological model of the local scale and boundary conditions for the site scale model is decreased as stepwise investigation, and boundary conditions for groundwater flow analysis on the site scale model for the former part of the Step 3 could be obtained. (author)

Economic Analysis of Small Scale Fish Pond Production in Oguta ...

African Journals Online (AJOL)

What are the costs and returns of small-scale fishpond enterprises? What problems hinder the development of small-scale fishpond production? Data were collected with the aid of structured questionnaires and interviews. Descriptive statistics, gross margin and likert scale were employed in data analysis. Gross margin ...

The Rationality/Emotional Defensiveness Scale--II. Convergent and discriminant correlational analysis in males and females with and without cancer.

Science.gov (United States)

Swan, G E; Carmelli, D; Dame, A; Rosenman, R H; Spielberger, C D

1992-05-01

The psychological correlates of the Rationality/Emotional Defensiveness Scale and its two subscales were examined in 1236 males and 863 females from the Western Collaborative Group Study. An additional 157 males and 164 females with some form of cancer other than of the skin were also included in this analysis. Characteristics measured included self-reported emotional control, anger expression, trait personality, depressive and neurotic symptomatology, Type A behavior, hostility, and social desirability. Results indicate that the Rationality/Emotional Defensiveness Scale is most strongly related to the suppression and control of emotions, especially anger. Scores on this scale also tend to be associated with less Type A behavior and hostility and with more social conformity. Analysis of the component subscale suggests that Antiemotionality, i.e. the extent to which an individual uses reason and logic to avoid interpersonally related emotions, is most strongly marked by the control of anger, while Rationality, i.e. the extent to which an individual uses reason and logic as a general approach to coping with the environment, is related to the control of anxiety and a higher level of trait curiosity. The psychological interpretation of the scale appears to be largely invariant across gender, unaffected by residualization of the total scale score for its association with Social Desirability, and, except for a few minor instances, unrelated to the diagnosis of cancer.

Scale-up of Escherichia coli growth and recombinant protein expression conditions from microwell to laboratory and pilot scale based on matched k(L)a.

Science.gov (United States)

Islam, R S; Tisi, D; Levy, M S; Lye, G J

2008-04-01

Fermentation optimization experiments are ideally performed at small scale to reduce time, cost and resource requirements. Currently microwell plates (MWPs) are under investigation for this purpose as the format is ideally suited to automated high-throughput experimentation. In order to translate an optimized small-scale fermentation process to laboratory and pilot scale stirred-tank reactors (STRs) it is necessary to characterize key engineering parameters at both scales given the differences in geometry and the mechanisms of aeration and agitation. In this study oxygen mass transfer coefficients are determined in three MWP formats and in 7.5 L and 75 L STRs. k(L)a values were determined in cell-free media using the dynamic gassing-out technique over a range of agitation conditions. Previously optimized culture conditions at the MWP scale were then scaled up to the larger STR scales on the basis of matched k(L)a values. The accurate reproduction of MWP (3 mL) E. coli BL21 (DE3) culture kinetics at the two larger scales was shown in terms of cell growth, protein expression, and substrate utilization for k(L)a values that provided effective mixing and gas-liquid distribution at each scale. This work suggests that k(L)a provides a useful initial scale-up criterion for MWP culture conditions which enabled a 15,000-fold scale translation in this particular case. This work complements our earlier studies on the application of DoE techniques to MWP fermentation optimization and in so doing provides a generic framework for the generation of large quantities of soluble protein in a rapid and cost-effective manner.

Integrative sparse principal component analysis of gene expression data.

Science.gov (United States)

Liu, Mengque; Fan, Xinyan; Fang, Kuangnan; Zhang, Qingzhao; Ma, Shuangge

2017-12-01

In the analysis of gene expression data, dimension reduction techniques have been extensively adopted. The most popular one is perhaps the PCA (principal component analysis). To generate more reliable and more interpretable results, the SPCA (sparse PCA) technique has been developed. With the "small sample size, high dimensionality" characteristic of gene expression data, the analysis results generated from a single dataset are often unsatisfactory. Under contexts other than dimension reduction, integrative analysis techniques, which jointly analyze the raw data of multiple independent datasets, have been developed and shown to outperform "classic" meta-analysis and other multidatasets techniques and single-dataset analysis. In this study, we conduct integrative analysis by developing the iSPCA (integrative SPCA) method. iSPCA achieves the selection and estimation of sparse loadings using a group penalty. To take advantage of the similarity across datasets and generate more accurate results, we further impose contrasted penalties. Different penalties are proposed to accommodate different data conditions. Extensive simulations show that iSPCA outperforms the alternatives under a wide spectrum of settings. The analysis of breast cancer and pancreatic cancer data further shows iSPCA's satisfactory performance. © 2017 WILEY PERIODICALS, INC.

Insulin/IGF-regulated size scaling of neuroendocrine cells expressing the bHLH transcription factor Dimmed in Drosophila.

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Jiangnan Luo

Full Text Available Neurons and other cells display a large variation in size in an organism. Thus, a fundamental question is how growth of individual cells and their organelles is regulated. Is size scaling of individual neurons regulated post-mitotically, independent of growth of the entire CNS? Although the role of insulin/IGF-signaling (IIS in growth of tissues and whole organisms is well established, it is not known whether it regulates the size of individual neurons. We therefore studied the role of IIS in the size scaling of neurons in the Drosophila CNS. By targeted genetic manipulations of insulin receptor (dInR expression in a variety of neuron types we demonstrate that the cell size is affected only in neuroendocrine cells specified by the bHLH transcription factor DIMMED (DIMM. Several populations of DIMM-positive neurons tested displayed enlarged cell bodies after overexpression of the dInR, as well as PI3 kinase and Akt1 (protein kinase B, whereas DIMM-negative neurons did not respond to dInR manipulations. Knockdown of these components produce the opposite phenotype. Increased growth can also be induced by targeted overexpression of nutrient-dependent TOR (target of rapamycin signaling components, such as Rheb (small GTPase, TOR and S6K (S6 kinase. After Dimm-knockdown in neuroendocrine cells manipulations of dInR expression have significantly less effects on cell size. We also show that dInR expression in neuroendocrine cells can be altered by up or down-regulation of Dimm. This novel dInR-regulated size scaling is seen during postembryonic development, continues in the aging adult and is diet dependent. The increase in cell size includes cell body, axon terminations, nucleus and Golgi apparatus. We suggest that the dInR-mediated scaling of neuroendocrine cells is part of a plasticity that adapts the secretory capacity to changing physiological conditions and nutrient-dependent organismal growth.

SINEX: SCALE shielding analysis GUI for X-Windows

International Nuclear Information System (INIS)

Browman, S.M.; Barnett, D.L.

1997-12-01

SINEX (SCALE Interface Environment for X-windows) is an X-Windows graphical user interface (GUI), that is being developed for performing SCALE radiation shielding analyses. SINEX enables the user to generate input for the SAS4/MORSE and QADS/QAD-CGGP shielding analysis sequences in SCALE. The code features will facilitate the use of both analytical sequences with a minimum of additional user input. Included in SINEX is the capability to check the geometry model by generating two-dimensional (2-D) color plots of the geometry model using a new version of the SCALE module, PICTURE. The most sophisticated feature, however, is the 2-D visualization display that provides a graphical representation on screen as the user builds a geometry model. This capability to interactively build a model will significantly increase user productivity and reduce user errors. SINEX will perform extensive error checking and will allow users to execute SCALE directly from the GUI. The interface will also provide direct on-line access to the SCALE manual

Life cycle analysis of kidney gene expression in male F344 rats.

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Joshua C Kwekel

Full Text Available Age is a predisposing condition for susceptibility to chronic kidney disease and progression as well as acute kidney injury that may arise due to the adverse effects of some drugs. Age-related differences in kidney biology, therefore, are a key concern in understanding drug safety and disease progression. We hypothesize that the underlying suite of genes expressed in the kidney at various life cycle stages will impact susceptibility to adverse drug reactions. Therefore, establishing changes in baseline expression data between these life stages is the first and necessary step in evaluating this hypothesis. Untreated male F344 rats were sacrificed at 2, 5, 6, 8, 15, 21, 78, and 104 weeks of age. Kidneys were collected for histology and gene expression analysis. Agilent whole-genome rat microarrays were used to query global expression profiles. An ANOVA (p1.5 in relative mRNA expression, was used to identify 3,724 unique differentially expressed genes (DEGs. Principal component analyses of these DEGs revealed three major divisions in life-cycle renal gene expression. K-means cluster analysis identified several groups of genes that shared age-specific patterns of expression. Pathway analysis of these gene groups revealed age-specific gene networks and functions related to renal function and aging, including extracellular matrix turnover, immune cell response, and renal tubular injury. Large age-related changes in expression were also demonstrated for the genes that code for qualified renal injury biomarkers KIM-1, Clu, and Tff3. These results suggest specific groups of genes that may underlie age-specific susceptibilities to adverse drug reactions and disease. This analysis of the basal gene expression patterns of renal genes throughout the life cycle of the rat will improve the use of current and future renal biomarkers and inform our assessments of kidney injury and disease.

Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules.

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Xiaolin Xiao

2014-01-01

Full Text Available Recent high-throughput efforts such as ENCODE have generated a large body of genome-scale transcriptional data in multiple conditions (e.g., cell-types and disease states. Leveraging these data is especially important for network-based approaches to human disease, for instance to identify coherent transcriptional modules (subnetworks that can inform functional disease mechanisms and pathological pathways. Yet, genome-scale network analysis across conditions is significantly hampered by the paucity of robust and computationally-efficient methods. Building on the Higher-Order Generalized Singular Value Decomposition, we introduce a new algorithmic approach for efficient, parameter-free and reproducible identification of network-modules simultaneously across multiple conditions. Our method can accommodate weighted (and unweighted networks of any size and can similarly use co-expression or raw gene expression input data, without hinging upon the definition and stability of the correlation used to assess gene co-expression. In simulation studies, we demonstrated distinctive advantages of our method over existing methods, which was able to recover accurately both common and condition-specific network-modules without entailing ad-hoc input parameters as required by other approaches. We applied our method to genome-scale and multi-tissue transcriptomic datasets from rats (microarray-based and humans (mRNA-sequencing-based and identified several common and tissue-specific subnetworks with functional significance, which were not detected by other methods. In humans we recapitulated the crosstalk between cell-cycle progression and cell-extracellular matrix interactions processes in ventricular zones during neocortex expansion and further, we uncovered pathways related to development of later cognitive functions in the cortical plate of the developing brain which were previously unappreciated. Analyses of seven rat tissues identified a multi

Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules.

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Xiao, Xiaolin; Moreno-Moral, Aida; Rotival, Maxime; Bottolo, Leonardo; Petretto, Enrico

2014-01-01

Recent high-throughput efforts such as ENCODE have generated a large body of genome-scale transcriptional data in multiple conditions (e.g., cell-types and disease states). Leveraging these data is especially important for network-based approaches to human disease, for instance to identify coherent transcriptional modules (subnetworks) that can inform functional disease mechanisms and pathological pathways. Yet, genome-scale network analysis across conditions is significantly hampered by the paucity of robust and computationally-efficient methods. Building on the Higher-Order Generalized Singular Value Decomposition, we introduce a new algorithmic approach for efficient, parameter-free and reproducible identification of network-modules simultaneously across multiple conditions. Our method can accommodate weighted (and unweighted) networks of any size and can similarly use co-expression or raw gene expression input data, without hinging upon the definition and stability of the correlation used to assess gene co-expression. In simulation studies, we demonstrated distinctive advantages of our method over existing methods, which was able to recover accurately both common and condition-specific network-modules without entailing ad-hoc input parameters as required by other approaches. We applied our method to genome-scale and multi-tissue transcriptomic datasets from rats (microarray-based) and humans (mRNA-sequencing-based) and identified several common and tissue-specific subnetworks with functional significance, which were not detected by other methods. In humans we recapitulated the crosstalk between cell-cycle progression and cell-extracellular matrix interactions processes in ventricular zones during neocortex expansion and further, we uncovered pathways related to development of later cognitive functions in the cortical plate of the developing brain which were previously unappreciated. Analyses of seven rat tissues identified a multi-tissue subnetwork of co-expressed

Multi-scale symbolic transfer entropy analysis of EEG

Science.gov (United States)

Yao, Wenpo; Wang, Jun

2017-10-01

From both global and local perspectives, we symbolize two kinds of EEG and analyze their dynamic and asymmetrical information using multi-scale transfer entropy. Multi-scale process with scale factor from 1 to 199 and step size of 2 is applied to EEG of healthy people and epileptic patients, and then the permutation with embedding dimension of 3 and global approach are used to symbolize the sequences. The forward and reverse symbol sequences are taken as the inputs of transfer entropy. Scale factor intervals of permutation and global way are (37, 57) and (65, 85) where the two kinds of EEG have satisfied entropy distinctions. When scale factor is 67, transfer entropy of the healthy and epileptic subjects of permutation, 0.1137 and 0.1028, have biggest difference. And the corresponding values of the global symbolization is 0.0641 and 0.0601 which lies in the scale factor of 165. Research results show that permutation which takes contribution of local information has better distinction and is more effectively applied to our multi-scale transfer entropy analysis of EEG.

Selecting numerical scales for pairwise comparisons

International Nuclear Information System (INIS)

Elliott, Michael A.

2010-01-01

It is often desirable in decision analysis problems to elicit from an individual the rankings of a population of attributes according to the individual's preference and to understand the degree to which each attribute is preferred to the others. A common method for obtaining this information involves the use of pairwise comparisons, which allows an analyst to convert subjective expressions of preference between two attributes into numerical values indicating preferences across the entire population of attributes. Key to the use of pairwise comparisons is the underlying numerical scale that is used to convert subjective linguistic expressions of preference into numerical values. This scale represents the psychological manner in which individuals perceive increments of preference among abstract attributes and it has important implications about the distribution and consistency of an individual's preferences. Three popular scale types, the traditional integer scales, balanced scales and power scales are examined. Results of a study of 64 individuals responding to a hypothetical decision problem show that none of these scales can accurately capture the preferences of all individuals. A study of three individuals working on an actual engineering decision problem involving the design of a decay heat removal system for a nuclear fission reactor show that the choice of scale can affect the preferred decision. It is concluded that applications of pairwise comparisons would benefit from permitting participants to choose the scale that best models their own particular way of thinking about the relative preference of attributes.

Macroscopic High-Temperature Structural Analysis Model of Small-Scale PCHE Prototype (II)

International Nuclear Information System (INIS)

Song, Kee Nam; Lee, Heong Yeon; Hong, Sung Deok; Park, Hong Yoon

2011-01-01

The IHX (intermediate heat exchanger) of a VHTR (very high-temperature reactor) is a core component that transfers the high heat generated by the VHTR at 950 .deg. C to a hydrogen production plant. Korea Atomic Energy Research Institute manufactured a small-scale prototype of a PCHE (printed circuit heat exchanger) that was being considered as a candidate for the IHX. In this study, as a part of high-temperature structural integrity evaluation of the small-scale PCHE prototype, we carried out high-temperature structural analysis modeling and macroscopic thermal and elastic structural analysis for the small-scale PCHE prototype under small-scale gas-loop test conditions. The modeling and analysis were performed as a precedent study prior to the performance test in the small-scale gas loop. The results obtained in this study will be compared with the test results for the small-scale PCHE. Moreover, these results will be used in the design of a medium-scale PCHE prototype

Scaling effects concerning the analysis of small break experiments

International Nuclear Information System (INIS)

Austregesilo Filho, H.

1985-01-01

Some scaling effects related to the experimental facilities as well as to the analytical models used for the design and safety analysis of nuclear power plants are discussed or the basis of phenomena expected to occur during small-break loss - of - coolant accidents. The results of isolated small-break experiments should not be directly extrapolated to the safety analysis of commercial reactors, due to the scaling distortions inherent to the test facilities. With respect to the analytical models used to simulate thermohydraulic processes in experimental facilities, their eventual dependence relative to the system dimension should be examined in order to assess their applicability to the safety analysis of commercial power plants. (Author) [pt

Perceiving Facial and Vocal Expressions of Emotion in Individuals with Williams Syndrome

Science.gov (United States)

Plesa-Skwerer, Daniela; Faja, Susan; Schofield, Casey; Verbalis, Alyssa; Tager-Flusberg, Helen

2006-01-01

People with Williams syndrome are extremely sociable, empathic, and expressive in communication. Some researchers suggest they may be especially sensitive to perceiving emotional expressions. We administered the Faces and Paralanguage subtests of the Diagnostic Analysis of Nonverbal Accuracy Scale (DANVA2), a standardized measure of emotion…

The scale analysis sequence for LWR fuel depletion

International Nuclear Information System (INIS)

Hermann, O.W.; Parks, C.V.

1991-01-01

The SCALE (Standardized Computer Analyses for Licensing Evaluation) code system is used extensively to perform away-from-reactor safety analysis (particularly criticality safety, shielding, heat transfer analyses) for spent light water reactor (LWR) fuel. Spent fuel characteristics such as radiation sources, heat generation sources, and isotopic concentrations can be computed within SCALE using the SAS2 control module. A significantly enhanced version of the SAS2 control module, which is denoted as SAS2H, has been made available with the release of SCALE-4. For each time-dependent fuel composition, SAS2H performs one-dimensional (1-D) neutron transport analyses (via XSDRNPM-S) of the reactor fuel assembly using a two-part procedure with two separate unit-cell-lattice models. The cross sections derived from a transport analysis at each time step are used in a point-depletion computation (via ORIGEN-S) that produces the burnup-dependent fuel composition to be used in the next spectral calculation. A final ORIGEN-S case is used to perform the complete depletion/decay analysis using the burnup-dependent cross sections. The techniques used by SAS2H and two recent applications of the code are reviewed in this paper. 17 refs., 5 figs., 5 tabs

Brain Responses to Dynamic Facial Expressions: A Normative Meta-Analysis

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Oksana Zinchenko

2018-06-01

Full Text Available Identifying facial expressions is crucial for social interactions. Functional neuroimaging studies show that a set of brain areas, such as the fusiform gyrus and amygdala, become active when viewing emotional facial expressions. The majority of functional magnetic resonance imaging (fMRI studies investigating face perception typically employ static images of faces. However, studies that use dynamic facial expressions (e.g., videos are accumulating and suggest that a dynamic presentation may be more sensitive and ecologically valid for investigating faces. By using quantitative fMRI meta-analysis the present study examined concordance of brain regions associated with viewing dynamic facial expressions. We analyzed data from 216 participants that participated in 14 studies, which reported coordinates for 28 experiments. Our analysis revealed bilateral fusiform and middle temporal gyri, left amygdala, left declive of the cerebellum and the right inferior frontal gyrus. These regions are discussed in terms of their relation to models of face processing.

Brain Responses to Dynamic Facial Expressions: A Normative Meta-Analysis.

Science.gov (United States)

Zinchenko, Oksana; Yaple, Zachary A; Arsalidou, Marie

2018-01-01

Identifying facial expressions is crucial for social interactions. Functional neuroimaging studies show that a set of brain areas, such as the fusiform gyrus and amygdala, become active when viewing emotional facial expressions. The majority of functional magnetic resonance imaging (fMRI) studies investigating face perception typically employ static images of faces. However, studies that use dynamic facial expressions (e.g., videos) are accumulating and suggest that a dynamic presentation may be more sensitive and ecologically valid for investigating faces. By using quantitative fMRI meta-analysis the present study examined concordance of brain regions associated with viewing dynamic facial expressions. We analyzed data from 216 participants that participated in 14 studies, which reported coordinates for 28 experiments. Our analysis revealed bilateral fusiform and middle temporal gyri, left amygdala, left declive of the cerebellum and the right inferior frontal gyrus. These regions are discussed in terms of their relation to models of face processing.

Global Gene Expression Analysis of Yeast Cells during Sake Brewing▿ †

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Wu, Hong; Zheng, Xiaohong; Araki, Yoshio; Sahara, Hiroshi; Takagi, Hiroshi; Shimoi, Hitoshi

2006-01-01

During the brewing of Japanese sake, Saccharomyces cerevisiae cells produce a high concentration of ethanol compared with other ethanol fermentation methods. We analyzed the gene expression profiles of yeast cells during sake brewing using DNA microarray analysis. This analysis revealed some characteristics of yeast gene expression during sake brewing and provided a scaffold for a molecular level understanding of the sake brewing process. PMID:16997994

[The French adaptation of the STAXI-2, C.D. Spielberger's State-trait anger expression inventory].

Science.gov (United States)

Borteyrou, X; Bruchon-Schweitzer, M; Spielberger, C D

2008-06-01

(principal axis analysis, followed by promax rotations). For the first part of the questionnaire (SAS), factor analysis suggested the presence of three factors with eigenvalues >1.0; but the factor structure obtained for males and females differed and was difficult to interpret. Moreover, the explained variance of Factors 2 and 3 was low. Velicer's MAP criteria and screen test established that one solution factor was more relevant. Confirmatory factor analysis suggested that the three factor solution was acceptable, but the unifactorial solution adjusted better to the data. For the second part of the questionnaire (TAS) factor analysis was conducted following the same procedure, and two factors were extracted. The explained variance of Factor 2 was very low. Velicer's MAP criteria and screen test suggested that the solution factor was more relevant. Moreover, the adjustment parameters of the original two-factor structure were not satisfactory. Finally, the analyses of the 32 items of anger expression and control yielded four factors with eigenvalues >1.0. All items loaded higher than 0.38 on the corresponding factor and lower than 0.30 in other factor. The factor structure of the AX scale was fairly robust, both for males and females. Internal consistency and test-retest reliability of the subscales were acceptable except for the SAS. The correlations of the six subscales with four criterion variables (Buss Durkee hostility inventory, Cook and Medley Ho scale, NEO PI-R Ho scale and Courtauld emotions control scale) were in the expected direction, establishing their convergent validity. In summary, the analysis reported in this study checked the factor structure of the STAXI-2 translated into French. The state anger dimension was also essentially confirmed, but no distinction was found between the three components: feeling angry, feeling like expressing anger verbally, and feeling like expressing anger physically. Moreover, the distinction between angry temperament and angry

Genomic analysis of expressed sequence tags in American black bear Ursus americanus

Science.gov (United States)

2010-01-01

Background Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). Results Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. Conclusion We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes. PMID:20338065

Genomic analysis of expressed sequence tags in American black bear Ursus americanus.

Science.gov (United States)

Zhao, Sen; Shao, Chunxuan; Goropashnaya, Anna V; Stewart, Nathan C; Xu, Yichi; Tøien, Øivind; Barnes, Brian M; Fedorov, Vadim B; Yan, Jun

2010-03-26

Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes.

Emotion Expression and Substance Use in Newly Parenting Adolescents and Young Adults.

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Desrosiers, Alethea; Sipsma, Heather; Divney, Anna; Magriples, Urania; Kershaw, Trace

2015-07-01

Deficits in emotion expression skills have been associated with alcohol and substance use, but the mechanisms through which these associations occur are not well understood. The current study investigated (a) associations between emotion expression and substance use (i.e., alcohol, cigarettes, and marijuana) in newly parenting adolescents and young adults and (b) whether symptoms of depression and stress mediate these associations in young mothers and fathers. Participants recruited from obstetrics and gynecology clinics completed the Center for Epidemiological Studies-Depression Scale, Perceived Stress Scale, Emotion Expression Scale for Children, and substance use items. Path analysis indicated that lower emotion expression at 6 months postpartum was significantly associated with more alcohol and marijuana use at 12 months postpartum for males but not females. Also among males, stress levels at 6 months postpartum partially mediated associations between emotion expression and alcohol and marijuana use at 12 months postpartum. Findings suggest that poor emotion expression skills are related to more substance use in young fathers, and levels of stress may partially account for this association. © 2015 Wiley Periodicals, Inc.

Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

Science.gov (United States)

Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

2014-01-01

Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

Semantic integration of gene expression analysis tools and data sources using software connectors

Science.gov (United States)

2013-01-01

Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools

A Serial Analysis of Gene Expression (SAGE) database analysis of chemosensitivity

DEFF Research Database (Denmark)

Stein, Wilfred D; Litman, Thomas; Fojo, Tito

2004-01-01

are their corresponding solid tumors. We used the Serial Analysis of Gene Expression (SAGE) database to identify differences between solid tumors and cell lines, hoping to detect genes that could potentially explain differences in drug sensitivity. SAGE libraries were available for both solid tumors and cell lines from...

Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

Directory of Open Access Journals (Sweden)

Yonglong Yu

2016-04-01

Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

Measuring the contribution of art therapy in multidisciplinary treatment of personality disorders: The construction of the Self-expression and Emotion Regulation in Art Therapy Scale (SERATS).

Science.gov (United States)

Haeyen, Suzanne; van Hooren, Susan; van der Veld, William M; Hutschemaekers, Giel

2018-02-01

Despite the use of art therapy in clinical practice, its appreciation and reported beneficial results, no instruments are available to measure specific effects of art therapy among patients with personality disorders cluster B/C in multidisciplinary treatment. In the present study, we described the development and psychometric evaluation of the Self-expression and Emotion Regulation in Art Therapy Scale (SERATS). Structural validity (exploratory and confirmatory factor analysis), reliability, construct validity and sensitivity to change were examined using two independent databases (n = 335; n = 34) of patients diagnosed with personality disorders cluster B/C. This resulted in a nine-item effect scale with a single factor with a high internal reliability and high test-retest reliability; it demonstrated discriminant validity and sensitivity to change. In conclusion, the SERATS is brief and content-valid and offers objective and reliable information on self-expression and emotion regulation in art therapy among patients with personality disorders cluster B/C. Although more research on construct validity is needed, the SERATS is a promising tool to be applied as an effect scale and as a monitoring tool during art therapy treatment. © 2017 The Authors Personality and Mental Health Published by John Wiley & Sons Ltd. © 2017 The Authors Personality and Mental Health Published by John Wiley & Sons Ltd.

Early Gene Expression in Wounded Human Keratinocytes Revealed by DNA Microarray Analysis

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Pascal Barbry

2006-04-01

Full Text Available Wound healing involves several steps: spreading of the cells, migration and proliferation. We have profiled gene expression during the early events of wound healing in normal human keratinocytes with a home-made DNA microarray containing about 1000 relevant human probes. An original wounding machine was used, that allows the wounding of up to 40% of the surface of a confluent monolayer of cultured cells grown on a Petri dish (compared with 5% with a classical ‘scratch’ method. The two aims of the present study were: (a to validate a limited number of genes by comparing the expression levels obtained with this technique with those found in the literature; (b to combine the use of the wounding machine with DNA microarray analysis for large-scale detection of the molecular events triggered during the early stages of the wound-healing process. The time-courses of RNA expression observed at 0.5, 1.5, 3, 6 and 15 h after wounding for genes such as c-Fos, c-Jun, Egr1, the plasminogen activator PLAU (uPA and the signal transducer and transcription activator STAT3, were consistent with previously published data. This suggests that our methodologies are able to perform quantitative measurement of gene expression. Transcripts encoding two zinc finger proteins, ZFP36 and ZNF161, and the tumour necrosis factor α-induced protein TNFAIP3, were also overexpressed after wounding. The role of the p38 mitogen-activated protein kinase (p38MAPK in wound healing was shown after the inhibition of p38 by SB203580, but our results also suggest the existence of surrogate activating pathways.

From Gene Expression to the Earth System: Isotopic Constraints on Nitrogen Cycling Across Scales

Science.gov (United States)

Houlton, B. Z.

2015-12-01

A central motivation of the Biogeosciences is to understand the cycling of biologically essential elements over multiple scales of space and time. This charge is vital to basic knowledge of Earth system functioning. It is also relevant to many of the global challenges we face, such as climate change, biodiversity conservation, and the multifaceted role of global fertilizer use in maximizing human health and well-being. Nitrogen is connected to all of these; yet it has been one of the more vexing elements to quantitatively appraise across systems and scales. Here I discuss how research in my group has been exploring the use of natural nitrogen isotope abundance (15N/14N) as a biogeochemical tracer - from the level of gene expression to nitrogen's role in global climate change. First, I present evidence for a positive correlation between the bacterial genes that encode for gaseous nitrogen production (i.e., nirS) and the 15N/14N of soil extractable nitrate pools across an array of terrestrial ecosystems. Second, I demonstrate how these local-scale results fit with our work on ecosystem-scale nitrogen isotope budgets, where we quantify a uniformly small isotope effect (i.e., supports the working hypothesis that bacterial denitrification is the major fractionating pathway of nitrogen loss from the terrestrial biosphere, much like the global ocean.

H2@Scale Resource and Market Analysis

Energy Technology Data Exchange (ETDEWEB)

Ruth, Mark

2017-07-12

This presentation overviews progress to date on the H2@Scale resource and market analysis work. The work finds, for example, that hydrogen demand of 60 MMT/yr is possible when transportation and industry are considered; resources are available to meet that demand; using renewable resources would reduce emissions and fossil use by over 15%; further impacts are possible when considering synergistic benefits; additional analysis is underway to improve understanding of potential markets and synergistic impacts; and further analysis will be necessary to estimate impacts due to spatial characteristics, feedback effects in the economy, and inertia characteristics.

Detecting differential protein expression in large-scale population proteomics

Energy Technology Data Exchange (ETDEWEB)

Ryu, Soyoung; Qian, Weijun; Camp, David G.; Smith, Richard D.; Tompkins, Ronald G.; Davis, Ronald W.; Xiao, Wenzhong

2014-06-17

Mass spectrometry-based high-throughput quantitative proteomics shows great potential in clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, methods are needed to appropriately handle issues/challenges unique to mass spectrometry data in order to detect as many biomarker proteins as possible. One issue is that different mass spectrometry experiments generate quite different total numbers of quantified peptides, which can result in more missing peptide abundances in an experiment with a smaller total number of quantified peptides. Another issue is that the quantification of peptides is sometimes absent, especially for less abundant peptides and such missing values contain the information about the peptide abundance. Here, we propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.

Semi-supervised consensus clustering for gene expression data analysis

OpenAIRE

Wang, Yunli; Pan, Youlian

2014-01-01

Background Simple clustering methods such as hierarchical clustering and k-means are widely used for gene expression data analysis; but they are unable to deal with noise and high dimensionality associated with the microarray gene expression data. Consensus clustering appears to improve the robustness and quality of clustering results. Incorporating prior knowledge in clustering process (semi-supervised clustering) has been shown to improve the consistency between the data partitioning and do...

Digital Gene Expression Profiling Analysis of Aged Mice under Moxibustion Treatment

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Nan Liu

2018-01-01

Full Text Available Aging is closely connected with death, progressive physiological decline, and increased risk of diseases, such as cancer, arteriosclerosis, heart disease, hypertension, and neurodegenerative diseases. It is reported that moxibustion can treat more than 300 kinds of diseases including aging related problems and can improve immune function and physiological functions. The digital gene expression profiling of aged mice with or without moxibustion treatment was investigated and the mechanisms of moxibustion in aged mice were speculated by gene ontology and pathway analysis in the study. Almost 145 million raw reads were obtained by digital gene expression analysis and about 140 million (96.55% were clean reads. Five differentially expressed genes with an adjusted P value 1 were identified between the control and moxibustion groups. They were Gm6563, Gm8116, Rps26-ps1, Nat8f4, and Igkv3-12. Gene ontology analysis was carried out by the GOseq R package and functional annotations of the differentially expressed genes related to translation, mRNA export from nucleus, mRNA transport, nuclear body, acetyltransferase activity, and so on. Kyoto Encyclopedia of Genes and Genomes database was used for pathway analysis and ribosome was the most significantly enriched pathway term.

Paired Expression Analysis of Tumor Cell Surface Antigens

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Rimas J. Orentas

2017-08-01

Full Text Available Adoptive immunotherapy with antibody-based therapy or with T cells transduced to express chimeric antigen receptors (CARs is useful to the extent that the cell surface membrane protein being targeted is not expressed on normal tissues. The most successful CAR-based (anti-CD19 or antibody-based therapy (anti-CD20 in hematologic malignancies has the side effect of eliminating the normal B cell compartment. Targeting solid tumors may not provide a similar expendable marker. Beyond antibody to Her2/NEU and EGFR, very few antibody-based and no CAR-based therapies have seen broad clinical application for solid tumors. To expand the way in which the surfaceome of solid tumors can be analyzed, we created an algorithm that defines the pairwise relative overexpression of surface antigens. This enables the development of specific immunotherapies that require the expression of two discrete antigens on the surface of the tumor target. This dyad analysis was facilitated by employing the Hotelling’s T-squared test (Hotelling–Lawley multivariate analysis of variance for two independent variables in comparison to a third constant entity (i.e., gene expression levels in normal tissues. We also present a unique consensus scoring mechanism for identifying transcripts that encode cell surface proteins. The unique application of our bioinformatics processing pipeline and statistical tools allowed us to compare the expression of two membrane protein targets as a pair, and to propose a new strategy based on implementing immunotherapies that require both antigens to be expressed on the tumor cell surface to trigger therapeutic effector mechanisms. Specifically, we found that, for MYCN amplified neuroblastoma, pairwise expression of ACVR2B or anaplastic lymphoma kinase (ALK with GFRA3, GFRA2, Cadherin 24, or with one another provided the strongest hits. For MYCN, non-amplified stage 4 neuroblastoma, neurotrophic tyrosine kinase 1, or ALK paired with GFRA2, GFRA3, SSK

Gait in children with cerebral palsy : observer reliability of Physician Rating Scale and Edinburgh Visual Gait Analysis Interval Testing scale

NARCIS (Netherlands)

Maathuis, KGB; van der Schans, CP; van Iperen, A; Rietman, HS; Geertzen, JHB

2005-01-01

The aim of this study was to test the inter- and intra-observer reliability of the Physician Rating Scale (PRS) and the Edinburgh Visual Gait Analysis Interval Testing (GAIT) scale for use in children with cerebral palsy (CP). Both assessment scales are quantitative observational scales, evaluating

Scale symmetry and virial theorem

International Nuclear Information System (INIS)

Westenholz, C. von

1978-01-01

Scale symmetry (or dilatation invariance) is discussed in terms of Noether's Theorem expressed in terms of a symmetry group action on phase space endowed with a symplectic structure. The conventional conceptual approach expressing invariance of some Hamiltonian under scale transformations is re-expressed in alternate form by infinitesimal automorphisms of the given symplectic structure. That is, the vector field representing scale transformations leaves the symplectic structure invariant. In this model, the conserved quantity or constant of motion related to scale symmetry is the virial. It is shown that the conventional virial theorem can be derived within this framework

Expansion of the wilderness values scale with three sub-scales: Personal maintenance, expression and learning, and societal maintenance

Science.gov (United States)

Rudy M. Schuster; Ken Cordell; Gary T. Green

2007-01-01

The purpose of this research was to expand the wilderness value scale administered in the 1994 and 2000 versions of the National Survey on Recreation and the Environment using questions included in the 2003 NSRE. A data set of 1,900 cases was randomly split in half. Validity of the additional questions was tested using principal component analysis, a confirmatory...

Molecular responses and expression analysis of genes in a ...

African Journals Online (AJOL)

STORAGESEVER

2009-06-17

Jun 17, 2009 ... Molecular responses and expression analysis of genes in a xerophytic desert shrub Haloxylon ammodendron .... physiological determination and cDNA-AFLP analysis, three groups of seeds were sowed in pots with sand and .... HaDR27. U. 234. PDR-like ABC transporter. AT1G59870. HaDR28. U. 135.

An Instructional Module on Mokken Scale Analysis

Science.gov (United States)

Wind, Stefanie A.

2017-01-01

Mokken scale analysis (MSA) is a probabilistic-nonparametric approach to item response theory (IRT) that can be used to evaluate fundamental measurement properties with less strict assumptions than parametric IRT models. This instructional module provides an introduction to MSA as a probabilistic-nonparametric framework in which to explore…

Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

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Kai Wang

2009-12-01

Full Text Available Co-expression networks are routinely used to study human diseases like obesity and diabetes. Systematic comparison of these networks between species has the potential to elucidate common mechanisms that are conserved between human and rodent species, as well as those that are species-specific characterizing evolutionary plasticity. We developed a semi-parametric meta-analysis approach for combining gene-gene co-expression relationships across expression profile datasets from multiple species. The simulation results showed that the semi-parametric method is robust against noise. When applied to human, mouse, and rat liver co-expression networks, our method out-performed existing methods in identifying gene pairs with coherent biological functions. We identified a network conserved across species that highlighted cell-cell signaling, cell-adhesion and sterol biosynthesis as main biological processes represented in genome-wide association study candidate gene sets for blood lipid levels. We further developed a heterogeneity statistic to test for network differences among multiple datasets, and demonstrated that genes with species-specific interactions tend to be under positive selection throughout evolution. Finally, we identified a human-specific sub-network regulated by RXRG, which has been validated to play a different role in hyperlipidemia and Type 2 diabetes between human and mouse. Taken together, our approach represents a novel step forward in integrating gene co-expression networks from multiple large scale datasets to leverage not only common information but also differences that are dataset-specific.

Neisseria meningitidis rifampicin resistant strains: analysis of protein differentially expressed

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Schininà Maria

2010-09-01

Full Text Available Abstract Background Several mutations have been described as responsible for rifampicin resistance in Neisseria meningitidis. However, the intriguing question on why these strains are so rare remains open. The aim of this study was to investigate the protein content and to identify differential expression in specific proteins in two rifampicin resistant and one susceptible meningococci using two-dimensional electrophoresis (2-DE combined with mass spectrometry. Results In our experimental conditions, able to resolve soluble proteins with an isoelectric point between 4 and 7, twenty-three proteins have been found differentially expressed in the two resistant strains compared to the susceptible. Some of them, involved in the main metabolic pathways, showed an increased expression, mainly in the catabolism of pyruvate and in the tricarboxylic acid cycle. A decreased expression of proteins belonging to gene regulation and to those involved in the folding of polypeptides has also been observed. 2-DE analysis showed the presence of four proteins displaying a shift in their isoelectric point in both resistant strains, confirmed by the presence of amino acid changes in the sequence analysis, absent in the susceptible. Conclusions The analysis of differentially expressed proteins suggests that an intricate series of events occurs in N. meningitidis rifampicin resistant strains and the results here reported may be considered a starting point in understanding their decreased invasion capacity. In fact, they support the hypothesis that the presence of more than one protein differentially expressed, having a role in the metabolism of the meningococcus, influences its ability to infect and to spread in the population. Different reports have described and discussed how a drug resistant pathogen shows a high biological cost for survival and that may also explain why, for some pathogens, the rate of resistant organisms is relatively low considering the

Computerised analysis of facial emotion expression in eating disorders

Science.gov (United States)

2017-01-01

Background Problems with social-emotional processing are known to be an important contributor to the development and maintenance of eating disorders (EDs). Diminished facial communication of emotion has been frequently reported in individuals with anorexia nervosa (AN). Less is known about facial expressivity in bulimia nervosa (BN) and in people who have recovered from AN (RecAN). This study aimed to pilot the use of computerised facial expression analysis software to investigate emotion expression across the ED spectrum and recovery in a large sample of participants. Method 297 participants with AN, BN, RecAN, and healthy controls were recruited. Participants watched film clips designed to elicit happy or sad emotions, and facial expressions were then analysed using FaceReader. Results The finding mirrored those from previous work showing that healthy control and RecAN participants expressed significantly more positive emotions during the positive clip compared to the AN group. There were no differences in emotion expression during the sad film clip. Discussion These findings support the use of computerised methods to analyse emotion expression in EDs. The findings also demonstrate that reduced positive emotion expression is likely to be associated with the acute stage of AN illness, with individuals with BN showing an intermediate profile. PMID:28575109

Computerised analysis of facial emotion expression in eating disorders.

Science.gov (United States)

Leppanen, Jenni; Dapelo, Marcela Marin; Davies, Helen; Lang, Katie; Treasure, Janet; Tchanturia, Kate

2017-01-01

Problems with social-emotional processing are known to be an important contributor to the development and maintenance of eating disorders (EDs). Diminished facial communication of emotion has been frequently reported in individuals with anorexia nervosa (AN). Less is known about facial expressivity in bulimia nervosa (BN) and in people who have recovered from AN (RecAN). This study aimed to pilot the use of computerised facial expression analysis software to investigate emotion expression across the ED spectrum and recovery in a large sample of participants. 297 participants with AN, BN, RecAN, and healthy controls were recruited. Participants watched film clips designed to elicit happy or sad emotions, and facial expressions were then analysed using FaceReader. The finding mirrored those from previous work showing that healthy control and RecAN participants expressed significantly more positive emotions during the positive clip compared to the AN group. There were no differences in emotion expression during the sad film clip. These findings support the use of computerised methods to analyse emotion expression in EDs. The findings also demonstrate that reduced positive emotion expression is likely to be associated with the acute stage of AN illness, with individuals with BN showing an intermediate profile.

A family of E. coli expression vectors for laboratory scale and high throughput soluble protein production

Directory of Open Access Journals (Sweden)

Bottomley Stephen P

2006-03-01

Full Text Available Abstract Background In the past few years, both automated and manual high-throughput protein expression and purification has become an accessible means to rapidly screen and produce soluble proteins for structural and functional studies. However, many of the commercial vectors encoding different solubility tags require different cloning and purification steps for each vector, considerably slowing down expression screening. We have developed a set of E. coli expression vectors with different solubility tags that allow for parallel cloning from a single PCR product and can be purified using the same protocol. Results The set of E. coli expression vectors, encode for either a hexa-histidine tag or the three most commonly used solubility tags (GST, MBP, NusA and all with an N-terminal hexa-histidine sequence. The result is two-fold: the His-tag facilitates purification by immobilised metal affinity chromatography, whilst the fusion domains act primarily as solubility aids during expression, in addition to providing an optional purification step. We have also incorporated a TEV recognition sequence following the solubility tag domain, which allows for highly specific cleavage (using TEV protease of the fusion protein to yield native protein. These vectors are also designed for ligation-independent cloning and they possess a high-level expressing T7 promoter, which is suitable for auto-induction. To validate our vector system, we have cloned four different genes and also one gene into all four vectors and used small-scale expression and purification techniques. We demonstrate that the vectors are capable of high levels of expression and that efficient screening of new proteins can be readily achieved at the laboratory level. Conclusion The result is a set of four rationally designed vectors, which can be used for streamlined cloning, expression and purification of target proteins in the laboratory and have the potential for being adaptable to a high

Transcriptome Sequencing, De Novo Assembly and Differential Gene Expression Analysis of the Early Development of Acipenser baeri.

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Wei Song

Full Text Available The molecular mechanisms that drive the development of the endangered fossil fish species Acipenser baeri are difficult to study due to the lack of genomic data. Recent advances in sequencing technologies and the reducing cost of sequencing offer exclusive opportunities for exploring important molecular mechanisms underlying specific biological processes. This manuscript describes the large scale sequencing and analyses of mRNA from Acipenser baeri collected at five development time points using the Illumina Hiseq2000 platform. The sequencing reads were de novo assembled and clustered into 278167 unigenes, of which 57346 (20.62% had 45837 known homologues proteins in Uniprot protein databases while 11509 proteins matched with at least one sequence of assembled unigenes. The remaining 79.38% of unigenes could stand for non-coding unigenes or unigenes specific to A. baeri. A number of 43062 unigenes were annotated into functional categories via Gene Ontology (GO annotation whereas 29526 unigenes were associated with 329 pathways by mapping to KEGG database. Subsequently, 3479 differentially expressed genes were scanned within developmental stages and clustered into 50 gene expression profiles. Genes preferentially expressed at each stage were also identified. Through GO and KEGG pathway enrichment analysis, relevant physiological variations during the early development of A. baeri could be better cognized. Accordingly, the present study gives insights into the transcriptome profile of the early development of A. baeri, and the information contained in this large scale transcriptome will provide substantial references for A. baeri developmental biology and promote its aquaculture research.

Front-end vision and multi-scale image analysis multi-scale computer vision theory and applications, written in Mathematica

CERN Document Server

Romeny, Bart M Haar

2008-01-01

Front-End Vision and Multi-Scale Image Analysis is a tutorial in multi-scale methods for computer vision and image processing. It builds on the cross fertilization between human visual perception and multi-scale computer vision (`scale-space') theory and applications. The multi-scale strategies recognized in the first stages of the human visual system are carefully examined, and taken as inspiration for the many geometric methods discussed. All chapters are written in Mathematica, a spectacular high-level language for symbolic and numerical manipulations. The book presents a new and effective

[Scale effect of Nanjing urban green infrastructure network pattern and connectivity analysis.

Science.gov (United States)

Yu, Ya Ping; Yin, Hai Wei; Kong, Fan Hua; Wang, Jing Jing; Xu, Wen Bin

2016-07-01

Based on ArcGIS, Erdas, GuidosToolbox, Conefor and other software platforms, using morphological spatial pattern analysis (MSPA) and landscape connectivity analysis methods, this paper quantitatively analysed the scale effect, edge effect and distance effect of the Nanjing urban green infrastructure network pattern in 2013 by setting different pixel sizes (P) and edge widths in MSPA analysis, and setting different dispersal distance thresholds in landscape connectivity analysis. The results showed that the type of landscape acquired based on the MSPA had a clear scale effect and edge effect, and scale effects only slightly affected landscape types, whereas edge effects were more obvious. Different dispersal distances had a great impact on the landscape connectivity, 2 km or 2.5 km dispersal distance was a critical threshold for Nanjing. When selecting the pixel size 30 m of the input data and the edge wide 30 m used in the morphological model, we could get more detailed landscape information of Nanjing UGI network. Based on MSPA and landscape connectivity, analysis of the scale effect, edge effect, and distance effect on the landscape types of the urban green infrastructure (UGI) network was helpful for selecting the appropriate size, edge width, and dispersal distance when developing these networks, and for better understanding the spatial pattern of UGI networks and the effects of scale and distance on the ecology of a UGI network. This would facilitate a more scientifically valid set of design parameters for UGI network spatiotemporal pattern analysis. The results of this study provided an important reference for Nanjing UGI networks and a basis for the analysis of the spatial and temporal patterns of medium-scale UGI landscape networks in other regions.

A Normalization-Free and Nonparametric Method Sharpens Large-Scale Transcriptome Analysis and Reveals Common Gene Alteration Patterns in Cancers.

Science.gov (United States)

Li, Qi-Gang; He, Yong-Han; Wu, Huan; Yang, Cui-Ping; Pu, Shao-Yan; Fan, Song-Qing; Jiang, Li-Ping; Shen, Qiu-Shuo; Wang, Xiao-Xiong; Chen, Xiao-Qiong; Yu, Qin; Li, Ying; Sun, Chang; Wang, Xiangting; Zhou, Jumin; Li, Hai-Peng; Chen, Yong-Bin; Kong, Qing-Peng

2017-01-01

Heterogeneity in transcriptional data hampers the identification of differentially expressed genes (DEGs) and understanding of cancer, essentially because current methods rely on cross-sample normalization and/or distribution assumption-both sensitive to heterogeneous values. Here, we developed a new method, Cross-Value Association Analysis (CVAA), which overcomes the limitation and is more robust to heterogeneous data than the other methods. Applying CVAA to a more complex pan-cancer dataset containing 5,540 transcriptomes discovered numerous new DEGs and many previously rarely explored pathways/processes; some of them were validated, both in vitro and in vivo , to be crucial in tumorigenesis, e.g., alcohol metabolism ( ADH1B ), chromosome remodeling ( NCAPH ) and complement system ( Adipsin ). Together, we present a sharper tool to navigate large-scale expression data and gain new mechanistic insights into tumorigenesis.

Meta-analysis of peripheral blood gene expression modules for COPD phenotypes.

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Dominik Reinhold

Full Text Available Chronic obstructive pulmonary disease (COPD occurs typically in current or former smokers, but only a minority of people with smoking history develops the disease. Besides environmental factors, genetics is an important risk factor for COPD. However, the relationship between genetics, environment and phenotypes is not well understood. Sample sizes for genome-wide expression studies based on lung tissue have been small due to the invasive nature of sample collection. Increasing evidence for the systemic nature of the disease makes blood a good alternative source to study the disease, but there have also been few large-scale blood genomic studies in COPD. Due to the complexity and heterogeneity of COPD, examining groups of interacting genes may have more relevance than identifying individual genes. Therefore, we used Weighted Gene Co-expression Network Analysis to find groups of genes (modules that are highly connected. However, module definitions may vary between individual data sets. To alleviate this problem, we used a consensus module definition based on two cohorts, COPDGene and ECLIPSE. We studied the relationship between the consensus modules and COPD phenotypes airflow obstruction and emphysema. We also used these consensus module definitions on an independent cohort (TESRA and performed a meta analysis involving all data sets. We found several modules that are associated with COPD phenotypes, are enriched in functional categories and are overrepresented for cell-type specific genes. Of the 14 consensus modules, three were strongly associated with airflow obstruction (meta p ≤ 0.0002, and two had some association with emphysema (meta p ≤ 0.06; some associations were stronger in the case-control cohorts, and others in the cases-only subcohorts. Gene Ontology terms that were overrepresented included "immune response" and "defense response." The cell types whose type-specific genes were overrepresented in modules (p < 0.05 included

Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline.

Science.gov (United States)

Chang, Lun-Ching; Lin, Hui-Min; Sibille, Etienne; Tseng, George C

2013-12-21

As high-throughput genomic technologies become accurate and affordable, an increasing number of data sets have been accumulated in the public domain and genomic information integration and meta-analysis have become routine in biomedical research. In this paper, we focus on microarray meta-analysis, where multiple microarray studies with relevant biological hypotheses are combined in order to improve candidate marker detection. Many methods have been developed and applied in the literature, but their performance and properties have only been minimally investigated. There is currently no clear conclusion or guideline as to the proper choice of a meta-analysis method given an application; the decision essentially requires both statistical and biological considerations. We performed 12 microarray meta-analysis methods for combining multiple simulated expression profiles, and such methods can be categorized for different hypothesis setting purposes: (1) HS(A): DE genes with non-zero effect sizes in all studies, (2) HS(B): DE genes with non-zero effect sizes in one or more studies and (3) HS(r): DE gene with non-zero effect in "majority" of studies. We then performed a comprehensive comparative analysis through six large-scale real applications using four quantitative statistical evaluation criteria: detection capability, biological association, stability and robustness. We elucidated hypothesis settings behind the methods and further apply multi-dimensional scaling (MDS) and an entropy measure to characterize the meta-analysis methods and data structure, respectively. The aggregated results from the simulation study categorized the 12 methods into three hypothesis settings (HS(A), HS(B), and HS(r)). Evaluation in real data and results from MDS and entropy analyses provided an insightful and practical guideline to the choice of the most suitable method in a given application. All source files for simulation and real data are available on the author's publication website.

Implementation of Grid-computing Framework for Simulation in Multi-scale Structural Analysis

Directory of Open Access Journals (Sweden)

Data Iranata

2010-05-01

Full Text Available A new grid-computing framework for simulation in multi-scale structural analysis is presented. Two levels of parallel processing will be involved in this framework: multiple local distributed computing environments connected by local network to form a grid-based cluster-to-cluster distributed computing environment. To successfully perform the simulation, a large-scale structural system task is decomposed into the simulations of a simplified global model and several detailed component models using various scales. These correlated multi-scale structural system tasks are distributed among clusters and connected together in a multi-level hierarchy and then coordinated over the internet. The software framework for supporting the multi-scale structural simulation approach is also presented. The program architecture design allows the integration of several multi-scale models as clients and servers under a single platform. To check its feasibility, a prototype software system has been designed and implemented to perform the proposed concept. The simulation results show that the software framework can increase the speedup performance of the structural analysis. Based on this result, the proposed grid-computing framework is suitable to perform the simulation of the multi-scale structural analysis.

Reliability and validity analysis of modified Nursing Stress Scale for Indian population.

Science.gov (United States)

Pathak, Vasundhara; Chakraborty, Tania; Mukhopadhyay, Suman

2013-01-01

The original Nursing Stress Scale (NSS) was structurally modified according to results of factorial analysis and a new scale was named as modified nursing stress scale (MNSS). This is the first study to modify and validate NSS for Indian nursing population. Factorial analysis showed different factor loading for two subscales and items were shifted according to their loading to provide a more meaningful structure. After relocation of Items 13, 14, and 15 into first factor, this factor was renamed as "emotional and painful conditions of patients" to provide a more appropriate name to the first factor. Items 24, 25, 26, 27, 28, and 29 were found to be distributed under two different factors; one of these two was renamed as "unpredictable changes" and another retained its original name (i.e., workload). This distribution was also supported by rational analysis. All other items were distributed under factors as in the original scale. Rest of the validity assessment was done with the modified scale. Thus, with minor changes in structure, the scale was found to have better content validity.

Psychometric analysis of two new scales: the evidence-based practice nursing leadership and work environment scales.

Science.gov (United States)

Pryse, Yvette; McDaniel, Anna; Schafer, John

2014-08-01

Those in nursing have been charged with practicing to the full extent of their education and training by the Institute of Medicine. Therefore, evidence-based practice (EBP) has never been more important to nursing than in the current healthcare environment. Frequently the burden of EBP is the responsibility of the bedside practitioner, but has been found to be a process that requires leadership and organizational support. A key underlying component of a strong EBP environment includes effective communications and collaboration among staff and nursing leadership. Developing measurement tools that examine the milieu and nursing leadership in which the staff nurse practices is an important component of understanding the factors that support or hinder EBP. The aim of this study is to report on the development and analysis of two new scales designed to explore leadership and organizational support for EBP. The EBP Nursing Leadership Scale (10 items) examines the staff nurses perception of support provided by the nurse manager for EBP, and the EBP Work Environment Scale (8 items) examines organizational support for EBP. Staff nurses who worked at least .5 FTE in direct patient care, from two inner city hospitals (n = 422) completed the scales. The scales were evaluated for internal consistency reliability with the Cronbach alpha technique, content validity using a panel of experts, and construct validity by The content validity index computed from expert rankings was .78 to 1.0 with an average of.96. Cronbach's alpha was .96 (n = 422) for the EBP Nursing Leadership Scale and .86 (n = 422) for the EBP Work Environment Scale. Factor analysis confirmed that each scale measured a unidimensional construct (p organizational influences on EBP. © 2014 Sigma Theta Tau International.

Rasch analysis suggested three unidimensional domains for Affiliate Stigma Scale: additional psychometric evaluation.

Science.gov (United States)

Chang, Chih-Cheng; Su, Jian-An; Tsai, Ching-Shu; Yen, Cheng-Fang; Liu, Jiun-Horng; Lin, Chung-Ying

2015-06-01

To examine the psychometrics of the Affiliate Stigma Scale using rigorous psychometric analysis: classical test theory (CTT) (traditional) and Rasch analysis (modern). Differential item functioning (DIF) items were also tested using Rasch analysis. Caregivers of relatives with mental illness (n = 453; mean age: 53.29 ± 13.50 years) were recruited from southern Taiwan. Each participant filled out four questionnaires: Affiliate Stigma Scale, Rosenberg Self-Esteem Scale, Beck Anxiety Inventory, and one background information sheet. CTT analyses showed that the Affiliate Stigma Scale had satisfactory internal consistency (α = 0.85-0.94) and concurrent validity (Rosenberg Self-Esteem Scale: r = -0.52 to -0.46; Beck Anxiety Inventory: r = 0.27-0.34). Rasch analyses supported the unidimensionality of three domains in the Affiliate Stigma Scale and indicated four DIF items (affect domain: 1; cognitive domain: 3) across gender. Our findings, based on rigorous statistical analysis, verified the psychometrics of the Affiliate Stigma Scale and reported its DIF items. We conclude that the three domains of the Affiliate Stigma Scale can be separately used and are suitable for measuring the affiliate stigma of caregivers of relatives with mental illness. Copyright © 2015 Elsevier Inc. All rights reserved.

The first facial expression recognition and analysis challenge

NARCIS (Netherlands)

Valstar, Michel F.; Jiang, Bihan; Mehu, Marc; Pantic, Maja; Scherer, Klaus

Automatic Facial Expression Recognition and Analysis, in particular FACS Action Unit (AU) detection and discrete emotion detection, has been an active topic in computer science for over two decades. Standardisation and comparability has come some way; for instance, there exist a number of commonly

CMT scaling analysis and distortion evaluation in passive integral test facility

International Nuclear Information System (INIS)

Deng Chengcheng; Qin Benke; Wang Han; Chang Huajian

2013-01-01

Core makeup tank (CMT) is the crucial device of AP1000 passive core cooling system, and reasonable scaling analysis of CMT plays a key role in the design of passive integral test facilities. H2TS method was used to perform scaling analysis for both circulating mode and draining mode of CMT. And then, the similarity criteria for CMT important processes were applied in the CMT scaling design of the ACME (advanced core-cooling mechanism experiment) facility now being built in China. Furthermore, the scaling distortion results of CMT characteristic Ⅱ groups of ACME were calculated. At last, the reason of scaling distortion was analyzed and the distortion evaluation was conducted for ACME facility. The dominant processes of CMT circulating mode can be adequately simulated in the ACME facility, but the steam condensation process during CMT draining is not well preserved because the excessive CMT mass leads to more energy to be absorbed by cold metal. However, comprehensive analysis indicates that the ACME facility with high-pressure simulation scheme is able to properly represent CMT's important phenomena and processes of prototype nuclear plant. (authors)

Stored energy analysis in the scaled-down test facilities

International Nuclear Information System (INIS)

Deng, Chengcheng; Chang, Huajian; Qin, Benke; Wu, Qiao

2016-01-01

Highlights: • Three methods are developed to evaluate stored energy in the scaled-down test facilities. • The mechanism behind stored energy distortion in the test facilities is revealed. • The application of stored energy analysis is demonstrated for the ACME facility of China. - Abstract: In the scaled-down test facilities that simulate the accident transient process of the prototype nuclear power plant, the stored energy release in the metal structures has an important influence on the accuracy and effectiveness of the experimental data. Three methods of stored energy analysis are developed, and the mechanism behind stored energy distortion in the test facilities is revealed. Moreover, the application of stored energy analysis is demonstrated for the ACME test facility newly built in China. The results show that the similarity requirements of three methods analyzing the stored energy release decrease gradually. The physical mechanism of stored energy release process can be characterized by the dimensionless numbers including Stanton number, Fourier number and Biot number. Under the premise of satisfying the overall similarity of natural circulation, the stored energy release process in the scale-down test facilities cannot maintain exact similarity. The results of the application of stored energy analysis illustrate that both the transient release process and integral total stored energy of the reactor pressure vessel wall of CAP1400 power plant can be well reproduced in the ACME test facility.

Rasch model analysis of the Depression, Anxiety and Stress Scales (DASS).

Science.gov (United States)

Shea, Tracey L; Tennant, Alan; Pallant, Julie F

2009-05-09

There is a growing awareness of the need for easily administered, psychometrically sound screening tools to identify individuals with elevated levels of psychological distress. Although support has been found for the psychometric properties of the Depression, Anxiety and Stress Scales (DASS) using classical test theory approaches it has not been subjected to Rasch analysis. The aim of this study was to use Rasch analysis to assess the psychometric properties of the DASS-21 scales, using two different administration modes. The DASS-21 was administered to 420 participants with half the sample responding to a web-based version and the other half completing a traditional pencil-and-paper version. Conformity of DASS-21 scales to a Rasch partial credit model was assessed using the RUMM2020 software. To achieve adequate model fit it was necessary to remove one item from each of the DASS-21 subscales. The reduced scales showed adequate internal consistency reliability, unidimensionality and freedom from differential item functioning for sex, age and mode of administration. Analysis of all DASS-21 items combined did not support its use as a measure of general psychological distress. A scale combining the anxiety and stress items showed satisfactory fit to the Rasch model after removal of three items. The results provide support for the measurement properties, internal consistency reliability, and unidimensionality of three slightly modified DASS-21 scales, across two different administration methods. The further use of Rasch analysis on the DASS-21 in larger and broader samples is recommended to confirm the findings of the current study.

Rasch model analysis of the Depression, Anxiety and Stress Scales (DASS)

Science.gov (United States)

Shea, Tracey L; Tennant, Alan; Pallant, Julie F

2009-01-01

Background There is a growing awareness of the need for easily administered, psychometrically sound screening tools to identify individuals with elevated levels of psychological distress. Although support has been found for the psychometric properties of the Depression, Anxiety and Stress Scales (DASS) using classical test theory approaches it has not been subjected to Rasch analysis. The aim of this study was to use Rasch analysis to assess the psychometric properties of the DASS-21 scales, using two different administration modes. Methods The DASS-21 was administered to 420 participants with half the sample responding to a web-based version and the other half completing a traditional pencil-and-paper version. Conformity of DASS-21 scales to a Rasch partial credit model was assessed using the RUMM2020 software. Results To achieve adequate model fit it was necessary to remove one item from each of the DASS-21 subscales. The reduced scales showed adequate internal consistency reliability, unidimensionality and freedom from differential item functioning for sex, age and mode of administration. Analysis of all DASS-21 items combined did not support its use as a measure of general psychological distress. A scale combining the anxiety and stress items showed satisfactory fit to the Rasch model after removal of three items. Conclusion The results provide support for the measurement properties, internal consistency reliability, and unidimensionality of three slightly modified DASS-21 scales, across two different administration methods. The further use of Rasch analysis on the DASS-21 in larger and broader samples is recommended to confirm the findings of the current study. PMID:19426512

Sports dance artistic expression culture analysis

OpenAIRE

Chen Zegang

2017-01-01

At present, the sports dance has entered every stage of the people’s life, has become the public’s favorite sport. Sports dance has been well developed. This article mainly uses the literature material law to carry on the detailed analysis to the sports dance constitution, elaborated in detail the sports dance artistic expression. The composition of sports dance elements; sports dance is a form of dance art show; sports dance through the dance art can be divided into three aspects, namely, fo...

Microarray Gene Expression Analysis to Evaluate Cell Type Specific Expression of Targets Relevant for Immunotherapy of Hematological Malignancies.

Directory of Open Access Journals (Sweden)

M J Pont

Full Text Available Cellular immunotherapy has proven to be effective in the treatment of hematological cancers by donor lymphocyte infusion after allogeneic hematopoietic stem cell transplantation and more recently by targeted therapy with chimeric antigen or T-cell receptor-engineered T cells. However, dependent on the tissue distribution of the antigens that are targeted, anti-tumor responses can be accompanied by undesired side effects. Therefore, detailed tissue distribution analysis is essential to estimate potential efficacy and toxicity of candidate targets for immunotherapy of hematological malignancies. We performed microarray gene expression analysis of hematological malignancies of different origins, healthy hematopoietic cells and various non-hematopoietic cell types from organs that are often targeted in detrimental immune responses after allogeneic stem cell transplantation leading to graft-versus-host disease. Non-hematopoietic cells were also cultured in the presence of IFN-γ to analyze gene expression under inflammatory circumstances. Gene expression was investigated by Illumina HT12.0 microarrays and quality control analysis was performed to confirm the cell-type origin and exclude contamination of non-hematopoietic cell samples with peripheral blood cells. Microarray data were validated by quantitative RT-PCR showing strong correlations between both platforms. Detailed gene expression profiles were generated for various minor histocompatibility antigens and B-cell surface antigens to illustrate the value of the microarray dataset to estimate efficacy and toxicity of candidate targets for immunotherapy. In conclusion, our microarray database provides a relevant platform to analyze and select candidate antigens with hematopoietic (lineage-restricted expression as potential targets for immunotherapy of hematological cancers.

Principal component analysis of the Norwegian version of the quality of life in late-stage dementia scale.

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Mjørud, Marit; Kirkevold, Marit; Røsvik, Janne; Engedal, Knut

2014-01-01

To investigate which factors the Quality of Life in Late-Stage Dementia (QUALID) scale holds when used among people with dementia (pwd) in nursing homes and to find out how the symptom load varies across the different severity levels of dementia. We included 661 pwd [mean age ± SD, 85.3 ± 8.6 years; 71.4% women]. The QUALID and the Clinical Dementia Rating (CDR) scale were applied. A principal component analysis (PCA) with varimax rotation and Kaiser normalization was applied to test the factor structure. Nonparametric analyses were applied to examine differences of symptom load across the three CDR groups. The mean QUALID score was 21.5 (±7.1), and the CDR scores of the three groups were 1 in 22.5%, 2 in 33.6% and 3 in 43.9%. The results of the statistical measures employed were the following: Crohnbach's α of QUALID, 0.74; Bartlett's test of sphericity, p Kaiser-Meyer-Olkin measure, 0.77. The PCA analysis resulted in three components accounting for 53% of the variance. The first component was 'tension' ('facial expression of discomfort', 'appears physically uncomfortable', 'verbalization suggests discomfort', 'being irritable and aggressive', 'appears calm', Crohnbach's α = 0.69), the second was 'well-being' ('smiles', 'enjoys eating', 'enjoys touching/being touched', 'enjoys social interaction', Crohnbach's α = 0.62) and the third was 'sadness' ('appears sad', 'cries', 'facial expression of discomfort', Crohnbach's α 0.65). The mean score on the components 'tension' and 'well-being' increased significantly with increasing severity levels of dementia. Three components of quality of life (qol) were identified. Qol decreased with increasing severity of dementia. © 2013 S. Karger AG, Basel.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

Science.gov (United States)

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-01-01

Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms. PMID:19706156

Analysis, scale modeling, and full-scale test of a railcar and spent-nuclear-fuel shipping cask in a high-velocity impact against a rigid barrier

International Nuclear Information System (INIS)

Huerta, M.

1981-06-01

This report describes the mathematical analysis, the physical scale modeling, and a full-scale crash test of a railcar spent-nuclear-fuel shipping system. The mathematical analysis utilized a lumped-parameter model to predict the structural response of the railcar and the shipping cask. The physical scale modeling analysis consisted of two crash tests that used 1/8-scale models to assess railcar and shipping cask damage. The full-scale crash test, conducted with retired railcar equipment, was carefully monitored with onboard instrumentation and high-speed photography. Results of the mathematical and scale modeling analyses are compared with the full-scale test. 29 figures

In silico analysis and verification of S100 gene expression in gastric cancer

International Nuclear Information System (INIS)

Liu, Ji; Li, Xue; Dong, Guang-Long; Zhang, Hong-Wei; Chen, Dong-Li; Du, Jian-Jun; Zheng, Jian-Yong; Li, Ji-Peng; Wang, Wei-Zhong

2008-01-01

The S100 protein family comprises 22 members whose protein sequences encompass at least one EF-hand Ca 2+ binding motif. They were involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. However, the expression status of S100 family members in gastric cancer was not known yet. Combined with analysis of series analysis of gene expression, virtual Northern blot and microarray data, the expression levels of S100 family members in normal and malignant stomach tissues were systematically investigated. The expression of S100A3 was further evaluated by quantitative RT-PCR. At least 5 S100 genes were found to be upregulated in gastric cance by in silico analysis. Among them, four genes, including S100A2, S100A4, S100A7 and S100A10, were reported to overexpressed in gastric cancer previously. The expression of S100A3 in eighty patients of gastric cancer was further examined. The results showed that the mean expression levels of S100A3 in gastric cancer tissues were 2.5 times as high as in adjacent non-tumorous tissues. S100A3 expression was correlated with tumor differentiation and TNM (Tumor-Node-Metastasis) stage of gastric cancer, which was relatively highly expressed in poorly differentiated and advanced gastric cancer tissues (P < 0.05). To our knowledge this is the first report of systematic evaluation of S100 gene expressions in gastric cancers by multiple in silico analysis. The results indicated that overexpression of S100 gene family members were characteristics of gastric cancers and S100A3 might play important roles in differentiation and progression of gastric cancer

Rationality, emotional expression and control: psychometric characteristics of a questionnaire for research in psycho-oncology.

Science.gov (United States)

Bleiker, E M; van der Ploeg, H M; Hendriks, J H; Leer, J W; Kleijn, W C

1993-12-01

In some studies rationality, anti-emotionality and the control of (negative) emotions were found to be psychological risk factors for cancer. In the present study instruments were developed in order to cross-validate the role of the 'rationality/anti-emotionality (RAE)'-concept and the 'emotional expression and control (EEC)'-concept. The psychometric characteristics of a RAE-scale and EEC-scales were investigated in 4302 healthy women attending a breast cancer screening programme in The Netherlands. Principal components analysis revealed three factors for the RAE-scale: (1) Rationality; (2) Emotionality; and (3) Understanding. The EEC-scales consist of three factors that indicate: (1) expression of emotions to oneself; (2) expression of emotions towards others; and (3) control of emotions. These RAE and EEC scales can be of importance in psycho-oncological research, especially when: (1) the more refined subscales are used; and (2) age of the subjects is taken into account.

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

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Gabriela D A Guardia

Full Text Available Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

Science.gov (United States)

Guardia, Gabriela D A; Pires, Luís Ferreira; Vêncio, Ricardo Z N; Malmegrim, Kelen C R; de Farias, Cléver R G

2015-01-01

Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

FACTOR ANALYSIS OF A SOCIAL SKILLS SCALE FOR HIGH SCHOOL STUDENTS.

Science.gov (United States)

Wang, H-Y; Lin, C-K

2015-10-01

The objective of this study was to develop a social skills scale for high school students in Taiwan. This study adopted stratified random sampling. A total of 1,729 high school students were included. The students ranged in age from 16 to 18 years. A Social Skills Scale was developed for this study and was designed for classroom teachers to fill out. The test-retest reliability of this scale was tested by Pearson's correlation coefficient. Exploratory factor analysis was used to determine construct validity. The Social Skills Scale had good overall test-retest reliability of .92, and the internal consistency of the five subscales was above .90. The results of the factor analysis showed that the Social Skills Scale covered the five domains of classroom learning skills, communication skills, individual initiative skills, interaction skills, and job-related social skills, and the five factors explained 68.34% of the variance. Thus, the Social Skills Scale had good reliability and validity and would be applicable to and could be promoted for use in schools.

Analysis of baseline gene expression levels from ...

Science.gov (United States)

The use of gene expression profiling to predict chemical mode of action would be enhanced by better characterization of variance due to individual, environmental, and technical factors. Meta-analysis of microarray data from untreated or vehicle-treated animals within the control arm of toxicogenomics studies has yielded useful information on baseline fluctuations in gene expression. A dataset of control animal microarray expression data was assembled by a working group of the Health and Environmental Sciences Institute's Technical Committee on the Application of Genomics in Mechanism Based Risk Assessment in order to provide a public resource for assessments of variability in baseline gene expression. Data from over 500 Affymetrix microarrays from control rat liver and kidney were collected from 16 different institutions. Thirty-five biological and technical factors were obtained for each animal, describing a wide range of study characteristics, and a subset were evaluated in detail for their contribution to total variability using multivariate statistical and graphical techniques. The study factors that emerged as key sources of variability included gender, organ section, strain, and fasting state. These and other study factors were identified as key descriptors that should be included in the minimal information about a toxicogenomics study needed for interpretation of results by an independent source. Genes that are the most and least variable, gender-selectiv

Molecular Characterization and Expression Analysis of Equine ( Gene in Horse (

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Ki-Duk Song

2014-05-01

Full Text Available The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog, we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks and non-synonymous substitution ratios (Ka revealed that the horse VEGFα underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR and quantitative-polymerase chain reaction (qPCR showed ubiquitous expression of VEGFα mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of VEGFα gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

Evolution and expression analysis of the soybean glutamate ...

Indian Academy of Sciences (India)

Evolution and expression analysis of the soybean glutamate decarboxylase gene family. TAE KYUNG HYUN, SEUNG HEE EOM, XIAO HAN and JU-SUNG KIM http://www.ias.ac.in/jbiosci. J. Biosci. 39(5), December 2014, 899–907, © Indian Academy of Sciences. Supplementary material. Supplementary figure 1.

Effects of in ovo electroporation on endogenous gene expression: genome-wide analysis

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Chambers David

2011-04-01

Full Text Available Abstract Background In ovo electroporation is a widely used technique to study gene function in developmental biology. Despite the widespread acceptance of this technique, no genome-wide analysis of the effects of in ovo electroporation, principally the current applied across the tissue and exogenous vector DNA introduced, on endogenous gene expression has been undertaken. Here, the effects of electric current and expression of a GFP-containing construct, via electroporation into the midbrain of Hamburger-Hamilton stage 10 chicken embryos, are analysed by microarray. Results Both current alone and in combination with exogenous DNA expression have a small but reproducible effect on endogenous gene expression, changing the expression of the genes represented on the array by less than 0.1% (current and less than 0.5% (current + DNA, respectively. The subset of genes regulated by electric current and exogenous DNA span a disparate set of cellular functions. However, no genes involved in the regional identity were affected. In sharp contrast to this, electroporation of a known transcription factor, Dmrt5, caused a much greater change in gene expression. Conclusions These findings represent the first systematic genome-wide analysis of the effects of in ovo electroporation on gene expression during embryonic development. The analysis reveals that this process has minimal impact on the genetic basis of cell fate specification. Thus, the study demonstrates the validity of the in ovo electroporation technique to study gene function and expression during development. Furthermore, the data presented here can be used as a resource to refine the set of transcriptional responders in future in ovo electroporation studies of specific gene function.

A Mokken scale analysis of the peer physical examination questionnaire.

Science.gov (United States)

Vaughan, Brett; Grace, Sandra

2018-01-01

Peer physical examination (PPE) is a teaching and learning strategy utilised in most health profession education programs. Perceptions of participating in PPE have been described in the literature, focusing on areas of the body students are willing, or unwilling, to examine. A small number of questionnaires exist to evaluate these perceptions, however none have described the measurement properties that may allow them to be used longitudinally. The present study undertook a Mokken scale analysis of the Peer Physical Examination Questionnaire (PPEQ) to evaluate its dimensionality and structure when used with Australian osteopathy students. Students enrolled in Year 1 of the osteopathy programs at Victoria University (Melbourne, Australia) and Southern Cross University (Lismore, Australia) were invited to complete the PPEQ prior to their first practical skills examination class. R, an open-source statistics program, was used to generate the descriptive statistics and perform a Mokken scale analysis. Mokken scale analysis is a non-parametric item response theory approach that is used to cluster items measuring a latent construct. Initial analysis suggested the PPEQ did not form a single scale. Further analysis identified three subscales: 'comfort', 'concern', and 'professionalism and education'. The properties of each subscale suggested they were unidimensional with variable internal structures. The 'comfort' subscale was the strongest of the three identified. All subscales demonstrated acceptable reliability estimation statistics (McDonald's omega > 0.75) supporting the calculation of a sum score for each subscale. The subscales identified are consistent with the literature. The 'comfort' subscale may be useful to longitudinally evaluate student perceptions of PPE. Further research is required to evaluate changes with PPE and the utility of the questionnaire with other health profession education programs.

Rasch model analysis of the Depression, Anxiety and Stress Scales (DASS

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Tennant Alan

2009-05-01

Full Text Available Abstract Background There is a growing awareness of the need for easily administered, psychometrically sound screening tools to identify individuals with elevated levels of psychological distress. Although support has been found for the psychometric properties of the Depression, Anxiety and Stress Scales (DASS using classical test theory approaches it has not been subjected to Rasch analysis. The aim of this study was to use Rasch analysis to assess the psychometric properties of the DASS-21 scales, using two different administration modes. Methods The DASS-21 was administered to 420 participants with half the sample responding to a web-based version and the other half completing a traditional pencil-and-paper version. Conformity of DASS-21 scales to a Rasch partial credit model was assessed using the RUMM2020 software. Results To achieve adequate model fit it was necessary to remove one item from each of the DASS-21 subscales. The reduced scales showed adequate internal consistency reliability, unidimensionality and freedom from differential item functioning for sex, age and mode of administration. Analysis of all DASS-21 items combined did not support its use as a measure of general psychological distress. A scale combining the anxiety and stress items showed satisfactory fit to the Rasch model after removal of three items. Conclusion The results provide support for the measurement properties, internal consistency reliability, and unidimensionality of three slightly modified DASS-21 scales, across two different administration methods. The further use of Rasch analysis on the DASS-21 in larger and broader samples is recommended to confirm the findings of the current study.

Protein expression analysis of inflammation-related colon carcinogenesis

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Yasui Yumiko

2009-01-01

Full Text Available Background: Chronic inflammation is a risk factor for colorectal cancer (CRC development. The aim of this study was to determine the differences in protein expression between CRC and the surrounding nontumorous colonic tissues in the mice that received azoxymethane (AOM and dextran sodium sulfate (DSS using a proteomic analysis. Materials and Methods: Male ICR mice were given a single intraperitoneal injection of AOM (10 mg/kg body weight, followed by 2% (w/v DSS in their drinking water for seven days, starting one week after the AOM injection. Colonic adenocarcinoma developed after 20 weeks and a proteomics analysis based on two-dimensional gel electrophoresis and ultraflex TOF/TOF mass spectrometry was conducted in the cancerous and nontumorous tissue specimens. Results: The proteomic analysis revealed 21 differentially expressed proteins in the cancerous tissues in comparison to the nontumorous tissues. There were five markedly increased proteins (beta-tropomyosin, tropomyosin 1 alpha isoform b, S100 calcium binding protein A9, and an unknown protein and 16 markedly decreased proteins (Car1 proteins, selenium-binding protein 1, HMG-CoA synthase, thioredoxin 1, 1 Cys peroxiredoxin protein 2, Fcgbp protein, Cytochrome c oxidase, subunit Va, ETHE1 protein, and 7 unknown proteins. Conclusions: There were 21 differentially expressed proteins in the cancerous tissues of the mice that received AOM and DSS. Their functions include metabolism, the antioxidant system, oxidative stress, mucin production, and inflammation. These findings may provide new insights into the mechanisms of inflammation-related colon carcinogenesis and the establishment of novel therapies and preventative strategies to treat carcinogenesis in the inflamed colon.

Maintaining scale as a realiable computational system for criticality safety analysis

International Nuclear Information System (INIS)

Bowmann, S.M.; Parks, C.V.; Martin, S.K.

1995-01-01

Accurate and reliable computational methods are essential for nuclear criticality safety analyses. The SCALE (Standardized Computer Analyses for Licensing Evaluation) computer code system was originally developed at Oak Ridge National Laboratory (ORNL) to enable users to easily set up and perform criticality safety analyses, as well as shielding, depletion, and heat transfer analyses. Over the fifteen-year life of SCALE, the mainstay of the system has been the criticality safety analysis sequences that have featured the KENO-IV and KENO-V.A Monte Carlo codes and the XSDRNPM one-dimensional discrete-ordinates code. The criticality safety analysis sequences provide automated material and problem-dependent resonance processing for each criticality calculation. This report details configuration management which is essential because SCALE consists of more than 25 computer codes (referred to as modules) that share libraries of commonly used subroutines. Changes to a single subroutine in some cases affect almost every module in SCALE exclamation point Controlled access to program source and executables and accurate documentation of modifications are essential to maintaining SCALE as a reliable code system. The modules and subroutine libraries in SCALE are programmed by a staff of approximately ten Code Managers. The SCALE Software Coordinator maintains the SCALE system and is the only person who modifies the production source, executables, and data libraries. All modifications must be authorized by the SCALE Project Leader prior to implementation

Global gene expression analysis for evaluation and design of biomaterials

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Nobutaka Hanagata, Taro Takemura and Takashi Minowa

2010-01-01

Full Text Available Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data.

Global gene expression analysis for evaluation and design of biomaterials

International Nuclear Information System (INIS)

Hanagata, Nobutaka; Takemura, Taro; Minowa, Takashi

2010-01-01

Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data. (topical review)

Evaluation of the Edinburgh Post Natal Depression Scale using Rasch analysis

Science.gov (United States)

Pallant, Julie F; Miller, Renée L; Tennant, Alan

2006-01-01

Background The Edinburgh Postnatal Depression Scale (EPDS) is a 10 item self-rating post-natal depression scale which has seen widespread use in epidemiological and clinical studies. Concern has been raised over the validity of the EPDS as a single summed scale, with suggestions that it measures two separate aspects, one of depressive feelings, the other of anxiety. Methods As part of a larger cross-sectional study conducted in Melbourne, Australia, a community sample (324 women, ranging in age from 18 to 44 years: mean = 32 yrs, SD = 4.6), was obtained by inviting primiparous women to participate voluntarily in this study. Data from the EPDS were fitted to the Rasch measurement model and tested for appropriate category ordering, for item bias through Differential Item Functioning (DIF) analysis, and for unidimensionality through tests of the assumption of local independence. Results Rasch analysis of the data from the ten item scale initially demonstrated a lack of fit to the model with a significant Item-Trait Interaction total chi-square (chi Square = 82.8, df = 40; p < .001). Removal of two items (items 7 and 8) resulted in a non-significant Item-Trait Interaction total chi-square with a residual mean value for items of -0.467 with a standard deviation of 0.850, showing fit to the model. No DIF existed in the final 8-item scale (EPDS-8) and all items showed fit to model expectations. Principal Components Analysis of the residuals supported the local independence assumption, and unidimensionality of the revised EPDS-8 scale. Revised cut points were identified for EPDS-8 to maintain the case identification of the original scale. Conclusion The results of this study suggest that EPDS, in its original 10 item form, is not a viable scale for the unidimensional measurement of depression. Rasch analysis suggests that a revised eight item version (EPDS-8) would provide a more psychometrically robust scale. The revised cut points of 7/8 and 9/10 for the EPDS-8 show high

A Pareto scale-inflated outlier model and its Bayesian analysis

OpenAIRE

Scollnik, David P. M.

2016-01-01

This paper develops a Pareto scale-inflated outlier model. This model is intended for use when data from some standard Pareto distribution of interest is suspected to have been contaminated with a relatively small number of outliers from a Pareto distribution with the same shape parameter but with an inflated scale parameter. The Bayesian analysis of this Pareto scale-inflated outlier model is considered and its implementation using the Gibbs sampler is discussed. The paper contains three wor...

Prognostic and clinical significance of histone deacetylase 1 expression in breast cancer: A meta-analysis.

Science.gov (United States)

Qiao, Weiqiang; Liu, Heyang; Liu, Ruidong; Liu, Qipeng; Zhang, Ting; Guo, Wanying; Li, Peng; Deng, Miao

2018-05-05

There are conflicting reports about the role of histone deacetylase 1 (HDAC1) in breast cancer prognosis. Here, we conducted a meta-analysis to investigate the prognostic significance of HDAC1 in breast cancer. We searched different databases to identify studies evaluating the association between HDAC1 expression and its prognostic value in breast cancer. The pooled hazard ratios (HRs) and odds radios (ORs) with 95% confidence intervals (95% CIs) were calculated from these studies to assess specific correlation. Our meta-analysis of four databases identified 7 eligible studies with 1429 total patients. We found that HDAC1 over-expression did not correlate with disease-free survival (DFS) and overall survival (OS) in breast cancer. Subgroup analysis indicated an association between up-regulated HDAC1 expression and better OS (HR = 0.47, 95% CI: 0.23-0.97; P = 0.04) in Asian breast cancer patients. However, false-positive report probability (FPRP) analysis and trial sequential analysis (TSA) indicated that the results need further validation. Furthermore, HDAC1 over-expression was associated with positive estrogen receptor (ER) expression (OR, 3.30; 95% CI, 1.11-9.83; P = 0.03) and negative human epidermal growth factor receptor 2 (HER2) expression (OR, 1.79; 95% CI, 1.22-2.61; P = 0.003), but there were no significant differences between patients based on age, tumor size, lymph node metastasis, nuclear grade, or progesterone receptor (PR) expression. Overall, our meta-analysis demonstrated an association between increased HDAC1 expression and better OS in Asian breast cancer patients. In addition, HDAC1 over-expression correlated with positive ER and negative HER2 expression in breast cancer. However, researches in large patients' randomised controlled trials (RCTs) are needed to confirm the results. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparative Criticality Analysis of Two Monte Carlo Codes on Centrifugal Atomizer: MCNPS and SCALE

International Nuclear Information System (INIS)

Kang, H-S; Jang, M-S; Kim, S-R; Park, J-M; Kim, K-N

2015-01-01

There are two well-known Monte Carlo codes for criticality analysis, MCNP5 and SCALE. MCNP5 is a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron or coupled neutron / photon / electron transport, including the capability to calculate eigenvalues for critical system as a main analysis code. SCALE provides a comprehensive, verified and validated, user-friendly tool set for criticality safety, reactor physics, radiation shielding, radioactive source term characterization, and sensitivity and uncertainty analysis. SCALE was conceived and funded by US NRC to perform standardized computer analysis for licensing evaluation and is used widely in the world. We performed a validation test of MCNP5 and a comparative analysis of Monte Carlo codes, MCNP5 and SCALE, in terms of the critical analysis of centrifugal atomizer. In the criticality analysis using MCNP5 code, we obtained the statistically reliable results by using a large number of source histories per cycle and performing of uncertainty analysis

Comparative Criticality Analysis of Two Monte Carlo Codes on Centrifugal Atomizer: MCNPS and SCALE

Energy Technology Data Exchange (ETDEWEB)

Kang, H-S; Jang, M-S; Kim, S-R [NESS, Daejeon (Korea, Republic of); Park, J-M; Kim, K-N [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2015-10-15

There are two well-known Monte Carlo codes for criticality analysis, MCNP5 and SCALE. MCNP5 is a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron or coupled neutron / photon / electron transport, including the capability to calculate eigenvalues for critical system as a main analysis code. SCALE provides a comprehensive, verified and validated, user-friendly tool set for criticality safety, reactor physics, radiation shielding, radioactive source term characterization, and sensitivity and uncertainty analysis. SCALE was conceived and funded by US NRC to perform standardized computer analysis for licensing evaluation and is used widely in the world. We performed a validation test of MCNP5 and a comparative analysis of Monte Carlo codes, MCNP5 and SCALE, in terms of the critical analysis of centrifugal atomizer. In the criticality analysis using MCNP5 code, we obtained the statistically reliable results by using a large number of source histories per cycle and performing of uncertainty analysis.

Lateralized Feeding Behavior is Associated with Asymmetrical Neuroanatomy and Lateralized Gene Expressions in the Brain in Scale-Eating Cichlid Fish

Science.gov (United States)

Lee, Hyuk Je; Schneider, Ralf F; Manousaki, Tereza; Kang, Ji Hyoun; Lein, Etienne; Franchini, Paolo

2017-01-01

Abstract Lateralized behavior (“handedness”) is unusual, but consistently found across diverse animal lineages, including humans. It is thought to reflect brain anatomical and/or functional asymmetries, but its neuro-molecular mechanisms remain largely unknown. Lake Tanganyika scale-eating cichlid fish, Perissodus microlepis show pronounced asymmetry in their jaw morphology as well as handedness in feeding behavior—biting scales preferentially only from one or the other side of their victims. This makes them an ideal model in which to investigate potential laterality in neuroanatomy and transcription in the brain in relation to behavioral handedness. After determining behavioral handedness in P. microlepis (preferred attack side), we estimated the volume of the hemispheres of brain regions and captured their gene expression profiles. Our analyses revealed that the degree of behavioral handedness is mirrored at the level of neuroanatomical asymmetry, particularly in the tectum opticum. Transcriptome analyses showed that different brain regions (tectum opticum, telencephalon, hypothalamus, and cerebellum) display distinct expression patterns, potentially reflecting their developmental interrelationships. For numerous genes in each brain region, their extent of expression differences between hemispheres was found to be correlated with the degree of behavioral lateralization. Interestingly, the tectum opticum and telencephalon showed divergent biases on the direction of up- or down-regulation of the laterality candidate genes (e.g., grm2) in the hemispheres, highlighting the connection of handedness with gene expression profiles and the different roles of these brain regions. Hence, handedness in predation behavior may be caused by asymmetric size of brain hemispheres and also by lateralized gene expressions in the brain. PMID:29069363

Stochastic biological response to radiation. Comprehensive analysis of gene expression

International Nuclear Information System (INIS)

Inoue, Tohru; Hirabayashi, Yoko

2012-01-01

Authors explain that the radiation effect on biological system is stochastic along the law of physics, differing from chemical effect, using instances of Cs-137 gamma-ray (GR) and benzene (BZ) exposures to mice and of resultant comprehensive analyses of gene expression. Single GR irradiation is done with Gamma Cell 40 (CSR) to C57BL/6 or C3H/He mouse at 0, 0.6 and 3 Gy. BE is given orally at 150 mg/kg/day for 5 days x 2 weeks. Bone marrow cells are sampled 1 month after the exposure. Comprehensive gene expression is analyzed by Gene Chip Mouse Genome 430 2.0 Array (Affymetrix) and data are processed by programs like case normalization, statistics, network generation, functional analysis etc. GR irradiation brings about changes of gene expression, which are classifiable in common genes variable commonly on the dose change and stochastic genes variable stochastically within each dose: e.g., with Welch-t-test, significant differences are between 0/3 Gy (dose-specific difference, 455 pbs (probe set), in stochastic 2113 pbs), 0/0.6 Gy (267 in 1284 pbs) and 0.6/3 Gy (532 pbs); and with one-way analysis of variation (ANOVA) and hierarchial/dendrographic analyses, 520 pbs are shown to involve the dose-dependent 226 and dose-specific 294 pbs. It is also shown that at 3 Gy, expression of common genes are rather suppressed, including those related to the proliferation/apoptosis of B/T cells, and of stochastic genes, related to cell division/signaling. Ven diagram of the common genes of above 520 pbs, stochastic 2113 pbs at 3 Gy and 1284 pbs at 0.6 Gy shows the overlapping genes 29, 2 and 4, respectively, indicating only 35 pbs are overlapping in total. Network analysis of changes by GR shows the rather high expression of genes around hub of cAMP response element binding protein (CREB) at 0.6 Gy, and rather variable expression around CREB hub/suppressed expression of kinesin hub at 3 Gy; in the network by BZ exposure, unchanged or low expression around p53 hub and suppression

Combined process automation for large-scale EEG analysis.

Science.gov (United States)

Sfondouris, John L; Quebedeaux, Tabitha M; Holdgraf, Chris; Musto, Alberto E

2012-01-01

Epileptogenesis is a dynamic process producing increased seizure susceptibility. Electroencephalography (EEG) data provides information critical in understanding the evolution of epileptiform changes throughout epileptic foci. We designed an algorithm to facilitate efficient large-scale EEG analysis via linked automation of multiple data processing steps. Using EEG recordings obtained from electrical stimulation studies, the following steps of EEG analysis were automated: (1) alignment and isolation of pre- and post-stimulation intervals, (2) generation of user-defined band frequency waveforms, (3) spike-sorting, (4) quantification of spike and burst data and (5) power spectral density analysis. This algorithm allows for quicker, more efficient EEG analysis. Copyright © 2011 Elsevier Ltd. All rights reserved.

Multivariate analysis of the geochemistry and mineralogy of soils along two continental-scale transects in North America

Science.gov (United States)

Drew, L.J.; Grunsky, E.C.; Sutphin, D.M.; Woodruff, L.G.

2010-01-01

Soils collected in 2004 along two North American continental-scale transects were subjected to geochemical and mineralogical analyses. In previous interpretations of these analyses, data were expressed in weight percent and parts per million, and thus were subject to the effect of the constant-sum phenomenon. In a new approach to the data, this effect was removed by using centered log-ratio transformations to 'open' the mineralogical and geochemical arrays. Multivariate analyses, including principal component and linear discriminant analyses, of the centered log-ratio data reveal the effects of soil-forming processes, including soil parent material, weathering, and soil age, at the continental-scale of the data arrays that were not readily apparent in the more conventionally presented data. Linear discriminant analysis of the data arrays indicates that the majority of the soil samples collected along the transects can be more successfully classified with Level 1 ecological regional-scale classification by the soil geochemistry than soil mineralogy. A primary objective of this study is to discover and describe, in a parsimonious way, geochemical processes that are both independent and inter-dependent and manifested through compositional data including estimates of the elements and corresponding mineralogy. ?? 2010.

Xylella fastidiosa gene expression analysis by DNA microarrays

Directory of Open Access Journals (Sweden)

Regiane F. Travensolo

2009-01-01

Full Text Available Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM2 and liquid BCYE. All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others. The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants.

Unintended changes in protein expression revealed by proteomic analysis of seeds from transgenic pea expressing a bean alpha-amylase inhibitor gene.

Science.gov (United States)

Chen, Hancai; Bodulovic, Greg; Hall, Prudence J; Moore, Andy; Higgins, Thomas J V; Djordjevic, Michael A; Rolfe, Barry G

2009-09-01

Seeds of genetically modified (GM) peas (Pisum sativum L.) expressing the gene for alpha-amylase inhibitor-1 (alphaAI1) from the common bean (Phaseolus vulgaris L. cv. Tendergreen) exhibit resistance to the pea weevil (Bruchus pisorum). A proteomic analysis was carried out to compare seeds from GM pea lines expressing the bean alphaAI1 protein and the corresponding alphaAI1-free segregating lines and non-GM parental line to identify unintended alterations to the proteome of GM peas due to the introduction of the gene for alphaAI1. Proteomic analysis showed that in addition to the presence of alphaAI1, 33 other proteins were differentially accumulated in the alphaAI1-expressing GM lines compared with their non-GM parental line and these were grouped into five expression classes. Among these 33 proteins, only three were found to be associated with the expression of alphaAI1 in the GM pea lines. The accumulation of the remaining 30 proteins appears to be associated with Agrobacterium-mediated transformation events. Sixteen proteins were identified after MALDI-TOF-TOF analysis. About 56% of the identified proteins with altered accumulation in the GM pea were storage proteins including legumin, vicilin or convicilin, phaseolin, cupin and valosin-containing protein. Two proteins were uniquely expressed in the alphaAI1-expressing GM lines and one new protein was present in both the alphaAI1-expressing GM lines and their alphaAI1-free segregating lines, suggesting that both transgenesis and transformation events led to demonstrable changes in the proteomes of the GM lines tested.

Anatomical specificity of vascular endothelial growth factor expression in glioblastomas: a voxel-based mapping analysis

Energy Technology Data Exchange (ETDEWEB)

Fan, Xing [Capital Medical University, Department of Neurosurgery, Beijing Tiantan Hospital, Beijing (China); Wang, Yinyan [Capital Medical University, Department of Neurosurgery, Beijing Tiantan Hospital, Beijing (China); Capital Medical University, Department of Neuropathology, Beijing Neurosurgical Institute, Beijing (China); Wang, Kai; Ma, Jun; Li, Shaowu [Capital Medical University, Department of Neuroradiology, Beijing Tiantan Hospital, Beijing (China); Liu, Shuai [Chinese Academy of Medical Sciences and Peking Union Medical College, Departments of Neurosurgery, Peking Union Medical College Hospital, Beijing (China); Liu, Yong [Chinese Academy of Sciences, Brainnetome Center, Institute of Automation, Beijing (China); Jiang, Tao [Capital Medical University, Department of Neurosurgery, Beijing Tiantan Hospital, Beijing (China); Beijing Academy of Critical Illness in Brain, Department of Clinical Oncology, Beijing (China)

2016-01-15

The expression of vascular endothelial growth factor (VEGF) is a common genetic alteration in malignant gliomas and contributes to the angiogenesis of tumors. This study aimed to investigate the anatomical specificity of VEGF expression levels in glioblastomas using voxel-based neuroimaging analysis. Clinical information, MR scans, and immunohistochemistry stains of 209 patients with glioblastomas were reviewed. All tumor lesions were segmented manually and subsequently registered to standard brain space. Voxel-based regression analysis was performed to correlate the brain regions of tumor involvement with the level of VEGF expression. Brain regions identified as significantly associated with high or low VEGF expression were preserved following permutation correction. High VEGF expression was detected in 123 (58.9 %) of the 209 patients. Voxel-based statistical analysis demonstrated that high VEGF expression was more likely in tumors located in the left frontal lobe and the right caudate and low VEGF expression was more likely in tumors that occurred in the posterior region of the right lateral ventricle. Voxel-based neuroimaging analysis revealed the anatomic specificity of VEGF expression in glioblastoma, which may further our understanding of genetic heterogeneity during tumor origination. This finding provides primary theoretical support for potential future application of customized antiangiogenic therapy. (orig.)

Anatomical specificity of vascular endothelial growth factor expression in glioblastomas: a voxel-based mapping analysis

International Nuclear Information System (INIS)

Fan, Xing; Wang, Yinyan; Wang, Kai; Ma, Jun; Li, Shaowu; Liu, Shuai; Liu, Yong; Jiang, Tao

2016-01-01

The expression of vascular endothelial growth factor (VEGF) is a common genetic alteration in malignant gliomas and contributes to the angiogenesis of tumors. This study aimed to investigate the anatomical specificity of VEGF expression levels in glioblastomas using voxel-based neuroimaging analysis. Clinical information, MR scans, and immunohistochemistry stains of 209 patients with glioblastomas were reviewed. All tumor lesions were segmented manually and subsequently registered to standard brain space. Voxel-based regression analysis was performed to correlate the brain regions of tumor involvement with the level of VEGF expression. Brain regions identified as significantly associated with high or low VEGF expression were preserved following permutation correction. High VEGF expression was detected in 123 (58.9 %) of the 209 patients. Voxel-based statistical analysis demonstrated that high VEGF expression was more likely in tumors located in the left frontal lobe and the right caudate and low VEGF expression was more likely in tumors that occurred in the posterior region of the right lateral ventricle. Voxel-based neuroimaging analysis revealed the anatomic specificity of VEGF expression in glioblastoma, which may further our understanding of genetic heterogeneity during tumor origination. This finding provides primary theoretical support for potential future application of customized antiangiogenic therapy. (orig.)

PWR core and spent fuel pool analysis using scale and nestle

International Nuclear Information System (INIS)

Murphy, J. E.; Maldonado, G. I.; St Clair, R.; Orr, D.

2012-01-01

The SCALE nuclear analysis code system [SCALE, 2011], developed and maintained at Oak Ridge National Laboratory (ORNL) is widely recognized as high quality software for analyzing nuclear systems. The SCALE code system is composed of several validated computer codes and methods with standard control sequences, such as the TRITON/NEWT lattice physics sequence, which supplies dependable and accurate analyses for industry, regulators, and academia. Although TRITON generates energy-collapsed and space-homogenized few group cross sections, SCALE does not include a full-core nodal neutron diffusion simulation module within. However, in the past few years, the open-source NESTLE core simulator [NESTLE, 2003], originally developed at North Carolina State Univ. (NCSU), has been updated and upgraded via collaboration between ORNL and the Univ. of Tennessee (UT), so it now has a growingly seamless coupling to the TRITON/NEWT lattice physics [Galloway, 2010]. This study presents the methodology used to couple lattice physics data between TRITON and NESTLE in order to perform a three-dimensional full-core analysis employing a 'real-life' Duke Energy PWR as the test bed. The focus for this step was to compare the key parameters of core reactivity and radial power distribution versus plant data. Following the core analysis, following a three cycle burn, a spent fuel pool analysis was done using information generated from NESTLE for the discharged bundles and was compared to Duke Energy spent fuel pool models. The KENO control module from SCALE was employed for this latter stage of the project. (authors)

PWR core and spent fuel pool analysis using scale and nestle

Energy Technology Data Exchange (ETDEWEB)

Murphy, J. E.; Maldonado, G. I. [Dept. of Nuclear Engineering, Univ. of Tennessee, Knoxville, TN 37996-2300 (United States); St Clair, R.; Orr, D. [Duke Energy, 526 S. Church St, Charlotte, NC 28202 (United States)

2012-07-01

The SCALE nuclear analysis code system [SCALE, 2011], developed and maintained at Oak Ridge National Laboratory (ORNL) is widely recognized as high quality software for analyzing nuclear systems. The SCALE code system is composed of several validated computer codes and methods with standard control sequences, such as the TRITON/NEWT lattice physics sequence, which supplies dependable and accurate analyses for industry, regulators, and academia. Although TRITON generates energy-collapsed and space-homogenized few group cross sections, SCALE does not include a full-core nodal neutron diffusion simulation module within. However, in the past few years, the open-source NESTLE core simulator [NESTLE, 2003], originally developed at North Carolina State Univ. (NCSU), has been updated and upgraded via collaboration between ORNL and the Univ. of Tennessee (UT), so it now has a growingly seamless coupling to the TRITON/NEWT lattice physics [Galloway, 2010]. This study presents the methodology used to couple lattice physics data between TRITON and NESTLE in order to perform a three-dimensional full-core analysis employing a 'real-life' Duke Energy PWR as the test bed. The focus for this step was to compare the key parameters of core reactivity and radial power distribution versus plant data. Following the core analysis, following a three cycle burn, a spent fuel pool analysis was done using information generated from NESTLE for the discharged bundles and was compared to Duke Energy spent fuel pool models. The KENO control module from SCALE was employed for this latter stage of the project. (authors)

Valence Scaling of Dynamic Facial Expressions Is Altered in High-Functioning Subjects with Autism Spectrum Disorders: An FMRI Study

Science.gov (United States)

Rahko, Jukka S.; Paakki, Jyri-Johan; Starck, Tuomo H.; Nikkinen, Juha; Pauls, David L.; Katsyri, Jari V.; Jansson-Verkasalo, Eira M.; Carter, Alice S.; Hurtig, Tuula M.; Mattila, Marja-Leena; Jussila, Katja K.; Remes, Jukka J.; Kuusikko-Gauffin, Sanna A.; Sams, Mikko E.; Bolte, Sven; Ebeling, Hanna E.; Moilanen, Irma K.; Tervonen, Osmo; Kiviniemi, Vesa

2012-01-01

FMRI was performed with the dynamic facial expressions fear and happiness. This was done to detect differences in valence processing between 25 subjects with autism spectrum disorders (ASDs) and 27 typically developing controls. Valence scaling was abnormal in ASDs. Positive valence induces lower deactivation and abnormally strong activity in ASD…

Clinical Significance of Resistin Expression in Osteoarthritis: A Meta-Analysis

Directory of Open Access Journals (Sweden)

Xiao-Chuan Li

2014-01-01

Full Text Available Background. The objective of this study was to conduct a systematic review of literature evaluating human resistin expression as a diagnostic factor in osteoarthritis development and to quantify the overall diagnostic effect. Method. Relevant studies were identified and evaluated for quality through multiple search strategies. Studies analyzing resistin expression in the development of OA were eligible for inclusion. Data from eligible studies were extracted and included into the meta-analysis using a random-effects model. Results. Four case-control studies consisting of a total of 375 OA patients and 214 controls as well as three sex-stratified analyses composed of 53 males and 104 females were incorporated into our meta-analysis. Our results revealed that resistin levels were significantly higher in male OA subjects and OA patients overall. Country-stratified analysis yielded significantly different estimates in resistin levels between male OA subjects and female OA subjects in the Canadian subgroup but not among the French and USA subgroups. Based on the resistin levels in OA cases and controls, resistin levels were heightened in OA patients in the Dutch population. Conclusion. These results support the hypothesis that high expression of resistin represents a significant and reproducible marker of poor progression in OA patients, especially in males.

Prognostic value of Notch-1 expression in hepatocellular carcinoma: a meta-analysis

Directory of Open Access Journals (Sweden)

Wu T

2015-10-01

Full Text Available Tao Wu,1 Min Jiao,1 Li Jing,1 Min-Cong Wang,1 Hai-Feng Sun,2 Qing Li,1 Yi-Yang Bai,1 Yong-Chang Wei,1 Ke-Jun Nan,1 Hui Guo1 1Department of Medical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, 2Department of Oncology, Shaanxi Cancer Hospital, Xi’an, People’s Republic of China Abstract: Association of Notch-1 expression with prognosis of patients with hepatocellular carcinoma (HCC remains controversial. We conducted a meta-analysis to reevaluate the association of Notch-1 expression with clinicopathological characteristics and prognosis of HCC. PubMed, Embase, Web of Science, and China National Knowledge Infrastructure were searched to look for relevant studies. The association between Notch-1 expression and clinicopathological parameters and overall survival (OS was then reassessed using the meta-analysis for odds ratio (OR or hazard ratio (HR and 95% confidence interval (CI. A total of seven studies, including 810 HCC patients, were eligible for the meta-analysis. Our data showed that high Notch-1 expression was able to predict poor OS (HR 1.50, 95% CI 1.17–1.83, P=0.0001. The pooled OR showed that high Notch-1 expression was significantly associated with tumor metastasis (OR 0.37, 95% CI 0.16–0.86, P=0.02 and tumor size >5 cm (OR 0.48, 95% CI 0.26–0.88, P=0.02. In contrast, there was no association between high Notch-1 expression and tumor differentiation, late TNM stage, tumor number, and portal vein invasion of HCC. In conclusion, Notch-1 overexpression might predict poorer survival and more aggressive behavior in patients with HCC. Keywords: hepatocellular carcinoma, Notch-1, prognosis, clinicopathological features, meta-analysis

Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat

Directory of Open Access Journals (Sweden)

Langridge Peter

2006-10-01

Full Text Available Abstract Background Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. Results We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChip® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation, recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases. Conclusion This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat.

EXP-PAC: providing comparative analysis and storage of next generation gene expression data.

Science.gov (United States)

Church, Philip C; Goscinski, Andrzej; Lefèvre, Christophe

2012-07-01

Microarrays and more recently RNA sequencing has led to an increase in available gene expression data. How to manage and store this data is becoming a key issue. In response we have developed EXP-PAC, a web based software package for storage, management and analysis of gene expression and sequence data. Unique to this package is SQL based querying of gene expression data sets, distributed normalization of raw gene expression data and analysis of gene expression data across experiments and species. This package has been populated with lactation data in the international milk genomic consortium web portal (http://milkgenomics.org/). Source code is also available which can be hosted on a Windows, Linux or Mac APACHE server connected to a private or public network (http://mamsap.it.deakin.edu.au/~pcc/Release/EXP_PAC.html). Copyright © 2012 Elsevier Inc. All rights reserved.

Expression analysis of argonaute, Dicer-like, and RNA-dependent ...

Indian Academy of Sciences (India)

DEFANG GAN

the first report of expression analysis of all CsDCL, CsAGO and CsRDR family genes in cucumber under .... tissues and organs were detected using online data and semi- ...... Wheeler B. S. 2013 Small RNAs, big impact: small RNA pathways.

Express-analysis of Radiocaesium Traces in Natural Water

International Nuclear Information System (INIS)

Remez, V.P.; Belyakova, E.G.

1999-01-01

To determine traces of radiocaesium in water solution, the sorbent on the base of ferric potassium hexacyanoferrate on cellulose carrier ANFEZH was worked out. The sorbent is capable to extract effectively the isotopes of caesium from various natural solutions (fresh and sea water, milk, juices and so on). The usage of sorbent allows practically completely concentrate the isotopes of caesium from water samples with the volume of tens and hundreds litres. The sorbent in quantity of 50-500 grams allows to extract 98±1% of caesium from natural water samples with the volume up to 1000 litres during 1-5 hours. The usage of this sorbent allowed to conduct the express analysis of multiple bore holes within the area of 30 km of Chernobyl Skaya NPP , drinking water and milk in the regions of Belorussia, Ukraine and Russia, hit by Chernobyl disaster and around NPP in Russia and America. The use of this express analysis reduced the time and required labour as compared with to precipitation methods

Source Code Analysis Laboratory (SCALe) for Energy Delivery Systems

Science.gov (United States)

2010-12-01

technical competence for the type of tests and calibrations SCALe undertakes. Testing and calibration laboratories that comply with ISO / IEC 17025 ...and exec t [ ISO / IEC 2005]. f a software system indicates that the SCALe analysis di by a CERT secure coding standard. Successful conforma antees that...to be more secure than non- systems. However, no study has yet been performed to p t ssment in accordance with ISO / IEC 17000: “a demonstr g to a

Three-dimensional analysis of free-electron laser performance using brightness scaled variables

Directory of Open Access Journals (Sweden)

M. Gullans

2008-06-01

Full Text Available A three-dimensional analysis of radiation generation in a free-electron laser (FEL is performed in the small signal regime. The analysis includes beam conditioning, harmonic generation, flat beams, and a new scaling of the FEL equations using the six-dimensional beam brightness. The six-dimensional beam brightness is an invariant under Liouvillian flow; therefore, any nondissipative manipulation of the phase space, performed, for example, in order to optimize FEL performance, must conserve this brightness. This scaling is more natural than the commonly used scaling with the one-dimensional growth rate. The brightness-scaled equations allow for the succinct characterization of the optimal FEL performance under various additional constraints. The analysis allows for the simple evaluation of gain enhancement schemes based on beam phase space manipulations such as emittance exchange and conditioning. An example comparing the gain in the first and third harmonics of round or flat and conditioned or unconditioned beams is presented.

Identification and expression analysis of genes associated with bovine blastocyst formation

Directory of Open Access Journals (Sweden)

Van Zeveren Alex

2007-06-01

Full Text Available Abstract Background Normal preimplantation embryo development encompasses a series of events including first cleavage division, activation of the embryonic genome, compaction and blastocyst formation. First lineage differentiation starts at the blastocyst stage with the formation of the trophectoderm and the inner cell mass. The main objective of this study was the detection, identification and expression analysis of genes associated with blastocyst formation in order to help us better understand this process. This information could lead to improvements of in vitro embryo production procedures. Results A subtractive cDNA library was constructed enriched for transcripts preferentially expressed at the blastocyst stage compared to the 2-cell and 8-cell stage. Sequence information was obtained for 65 randomly selected clones. The RNA expression levels of 12 candidate genes were determined throughout 3 stages of preimplantation embryo development (2-cell, 8-cell and blastocyst and compared with the RNA expression levels of in vivo "golden standard" embryos using real-time PCR. The RNA expression profiles of 9 (75% transcripts (KRT18, FN1, MYL6, ATP1B3, FTH1, HINT1, SLC25A5, ATP6V0B, RPL10 were in agreement with the subtractive cDNA cloning approach, whereas for the remaining 3 (25% (ACTN1, COPE, EEF1A1 the RNA expression level was equal or even higher at the earlier developmental stages compared to the blastocyst stage. Moreover, significant differences in RNA expression levels were observed between in vitro and in vivo produced embryos. By immunofluorescent labelling, the protein expression of KRT18, FN1 and MYL6 was determined throughout bovine preimplantation embryo development and showed the same pattern as the RNA expression analyses. Conclusion By subtractive cDNA cloning, candidate genes involved in blastocyst formation were identified. For several candidate genes, important differences in gene expression were observed between in vivo and in

Rasch analysis of the Rosenberg Self-Esteem Scale with African Americans.

Science.gov (United States)

Chao, Ruth Chu-Lien; Vidacovich, Courtney; Green, Kathy E

2017-03-01

Effectively diagnosing African Americans' self-esteem has posed an unresolved challenge. To address this assessment issue, we conducted exploratory factor analysis and Rasch analysis to assess the psychometric characteristics of the Rosenberg Self-Esteem Scale (RSES, Rosenberg, 1965) for African American college students. The dimensional structure of the RSES was first identified with the first subsample (i.e., calibration subsample) and then held up under cross-validation with a second subsample (i.e., validation subsample). Exploratory factor analysis and Rasch analysis both supported unidimensionality of the measure, with that finding replicated for a random split of the sample. Response scale use was generally appropriate, items were endorsed at a high level reflecting high levels of self-esteem, and person separation and reliability of person separation were adequate, and reflected results similar to those found in prior research. However, as some categories were infrequently used, we also collapsed scale points and found a slight improvement in scale and item indices. No differential item functioning was found by sex or having received professional assistance versus not; there were no mean score differences by age group, marital status, or year in college. Two items were seen as problematic. Implications for theory and research on multicultural mental health are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression

NARCIS (Netherlands)

van Kampen, A. H.; van Schaik, B. D.; Pauws, E.; Michiels, E. M.; Ruijter, J. M.; Caron, H. N.; Versteeg, R.; Heisterkamp, S. H.; Leunissen, J. A.; Baas, F.; van der Mee, M.

2000-01-01

MOTIVATION: SAGE enables the determination of genome-wide mRNA expression profiles. A comprehensive analysis of SAGE data requires software, which integrates (statistical) data analysis methods with a database system. Furthermore, to facilitate data sharing between users, the application should

ChIP-on-chip analysis identifies IL-22 as direct target gene of ectopically expressed FOXP3 transcription factor in human T cells

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Jeron Andreas

2012-12-01

Full Text Available Abstract Background The transcription factor (TF forkhead box P3 (FOXP3 is constitutively expressed at high levels in naturally occurring CD4+CD25+ regulatory T cells (nTregs. It is not only the most accepted marker for that cell population but is also considered lineage determinative. Chromatin immunoprecipitation (ChIP of TFs in combination with genomic tiling microarray analysis (ChIP-on-chip has been shown to be an appropriate tool for identifying FOXP3 transcription factor binding sites (TFBSs on a genome-wide scale. In combination with microarray expression analysis, the ChIP-on-chip technique allows identification of direct FOXP3 target genes. Results ChIP-on-chip analysis of the human FOXP3 expressed in resting and PMA/ionomycin–stimulated Jurkat T cells revealed several thousand putative FOXP3 binding sites and demonstrated the importance of intronic regions for FOXP3 binding. The analysis of expression data showed that the stimulation-dependent down-regulation of IL-22 was correlated with direct FOXP3 binding in the IL-22 promoter region. This association was confirmed by real-time PCR analysis of ChIP-DNA. The corresponding ChIP-region also contained a matching FOXP3 consensus sequence. Conclusions Knowledge of the general distribution patterns of FOXP3 TFBSs in the human genome under resting and activated conditions will contribute to a better understanding of this TF and its influence on direct target genes, as well as its importance for the phenotype and function of Tregs. Moreover, FOXP3-dependent repression of Th17-related IL-22 may be relevant to an understanding of the phenomenon of Treg/Th17 cell plasticity.

Applications of Convex Analysis to Multidimensional Scaling

OpenAIRE

Jan de Leeuw

2011-01-01

In this paper we discuss the convergence of an algorithm for metric and nonmetric multidimensional scaling that is very similar to the C-matrix algorithm of Guttman. The paper improves some earlier results in two respects. In the first place the analysis is extended to cover general Minkovski metrics, in the second place a more elementary proof of convergence based on results of Robert is presented.

Serial analysis of gene expression (SAGE) in normal human trabecular meshwork.

Science.gov (United States)

Liu, Yutao; Munro, Drew; Layfield, David; Dellinger, Andrew; Walter, Jeffrey; Peterson, Katherine; Rickman, Catherine Bowes; Allingham, R Rand; Hauser, Michael A

2011-04-08

To identify the genes expressed in normal human trabecular meshwork tissue, a tissue critical to the pathogenesis of glaucoma. Total RNA was extracted from human trabecular meshwork (HTM) harvested from 3 different donors. Extracted RNA was used to synthesize individual SAGE (serial analysis of gene expression) libraries using the I-SAGE Long kit from Invitrogen. Libraries were analyzed using SAGE 2000 software to extract the 17 base pair sequence tags. The extracted sequence tags were mapped to the genome using SAGE Genie map. A total of 298,834 SAGE tags were identified from all HTM libraries (96,842, 88,126, and 113,866 tags, respectively). Collectively, there were 107,325 unique tags. There were 10,329 unique tags with a minimum of 2 counts from a single library. These tags were mapped to known unique Unigene clusters. Approximately 29% of the tags (orphan tags) did not map to a known Unigene cluster. Thirteen percent of the tags mapped to at least 2 Unigene clusters. Sequence tags from many glaucoma-related genes, including myocilin, optineurin, and WD repeat domain 36, were identified. This is the first time SAGE analysis has been used to characterize the gene expression profile in normal HTM. SAGE analysis provides an unbiased sampling of gene expression of the target tissue. These data will provide new and valuable information to improve understanding of the biology of human aqueous outflow.

Using the Positive and Negative Syndrome Scale (PANSS) to Define Different Domains of Negative Symptoms: Prediction of Everyday Functioning by Impairments in Emotional Expression and Emotional Experience.

Science.gov (United States)

Harvey, Philip D; Khan, Anzalee; Keefe, Richard S E

2017-12-01

Background: Reduced emotional experience and expression are two domains of negative symptoms. The authors assessed these two domains of negative symptoms using previously developed Positive and Negative Syndrome Scale (PANSS) factors. Using an existing dataset, the authors predicted three different elements of everyday functioning (social, vocational, and everyday activities) with these two factors, as well as with performance on measures of functional capacity. Methods: A large (n=630) sample of people with schizophrenia was used as the data source of this study. Using regression analyses, the authors predicted the three different aspects of everyday functioning, first with just the two Positive and Negative Syndrome Scale factors and then with a global negative symptom factor. Finally, we added neurocognitive performance and functional capacity as predictors. Results: The Positive and Negative Syndrome Scale reduced emotional experience factor accounted for 21 percent of the variance in everyday social functioning, while reduced emotional expression accounted for no variance. The total Positive and Negative Syndrome Scale negative symptom factor accounted for less variance (19%) than the reduced experience factor alone. The Positive and Negative Syndrome Scale expression factor accounted for, at most, one percent of the variance in any of the functional outcomes, with or without the addition of other predictors. Implications: Reduced emotional experience measured with the Positive and Negative Syndrome Scale, often referred to as "avolition and anhedonia," specifically predicted impairments in social outcomes. Further, reduced experience predicted social impairments better than emotional expression or the total Positive and Negative Syndrome Scale negative symptom factor. In this cross-sectional study, reduced emotional experience was specifically related with social outcomes, accounting for essentially no variance in work or everyday activities, and being the

Evaluation of the Edinburgh Post Natal Depression Scale using Rasch analysis

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Tennant Alan

2006-06-01

Full Text Available Abstract Background The Edinburgh Postnatal Depression Scale (EPDS is a 10 item self-rating post-natal depression scale which has seen widespread use in epidemiological and clinical studies. Concern has been raised over the validity of the EPDS as a single summed scale, with suggestions that it measures two separate aspects, one of depressive feelings, the other of anxiety. Methods As part of a larger cross-sectional study conducted in Melbourne, Australia, a community sample (324 women, ranging in age from 18 to 44 years: mean = 32 yrs, SD = 4.6, was obtained by inviting primiparous women to participate voluntarily in this study. Data from the EPDS were fitted to the Rasch measurement model and tested for appropriate category ordering, for item bias through Differential Item Functioning (DIF analysis, and for unidimensionality through tests of the assumption of local independence. Results Rasch analysis of the data from the ten item scale initially demonstrated a lack of fit to the model with a significant Item-Trait Interaction total chi-square (chi Square = 82.8, df = 40; p Conclusion The results of this study suggest that EPDS, in its original 10 item form, is not a viable scale for the unidimensional measurement of depression. Rasch analysis suggests that a revised eight item version (EPDS-8 would provide a more psychometrically robust scale. The revised cut points of 7/8 and 9/10 for the EPDS-8 show high levels of agreement with the original case identification for the EPDS-10.

Comparative transcriptome analysis reveals differentially expressed genes associated with sex expression in garden asparagus (Asparagus officinalis).

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Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gao, Wu-Jun

2017-08-22

Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood. De novo transcriptome sequencing via Illumina paired-end sequencing revealed more than 26 billion bases of high-quality sequence data from male and female asparagus flower buds. A total of 72,626 unigenes with an average length of 979 bp were assembled. In comparative transcriptome analysis, 4876 differentially expressed genes (DEGs) were identified in the possible sex-determining stage of female and male/supermale flower buds. Of these DEGs, 433, including 285 male/supermale-biased and 149 female-biased genes, were annotated as flower related. Of the male/supermale-biased flower-related genes, 102 were probably involved in anther development. In addition, 43 DEGs implicated in hormone response and biosynthesis putatively associated with sex expression and reproduction were discovered. Moreover, 128 transcription factor (TF)-related genes belonging to various families were found to be differentially expressed, and this finding implied the essential roles of TF in sex determination or differentiation in asparagus. Correlation analysis indicated that miRNA-DEG pairs were also implicated in asparagus sexual development. Our study identified a large number of DEGs involved in the sex expression and reproduction of asparagus, including known genes participating in plant reproduction, plant hormone signaling, TF encoding, and genes with unclear functions. We also found that miRNAs might be involved in the sex differentiation process. Our study could provide a valuable basis for further investigations on the regulatory networks of sex determination and differentiation in asparagus and facilitate further genetic and genomic studies on this dioecious species.

Systematic analysis of gene expression pattern in has-miR-197 over-expressed human uterine leiomyoma cells.

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Ling, Jing; Wu, Xiaoli; Fu, Ziyi; Tan, Jie; Xu, Qing

2015-10-01

Our previous study showed that the expression of miR-197 in leiomyoma was down-regulated compared with myometrium. Further, miR-197 has been identified to affect uterine leiomyoma cell proliferation, apoptosis, and metastasis ability, though the responsible molecular mechanism has not been well elucidated. In this study, we sought to determine the expression patterns of miR-197 targeted genes and to explore their potential functions, participating Pathways and the networks that are involved in the biological behavior of human uterine leiomyoma. After transfection of human uterine leiomyoma cells with miR-197, we confirmed the expression level of miR-197 using quantitative real-time PCR (qRT-PCR), and we detected the gene expression profiles after miR-197 over-expression through DNA microarray analysis. Further, we performed GO and Pathway analysis. The dominantly dys-regulated genes, which were up- or down-regulated by more than 10-fold, compared with parental cells, were confirmed using qRT-PCR technology. Compared with the control group, miR-197 was up-regulated by 30-fold after miR-197 lentiviral transfection. The microarray data showed that 872 genes were dys-regulated by more than 2-fold in human uterine leiomyoma cells after miR-197 overexpression, including 537 up-regulated and 335 down-regulated genes. The GO analysis indicated that the dys-regulated genes were primarily involved in response to stimuli, multicellular organ processes, and the signaling of biological progression. Further, Pathway analysis data showed that these genes participated in regulating several signaling Pathways, including the JAK/STAT signaling Pathway, the Toll-like receptor signaling Pathway, and cytokine-cytokine receptor interaction. The qRT-PCR results confirmed that 17 of the 66 selected genes, which were up- or down-regulated more than 10-fold by miR-197, were consistent with the microarray results, including tumorigenesis-related genes, such as DRT7, SLC549, SFMBT2, FLJ37956

Comparative analysis of clustering methods for gene expression time course data

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Ivan G. Costa

2004-01-01

Full Text Available This work performs a data driven comparative study of clustering methods used in the analysis of gene expression time courses (or time series. Five clustering methods found in the literature of gene expression analysis are compared: agglomerative hierarchical clustering, CLICK, dynamical clustering, k-means and self-organizing maps. In order to evaluate the methods, a k-fold cross-validation procedure adapted to unsupervised methods is applied. The accuracy of the results is assessed by the comparison of the partitions obtained in these experiments with gene annotation, such as protein function and series classification.

Lateralized Feeding Behavior is Associated with Asymmetrical Neuroanatomy and Lateralized Gene Expressions in the Brain in Scale-Eating Cichlid Fish.

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Lee, Hyuk Je; Schneider, Ralf F; Manousaki, Tereza; Kang, Ji Hyoun; Lein, Etienne; Franchini, Paolo; Meyer, Axel

2017-11-01

Lateralized behavior ("handedness") is unusual, but consistently found across diverse animal lineages, including humans. It is thought to reflect brain anatomical and/or functional asymmetries, but its neuro-molecular mechanisms remain largely unknown. Lake Tanganyika scale-eating cichlid fish, Perissodus microlepis show pronounced asymmetry in their jaw morphology as well as handedness in feeding behavior-biting scales preferentially only from one or the other side of their victims. This makes them an ideal model in which to investigate potential laterality in neuroanatomy and transcription in the brain in relation to behavioral handedness. After determining behavioral handedness in P. microlepis (preferred attack side), we estimated the volume of the hemispheres of brain regions and captured their gene expression profiles. Our analyses revealed that the degree of behavioral handedness is mirrored at the level of neuroanatomical asymmetry, particularly in the tectum opticum. Transcriptome analyses showed that different brain regions (tectum opticum, telencephalon, hypothalamus, and cerebellum) display distinct expression patterns, potentially reflecting their developmental interrelationships. For numerous genes in each brain region, their extent of expression differences between hemispheres was found to be correlated with the degree of behavioral lateralization. Interestingly, the tectum opticum and telencephalon showed divergent biases on the direction of up- or down-regulation of the laterality candidate genes (e.g., grm2) in the hemispheres, highlighting the connection of handedness with gene expression profiles and the different roles of these brain regions. Hence, handedness in predation behavior may be caused by asymmetric size of brain hemispheres and also by lateralized gene expressions in the brain. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A scaling analysis of electronic localization in two-dimensional random media

International Nuclear Information System (INIS)

Ye Zhen

2003-01-01

By an improved scaling analysis, we suggest that there may appear two possibilities concerning the electronic localization in two-dimensional random media. The first is that all electronic states are localized in two dimensions, as conjectured previously. The second possibility is that electronic behaviors in two- and three-dimensional random systems are similar, in agreement with a recent calculation based on a direct calculation of the conductance with the use of the Kubo formula. In this case, non-localized states are possible in two dimensions, and have some peculiar properties. A few predictions are proposed. Moreover, the present analysis accommodates results from the previous scaling analysis

Estimating Most Productive Scale Size in Data Envelopment Analysis with Integer Value Data

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Dwi Sari, Yunita; Angria S, Layla; Efendi, Syahril; Zarlis, Muhammad

2018-01-01

The most productive scale size (MPSS) is a measurement that states how resources should be organized and utilized to achieve optimal results. The most productive scale size (MPSS) can be used as a benchmark for the success of an industry or company in producing goods or services. To estimate the most productive scale size (MPSS), each decision making unit (DMU) should pay attention the level of input-output efficiency, by data envelopment analysis (DEA) method decision making unit (DMU) can identify units used as references that can help to find the cause and solution from inefficiencies can optimize productivity that main advantage in managerial applications. Therefore, data envelopment analysis (DEA) is chosen to estimating most productive scale size (MPSS) that will focus on the input of integer value data with the CCR model and the BCC model. The purpose of this research is to find the best solution for estimating most productive scale size (MPSS) with input of integer value data in data envelopment analysis (DEA) method.

Exploring Incomplete Rating Designs with Mokken Scale Analysis

Science.gov (United States)

Wind, Stefanie A.; Patil, Yogendra J.

2018-01-01

Recent research has explored the use of models adapted from Mokken scale analysis as a nonparametric approach to evaluating rating quality in educational performance assessments. A potential limiting factor to the widespread use of these techniques is the requirement for complete data, as practical constraints in operational assessment systems…

Molecular cloning and expression analysis of a zeta-class ...

African Journals Online (AJOL)

Jane

2011-07-27

Jul 27, 2011 ... sugar-signalling pathway (Chi et al., 2010). All the earlier mentioned ... real-time qPCR analysis was the ABI PRISM7500 real-time PCR system. ... Construction of prokaryotic expression vector of Sc-GST gene. pET29a (+) ...

A resampling-based meta-analysis for detection of differential gene expression in breast cancer

International Nuclear Information System (INIS)

Gur-Dedeoglu, Bala; Konu, Ozlen; Kir, Serkan; Ozturk, Ahmet Rasit; Bozkurt, Betul; Ergul, Gulusan; Yulug, Isik G

2008-01-01

Accuracy in the diagnosis of breast cancer and classification of cancer subtypes has improved over the years with the development of well-established immunohistopathological criteria. More recently, diagnostic gene-sets at the mRNA expression level have been tested as better predictors of disease state. However, breast cancer is heterogeneous in nature; thus extraction of differentially expressed gene-sets that stably distinguish normal tissue from various pathologies poses challenges. Meta-analysis of high-throughput expression data using a collection of statistical methodologies leads to the identification of robust tumor gene expression signatures. A resampling-based meta-analysis strategy, which involves the use of resampling and application of distribution statistics in combination to assess the degree of significance in differential expression between sample classes, was developed. Two independent microarray datasets that contain normal breast, invasive ductal carcinoma (IDC), and invasive lobular carcinoma (ILC) samples were used for the meta-analysis. Expression of the genes, selected from the gene list for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes were tested on 10 independent primary IDC samples and matched non-tumor controls by real-time qRT-PCR. Other existing breast cancer microarray datasets were used in support of the resampling-based meta-analysis. The two independent microarray studies were found to be comparable, although differing in their experimental methodologies (Pearson correlation coefficient, R = 0.9389 and R = 0.8465 for ductal and lobular samples, respectively). The resampling-based meta-analysis has led to the identification of a highly stable set of genes for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes. The expression results of the selected genes obtained through real-time qRT-PCR supported the meta-analysis results. The

A resampling-based meta-analysis for detection of differential gene expression in breast cancer

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Ergul Gulusan

2008-12-01

Full Text Available Abstract Background Accuracy in the diagnosis of breast cancer and classification of cancer subtypes has improved over the years with the development of well-established immunohistopathological criteria. More recently, diagnostic gene-sets at the mRNA expression level have been tested as better predictors of disease state. However, breast cancer is heterogeneous in nature; thus extraction of differentially expressed gene-sets that stably distinguish normal tissue from various pathologies poses challenges. Meta-analysis of high-throughput expression data using a collection of statistical methodologies leads to the identification of robust tumor gene expression signatures. Methods A resampling-based meta-analysis strategy, which involves the use of resampling and application of distribution statistics in combination to assess the degree of significance in differential expression between sample classes, was developed. Two independent microarray datasets that contain normal breast, invasive ductal carcinoma (IDC, and invasive lobular carcinoma (ILC samples were used for the meta-analysis. Expression of the genes, selected from the gene list for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes were tested on 10 independent primary IDC samples and matched non-tumor controls by real-time qRT-PCR. Other existing breast cancer microarray datasets were used in support of the resampling-based meta-analysis. Results The two independent microarray studies were found to be comparable, although differing in their experimental methodologies (Pearson correlation coefficient, R = 0.9389 and R = 0.8465 for ductal and lobular samples, respectively. The resampling-based meta-analysis has led to the identification of a highly stable set of genes for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes. The expression results of the selected genes obtained through real

Facial Expressivity at 4 Months: A Context by Expression Analysis.

Science.gov (United States)

Bennett, David S; Bendersky, Margaret; Lewis, Michael

2002-01-01

The specificity predicted by differential emotions theory (DET) for early facial expressions in response to 5 different eliciting situations was studied in a sample of 4-month-old infants (n = 150). Infants were videotaped during tickle, sour taste, jack-in-the-box, arm restraint, and masked-stranger situations and their expressions were coded second by second. Infants showed a variety of facial expressions in each situation; however, more infants exhibited positive (joy and surprise) than negative expressions (anger, disgust, fear, and sadness) across all situations except sour taste. Consistent with DET-predicted specificity, joy expressions were the most common in response to tickling, and were less common in response to other situations. Surprise expressions were the most common in response to the jack-in-the-box, as predicted, but also were the most common in response to the arm restraint and masked-stranger situations, indicating a lack of specificity. No evidence of predicted specificity was found for anger, disgust, fear, and sadness expressions. Evidence of individual differences in expressivity within situations, as well as stability in the pattern across situations, underscores the need to examine both child and contextual factors in studying emotional development. The results provide little support for the DET postulate of situational specificity and suggest that a synthesis of differential emotions and dynamic systems theories of emotional expression should be considered.

Two-dimensional DFA scaling analysis applied to encrypted images

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Vargas-Olmos, C.; Murguía, J. S.; Ramírez-Torres, M. T.; Mejía Carlos, M.; Rosu, H. C.; González-Aguilar, H.

2015-01-01

The technique of detrended fluctuation analysis (DFA) has been widely used to unveil scaling properties of many different signals. In this paper, we determine scaling properties in the encrypted images by means of a two-dimensional DFA approach. To carry out the image encryption, we use an enhanced cryptosystem based on a rule-90 cellular automaton and we compare the results obtained with its unmodified version and the encryption system AES. The numerical results show that the encrypted images present a persistent behavior which is close to that of the 1/f-noise. These results point to the possibility that the DFA scaling exponent can be used to measure the quality of the encrypted image content.

Psychometric Analysis of the Work/Life Balance Self-Assessment Scale.

Science.gov (United States)

Smeltzer, Suzanne C; Cantrell, Mary Ann; Sharts-Hopko, Nancy C; Heverly, Mary Ann; Jenkinson, Amanda; Nthenge, Serah

2016-01-01

This study investigated the psychometric properties of the Work/Life Balance Self-Assessment scale among nurse faculty involved in doctoral education. A national random sample of 554 respondents completed the Work/Life Balance Self-Assessment scale, which addresses 3 factors: work interference with personal life (WIPL), personal life interference with work (PLIW), and work/personal life enhancement (WPLE). A principal components analysis with varimax rotation revealed 3 internally consistent aspects of work-life balance, explaining 40.5% of the variance. The Cronbach's alpha coefficients for reliability of the scale were .88 for the total scale and for the subscales, .93 (WIPL), .85 (PLIW), and .69 (WPLE). The Work/Life Balance Self-Assessment scale appears to be a reliable and valid instrument to examine work-life balance among nurse faculty.

Gene expression analysis of FABP4 in gastric cancer

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Abdulkarim Yasin Karim

2016-06-01

Full Text Available Purpose: Gastric cancer has high incidence and mortality rate in several countries and is still one of the most frequent and lethal disease. In this study, we aimed to determine diagnostic markers in gastric cancer by molecular techniques; include mRNA expression analysis of FABP4 gene. Fatty acid binding protein 4 (FABP4 gene encodes the fatty acid binding protein found in adipocytes. The protein encoded by FABP4 are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. Material and Methods: Total RNA were extracted from paired tumor and normal tissues of 47 gastric cancer. The mRNA expression level of FABP4 was measured employing semi- quantitative reverse transcription- polymerase chain reaction (RT- PCR. Results: The mRNA expression level of FABP4 was significantly decreased (down- regulated. Conclusion: Down-regulation of FABP4 gene seems to occur at the initial steps of gastric cancer development. In order to confirm the relationship between the gastric tumor and FABP4 gene, further analysis like immunohistochemistry and epigenetc techniques are necessary. [Cukurova Med J 2016; 41(2.000: 248-252

Microarray Expression Profile and Functional Analysis of Circular RNAs in Osteosarcoma

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Weihai Liu

2017-09-01

Full Text Available Background/Aims: Osteosarcoma (OS is the most common primary malignant bone tumor in children and adolescents. However, the molecular mechanisms regulating osteosarcoma tumorigenesis and progression are still poorly understood. Circular RNAs (circRNAs have been identified as microRNA sponges and are involved in many important biological processes. This study aims to investigate the global changes in the expression pattern of circRNAs in osteosarcoma and provide a comprehensive understanding of differentially expressed circRNAs. Methods: Microarray based circRNA expression was determined in osteosarcoma cell lines and compared with hFOB1.19, which was used as the normal control. We confirmed the microarray data by real time-qPCR in both osteosarcoma cell lines and tissues. The circRNA/microRNA/mRNA interaction network was predicted using bioinformatics. Gene Ontology analysis and 4 annotation tools for pathway analysis (KEGG, Biocarta, PANTHER and Reactome were used to predict the functions of differentially expressed circRNAs. Results: We revealed a number of differentially expressed circRNAs and 12 of them were confirmed, which suggests a potential role of circRNAs in OS. Among these differentially expressed circRNAs, hsa_circRNA_103801 was up-regulated in both osteosarcoma cell lines and tissues, while hsa_circRNA_104980 was down-regulated. The most likely potential target miRNAs for hsa_circRNA_103801 include hsa-miR-370-3p, hsa-miR-338-3p and hsa-miR-877-3p, while the most potential target miRNAs of hsa_circRNA_104980 consist of hsa-miR-1298-3p and hsa-miR-660-3p. Functional analysis found that hsa_circRNA_103801 was involved in pathways in cancer, such as the HIF-1, VEGF and angiogenesis pathway, the Rap1 signaling pathway and the PI3K-Akt signaling pathway, while hsa_circRNA_104980 was related to some pathways such as the tight junction pathway. Conclusions: This study has identified the comprehensive expression profile of circRNAs in

Analysis of multi-scale chaotic characteristics of wind power based on Hilbert–Huang transform and Hurst analysis

International Nuclear Information System (INIS)

Liang, Zhengtang; Liang, Jun; Zhang, Li; Wang, Chengfu; Yun, Zhihao; Zhang, Xu

2015-01-01

Highlights: • A scale division method of wind power based on HHT and Hurst analysis is proposed. • The time–frequency components of wind power show different fractal structures. • These components are superposed and reconstructed into three scale subsequences. • Each subsequence has a chaotic characteristic and shows its own properties. • The EMD-LSSVM + ELM method improves the short-term wind power forecasting accuracy. - Abstract: The causes of uncertainty in wind farm power generation are not yet fully understood. A method for the scale division of wind power based on the Hilbert–Huang transform (HHT) and Hurst analysis is proposed in this paper, which allows the various multi-scale chaotic characteristics of wind power to be investigated to reveal further information about the dynamic behavior of wind power. First, the time–frequency characteristics of wind power are analyzed using the HHT, and then Hurst analysis is applied to analyze the stochastic/persistent characteristics of the different time–frequency components. Second, based on their fractal structures, the components are superposed and reconstructed into three series, which are defined as the Micro-, Meso- and Macro-scale subsequences. Finally, indices related to the statistical and behavioral characteristics of the subsequences are calculated and used to analyze their nonlinear dynamic behavior. The data collected from a wind farm of Hebei Province, China, are selected for case studies. The simulation results reveal that (1) although the time–frequency components can be decomposed, the different fractal structures of the signal are also derived from the original series; (2) the three scale subsequences all present chaotic characteristics and each of them exhibits its own unique properties. The Micro-scale subsequence shows strong randomness and contributes the least to the overall fluctuations; the Macro-scale subsequence is the steadiest and exhibits the most significant tendency

Exploring Rating Quality in Rater-Mediated Assessments Using Mokken Scale Analysis

Science.gov (United States)

Wind, Stefanie A.; Engelhard, George, Jr.

2016-01-01

Mokken scale analysis is a probabilistic nonparametric approach that offers statistical and graphical tools for evaluating the quality of social science measurement without placing potentially inappropriate restrictions on the structure of a data set. In particular, Mokken scaling provides a useful method for evaluating important measurement…

Factor Analysis of the Brazilian Version of UPPS Impulsive Behavior Scale

Science.gov (United States)

Sediyama, Cristina Y. N.; Moura, Ricardo; Garcia, Marina S.; da Silva, Antonio G.; Soraggi, Carolina; Neves, Fernando S.; Albuquerque, Maicon R.; Whiteside, Setephen P.; Malloy-Diniz, Leandro F.

2017-01-01

Objective: To examine the internal consistency and factor structure of the Brazilian adaptation of the UPPS Impulsive Behavior Scale. Methods: UPPS is a self-report scale composed by 40 items assessing four factors of impulsivity: (a) urgency, (b) lack of premeditation; (c) lack of perseverance; (d) sensation seeking. In the present study 384 participants (278 women and 106 men), who were recruited from schools, universities, leisure centers and workplaces fulfilled the UPPS scale. An exploratory factor analysis was performed by using Varimax factor rotation and Kaiser Normalization, and we also conducted two confirmatory analyses to test the independency of the UPPS components found in previous analysis. Results: Results showed a decrease in mean UPPS total scores with age and this analysis showed that the youngest participants (below 30 years) scored significantly higher than the other groups over 30 years. No difference in gender was found. Cronbach’s alpha, results indicated satisfactory values for all subscales, with similar high values for the subscales and confirmatory factor analysis indexes also indicated a poor model fit. The results of two exploratory factor analysis were satisfactory. Conclusion: Our results showed that the Portuguese version has the same four-factor structure of the original and previous translations of the UPPS. PMID:28484414

Factor Analysis of the Brazilian Version of UPPS Impulsive Behavior Scale

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Leandro F. Malloy-Diniz

2017-04-01

Full Text Available Objective: To examine the internal consistency and factor structure of the Brazilian adaptation of the UPPS Impulsive Behavior Scale.Methods: UPPS is a self-report scale composed by 40 items assessing four factors of impulsivity: (a urgency, (b lack of premeditation; (c lack of perseverance; (d sensation seeking. In the present study 384 participants (278 women and 106 men, who were recruited from schools, universities, leisure centers and workplaces fulfilled the UPPS scale. An exploratory factor analysis was performed by using Varimax factor rotation and Kaiser Normalization, and we also conducted two confirmatory analyses to test the independency of the UPPS components found in previous analysis.Results: Results showed a decrease in mean UPPS total scores with age and this analysis showed that the youngest participants (below 30 years scored significantly higher than the other groups over 30 years. No difference in gender was found. Cronbach’s alpha, results indicated satisfactory values for all subscales, with similar high values for the subscales and confirmatory factor analysis indexes also indicated a poor model fit. The results of two exploratory factor analysis were satisfactory.Conclusion: Our results showed that the Portuguese version has the same four-factor structure of the original and previous translations of the UPPS.

Factor Analysis of the Brazilian Version of UPPS Impulsive Behavior Scale.

Science.gov (United States)

Sediyama, Cristina Y N; Moura, Ricardo; Garcia, Marina S; da Silva, Antonio G; Soraggi, Carolina; Neves, Fernando S; Albuquerque, Maicon R; Whiteside, Setephen P; Malloy-Diniz, Leandro F

2017-01-01

Objective: To examine the internal consistency and factor structure of the Brazilian adaptation of the UPPS Impulsive Behavior Scale. Methods: UPPS is a self-report scale composed by 40 items assessing four factors of impulsivity: (a) urgency, (b) lack of premeditation; (c) lack of perseverance; (d) sensation seeking. In the present study 384 participants (278 women and 106 men), who were recruited from schools, universities, leisure centers and workplaces fulfilled the UPPS scale. An exploratory factor analysis was performed by using Varimax factor rotation and Kaiser Normalization, and we also conducted two confirmatory analyses to test the independency of the UPPS components found in previous analysis. Results: Results showed a decrease in mean UPPS total scores with age and this analysis showed that the youngest participants (below 30 years) scored significantly higher than the other groups over 30 years. No difference in gender was found. Cronbach's alpha, results indicated satisfactory values for all subscales, with similar high values for the subscales and confirmatory factor analysis indexes also indicated a poor model fit. The results of two exploratory factor analysis were satisfactory. Conclusion: Our results showed that the Portuguese version has the same four-factor structure of the original and previous translations of the UPPS.

Using scale and feather traits for module construction provides a functional approach to chicken epidermal development.

Science.gov (United States)

Bao, Weier; Greenwold, Matthew J; Sawyer, Roger H

2017-11-01

Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules.

The Rat Grimace Scale: A partially automated method for quantifying pain in the laboratory rat via facial expressions

Directory of Open Access Journals (Sweden)

Zhan Shu

2011-07-01

Full Text Available Abstract We recently demonstrated the utility of quantifying spontaneous pain in mice via the blinded coding of facial expressions. As the majority of preclinical pain research is in fact performed in the laboratory rat, we attempted to modify the scale for use in this species. We present herein the Rat Grimace Scale, and show its reliability, accuracy, and ability to quantify the time course of spontaneous pain in the intraplantar complete Freund's adjuvant, intraarticular kaolin-carrageenan, and laparotomy (post-operative pain assays. The scale's ability to demonstrate the dose-dependent analgesic efficacy of morphine is also shown. In addition, we have developed software, Rodent Face Finder®, which successfully automates the most labor-intensive step in the process. Given the known mechanistic dissociations between spontaneous and evoked pain, and the primacy of the former as a clinical problem, we believe that widespread adoption of spontaneous pain measures such as the Rat Grimace Scale might lead to more successful translation of basic science findings into clinical application.

The Development and Validation of the Instructional Dissent Scale

Science.gov (United States)

Goodboy, Alan K.

2011-01-01

Two studies (N = 420) were conducted to develop and validate the instructional dissent scale (IDS) for use in the college classroom. Participants in study 1 were 210 students who completed the IDS pilot inventory which was subjected to an exploratory factor analysis yielding three distinct factors of dissent (i.e., expressive, rhetorical,…

Development of multitissue microfluidic dynamic array for assessing changes in gene expression associated with channel catfish appetite, growth, metabolism, and intestinal health

Science.gov (United States)

Large-scale, gene expression methods allow for high throughput analysis of physiological pathways at a fraction of the cost of individual gene expression analysis. Systems, such as the Fluidigm quantitative PCR array described here, can provide powerful assessments of the effects of diet, environme...

Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response

Directory of Open Access Journals (Sweden)

Nasrine Bendjilali

2017-01-01

Full Text Available Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen.

Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response.

Science.gov (United States)

Bendjilali, Nasrine; MacLeon, Samuel; Kalra, Gurmannat; Willis, Stephen D; Hossian, A K M Nawshad; Avery, Erica; Wojtowicz, Olivia; Hickman, Mark J

2017-01-05

Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq) analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR) consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen. Copyright © 2017 Bendjilali et al.

Psychometric Analysis of Role Conflict and Ambiguity Scales in Academia

Science.gov (United States)

Khan, Anwar; Yusoff, Rosman Bin Md.; Khan, Muhammad Muddassar; Yasir, Muhammad; Khan, Faisal

2014-01-01

A comprehensive Psychometric Analysis of Rizzo et al.'s (1970) Role Conflict & Ambiguity (RCA) scales were performed after its distribution among 600 academic staff working in six universities of Pakistan. The reliability analysis includes calculation of Cronbach Alpha Coefficients and Inter-Items statistics, whereas validity was determined by…

Global scaling analysis for the pebble bed advanced high temperature reactor

International Nuclear Information System (INIS)

Blandford, E.D.; Peterson, P.F.

2009-01-01

Scaled Integral Effects Test (IET) facilities play a critical role in the design certification process of innovative reactor designs. Best-estimate system analysis codes, which minimize deliberate conservatism, require confirmatory data during the validation process to ensure an acceptable level of accuracy as defined by the regulator. The modular Pebble Bed Advanced High Temperature Reactor (PB-AHTR), with a nominal power output of 900 MWth, is the most recent UC Berkeley design for a liquid fluoride salt cooled, solid fuel reactor. The PB-AHTR takes advantage of technologies developed for gas-cooled high temperature thermal and fast reactors, sodium fast reactors, and molten salt reactors. In this paper, non-dimensional scaling groups and similarity criteria are presented at the global system level for a loss of forced circulation transient, where single-phase natural circulation is the primary mechanism for decay heat removal following a primary pump trip. Due to very large margin to fuel damage temperatures, the peak metal temperature of primary-loop components was identified as the key safety parameter of interest. Fractional Scaling Analysis (FSA) methods were used to quantify the intensity of each transfer process during the transient and subsequently rank them by their relative importance while identifying key sources of distortion between the prototype and model. The results show that the development of a scaling hierarchy at the global system level informs the bottom-up scaling analysis. (author)

Notes on a Dramaturgical Analysis of Unequal Small-Scale Corruption Experiences

OpenAIRE

Edgar Daniel Manchinelly Mota

2017-01-01

In the last two decades, corruption has emerged as a relevant subject on a worldwide scale, because of its negative effects on the economy and State institutions, among other things. Research has focused on the macro aspects of corruption, emphasizing its causes and consequences. However, small-scale corruption has not been studied in such detail. This document proposes a theoretical-methodological framework for a dramaturgical analysis of small-scale corruption, with the aim of demonstrating...

Analysis of the 2H-evaporator scale samples (HTF-17-56, -57)

Energy Technology Data Exchange (ETDEWEB)

Hay, M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Coleman, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Diprete, D. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

2017-09-13

Savannah River National Laboratory analyzed scale samples from both the wall and cone sections of the 242-16H Evaporator prior to chemical cleaning. The samples were analyzed for uranium and plutonium isotopes required for a Nuclear Criticality Safety Assessment of the scale removal process. The analysis of the scale samples found the material to contain crystalline nitrated cancrinite and clarkeite. Samples from both the wall and cone contain depleted uranium. Uranium concentrations of 16.8 wt% 4.76 wt% were measured in the wall and cone samples, respectively. The ratio of plutonium isotopes in both samples is ~85% Pu-239 and ~15% Pu-238 by mass and shows approximately the same 3.5 times higher concentration in the wall sample versus the cone sample as observed in the uranium concentrations. The mercury concentrations measured in the scale samples were higher than previously reported values. The wall sample contains 19.4 wt% mercury and the cone scale sample 11.4 wt% mercury. The results from the current scales samples show reasonable agreement with previous 242-16H Evaporator scale sample analysis; however, the uranium concentration in the current wall sample is substantially higher than previous measurements.

Expression analysis of G Protein-Coupled Receptors in mouse macrophages.

Science.gov (United States)

Lattin, Jane E; Schroder, Kate; Su, Andrew I; Walker, John R; Zhang, Jie; Wiltshire, Tim; Saijo, Kaoru; Glass, Christopher K; Hume, David A; Kellie, Stuart; Sweet, Matthew J

2008-04-29

Monocytes and macrophages express an extensive repertoire of G Protein-Coupled Receptors (GPCRs) that regulate inflammation and immunity. In this study we performed a systematic micro-array analysis of GPCR expression in primary mouse macrophages to identify family members that are either enriched in macrophages compared to a panel of other cell types, or are regulated by an inflammatory stimulus, the bacterial product lipopolysaccharide (LPS). Several members of the P2RY family had striking expression patterns in macrophages; P2ry6 mRNA was essentially expressed in a macrophage-specific fashion, whilst P2ry1 and P2ry5 mRNA levels were strongly down-regulated by LPS. Expression of several other GPCRs was either restricted to macrophages (e.g. Gpr84) or to both macrophages and neural tissues (e.g. P2ry12, Gpr85). The GPCR repertoire expressed by bone marrow-derived macrophages and thioglycollate-elicited peritoneal macrophages had some commonality, but there were also several GPCRs preferentially expressed by either cell population. The constitutive or regulated expression in macrophages of several GPCRs identified in this study has not previously been described. Future studies on such GPCRs and their agonists are likely to provide important insights into macrophage biology, as well as novel inflammatory pathways that could be future targets for drug discovery.

TiGER: a database for tissue-specific gene expression and regulation.

Science.gov (United States)

Liu, Xiong; Yu, Xueping; Zack, Donald J; Zhu, Heng; Qian, Jiang

2008-06-09

Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation). The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM) detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.

TiGER: A database for tissue-specific gene expression and regulation

Directory of Open Access Journals (Sweden)

Zack Donald J

2008-06-01

Full Text Available Abstract Background Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. Results The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation. The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. Conclusion We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.

Elucidating gene function and function evolution through comparison of co-expression networks in plants

Directory of Open Access Journals (Sweden)

Marek eMutwil

2014-08-01

Full Text Available The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species, Frontiers in Plant Science 2:23. In this paper we applied cross-species analysis to co-expression networks of genes involved in cellulose biosynthesis. We show that the co-expression networks from different species are highly similar, indicating that whole biological pathways are conserved across species. This finding has two important implications. First, the analysis can transfer gene function annotation from well-studied plants, such as Arabidopsis, to other, uncharacterized plant species. As the analysis finds genes that have similar sequence and similar expression pattern across different organisms, functionally equivalent genes can be identified. Second, since co-expression analyses are often noisy, a comparative analysis should have higher performance, as parts of co-expression networks that are conserved are more likely to be functionally relevant. In this Focused Review, we outline the comparative analysis done in the original paper and comment on the recent advances and approaches that allow comparative analyses of co-function networks. We hypothesize that, in comparison to simple co-expression analysis, comparative analysis would yield more accurate gene function predictions. Finally, by combining comparative analysis with genomic information of green plants, we propose a possible composition of cellulose biosynthesis machinery during earlier stages of plant evolution.

Multi-scale Analysis of MEMS Sensors Subject to Drop Impacts

Directory of Open Access Journals (Sweden)

Sarah Zerbini

2007-09-01

Full Text Available The effect of accidental drops on MEMS sensors are examined within the frame-work of a multi-scale finite element approach. With specific reference to a polysilicon MEMSaccelerometer supported by a naked die, the analysis is decoupled into macro-scale (at dielength-scale and meso-scale (at MEMS length-scale simulations, accounting for the verysmall inertial contribution of the sensor to the overall dynamics of the device. Macro-scaleanalyses are adopted to get insights into the link between shock waves caused by the impactagainst a target surface and propagating inside the die, and the displacement/acceleration his-tories at the MEMS anchor points. Meso-scale analyses are adopted to detect the most stresseddetails of the sensor and to assess whether the impact can lead to possible localized failures.Numerical results show that the acceleration at sensor anchors cannot be considered an ob-jective indicator for drop severity. Instead, accurate analyses at sensor level are necessary toestablish how MEMS can fail because of drops.

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

Directory of Open Access Journals (Sweden)

Settles Matthew L

2009-05-01

-antisense transcript pairs, analysis of the gene ontology terms showed a significant over-representation of transcripts involved in energy production. These included several representations of ATP synthase, photosystem proteins and RUBISCO, which indicated that photosynthesis is likely to be regulated by antisense transcripts. Conclusion This study demonstrated the novel use of an adapted labeling protocol and a 3'IVT GeneChip array for large-scale identification of antisense transcription in wheat. The results show that antisense transcription is relatively abundant in wheat, and may affect the expression of valuable agronomic phenotypes. Future work should select potentially interesting transcript pairs for further functional characterization to determine biological activity.

Manufacturing Cost Analysis for YSZ-Based FlexCells at Pilot and Full Scale Production Scales

Energy Technology Data Exchange (ETDEWEB)

Scott Swartz; Lora Thrun; Robin Kimbrell; Kellie Chenault

2011-05-01

Significant reductions in cell costs must be achieved in order to realize the full commercial potential of megawatt-scale SOFC power systems. The FlexCell designed by NexTech Materials is a scalable SOFC technology that offers particular advantages over competitive technologies. In this updated topical report, NexTech analyzes its FlexCell design and fabrication process to establish manufacturing costs at both pilot scale (10 MW/year) and full-scale (250 MW/year) production levels and benchmarks this against estimated anode supported cell costs at the 250 MW scale. This analysis will show that even with conservative assumptions for yield, materials usage, and cell power density, a cost of $35 per kilowatt can be achieved at high volume. Through advancements in cell size and membrane thickness, NexTech has identified paths for achieving cell manufacturing costs as low as $27 per kilowatt for its FlexCell technology. Also in this report, NexTech analyzes the impact of raw material costs on cell cost, showing the significant increases that result if target raw material costs cannot be achieved at this volume.

Laminar flow and convective transport processes scaling principles and asymptotic analysis

CERN Document Server

Brenner, Howard

1992-01-01

Laminar Flow and Convective Transport Processes: Scaling Principles and Asymptotic Analysis presents analytic methods for the solution of fluid mechanics and convective transport processes, all in the laminar flow regime. This book brings together the results of almost 30 years of research on the use of nondimensionalization, scaling principles, and asymptotic analysis into a comprehensive form suitable for presentation in a core graduate-level course on fluid mechanics and the convective transport of heat. A considerable amount of material on viscous-dominated flows is covered.A unique feat

Scale-up from microtiter plate to laboratory fermenter: evaluation by online monitoring techniques of growth and protein expression in Escherichia coli and Hansenula polymorpha fermentations

Directory of Open Access Journals (Sweden)

Engelbrecht Christoph

2009-12-01

Full Text Available Abstract Background In the past decade, an enormous number of new bioprocesses have evolved in the biotechnology industry. These bioprocesses have to be developed fast and at a maximum productivity. Up to now, only few microbioreactors were developed to fulfill these demands and to facilitate sample processing. One predominant reaction platform is the shaken microtiter plate (MTP, which provides high-throughput at minimal expenses in time, money and work effort. By taking advantage of this simple and efficient microbioreactor array, a new online monitoring technique for biomass and fluorescence, called BioLector, has been recently developed. The combination of high-throughput and high information content makes the BioLector a very powerful tool in bioprocess development. Nevertheless, the scalabilty of results from the micro-scale to laboratory or even larger scales is very important for short development times. Therefore, engineering parameters regarding the reactor design and its operation conditions play an important role even on a micro-scale. In order to evaluate the scale-up from a microtiter plate scale (200 μL to a stirred tank fermenter scale (1.4 L, two standard microbial expression systems, Escherichia coli and Hansenula polymorpha, were fermented in parallel at both scales and compared with regard to the biomass and protein formation. Results Volumetric mass transfer coefficients (kLa ranging from 100 to 350 1/h were obtained in 96-well microtiter plates. Even with a suboptimal mass transfer condition in the microtiter plate compared to the stirred tank fermenter (kLa = 370-600 1/h, identical growth and protein expression kinetics were attained in bacteria and yeast fermentations. The bioprocess kinetics were evaluated by optical online measurements of biomass and protein concentrations exhibiting the same fermentation times and maximum signal deviations below 10% between the scales. In the experiments, the widely applied green

thermal analysis of a small scale solid waste-fired steam boiler

African Journals Online (AJOL)

user

Thermal analysis of a small scale solid waste-fired steam generator is presented in this paper. The analysis was based on the chosen design specifications which are operating steam ... include: wind, bio-energy, geothermal, solar thermal,.

Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: A systematic expression analysis

International Nuclear Information System (INIS)

Hamm, Alexander; Knuechel, Ruth; Dahl, Edgar; Veeck, Juergen; Bektas, Nuran; Wild, Peter J; Hartmann, Arndt; Heindrichs, Uwe; Kristiansen, Glen; Werbowetski-Ogilvie, Tamra; Del Maestro, Rolando

2008-01-01

The inter-alpha-trypsin inhibitors (ITI) are a family of plasma protease inhibitors, assembled from a light chain – bikunin, encoded by AMBP – and five homologous heavy chains (encoded by ITIH1, ITIH2, ITIH3, ITIH4, and ITIH5), contributing to extracellular matrix stability by covalent linkage to hyaluronan. So far, ITIH molecules have been shown to play a particularly important role in inflammation and carcinogenesis. We systematically investigated differential gene expression of the ITIH gene family, as well as AMBP and the interacting partner TNFAIP6 in 13 different human tumor entities (of breast, endometrium, ovary, cervix, stomach, small intestine, colon, rectum, lung, thyroid, prostate, kidney, and pancreas) using cDNA dot blot analysis (Cancer Profiling Array, CPA), semiquantitative RT-PCR and immunohistochemistry. We found that ITIH genes are clearly downregulated in multiple human solid tumors, including breast, colon and lung cancer. Thus, ITIH genes may represent a family of putative tumor suppressor genes that should be analyzed in greater detail in the future. For an initial detailed analysis we chose ITIH2 expression in human breast cancer. Loss of ITIH2 expression in 70% of cases (n = 50, CPA) could be confirmed by real-time PCR in an additional set of breast cancers (n = 36). Next we studied ITIH2 expression on the protein level by analyzing a comprehensive tissue micro array including 185 invasive breast cancer specimens. We found a strong correlation (p < 0.001) between ITIH2 expression and estrogen receptor (ER) expression indicating that ER may be involved in the regulation of this ECM molecule. Altogether, this is the first systematic analysis on the differential expression of ITIH genes in human cancer, showing frequent downregulation that may be associated with initiation and/or progression of these malignancies

The Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT): Data Analysis and Visualization for Geoscience Data

Energy Technology Data Exchange (ETDEWEB)

Williams, Dean [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Doutriaux, Charles [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Patchett, John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Williams, Sean [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Shipman, Galen [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Miller, Ross [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Steed, Chad [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Krishnan, Harinarayan [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Silva, Claudio [NYU Polytechnic School of Engineering, New York, NY (United States); Chaudhary, Aashish [Kitware, Inc., Clifton Park, NY (United States); Bremer, Peer-Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pugmire, David [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bethel, E. Wes [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Childs, Hank [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Prabhat, Mr. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Geveci, Berk [Kitware, Inc., Clifton Park, NY (United States); Bauer, Andrew [Kitware, Inc., Clifton Park, NY (United States); Pletzer, Alexander [Tech-X Corp., Boulder, CO (United States); Poco, Jorge [NYU Polytechnic School of Engineering, New York, NY (United States); Ellqvist, Tommy [NYU Polytechnic School of Engineering, New York, NY (United States); Santos, Emanuele [Federal Univ. of Ceara, Fortaleza (Brazil); Potter, Gerald [NASA Johnson Space Center, Houston, TX (United States); Smith, Brian [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Maxwell, Thomas [NASA Johnson Space Center, Houston, TX (United States); Kindig, David [Tech-X Corp., Boulder, CO (United States); Koop, David [NYU Polytechnic School of Engineering, New York, NY (United States)

2013-05-01

To support interactive visualization and analysis of complex, large-scale climate data sets, UV-CDAT integrates a powerful set of scientific computing libraries and applications to foster more efficient knowledge discovery. Connected through a provenance framework, the UV-CDAT components can be loosely coupled for fast integration or tightly coupled for greater functionality and communication with other components. This framework addresses many challenges in the interactive visual analysis of distributed large-scale data for the climate community.

Comparative analysis of the PCA3 gene expression in sediments and exosomes isolated from urine

Directory of Open Access Journals (Sweden)

D. S. Mikhaylenko

2017-01-01

Full Text Available Introduction. Prostate cancer (PCa is one of the common oncological diseases in men. Expression of the PCA3 gene in urine is currently used as a molecular genetic marker of PCa.Objective: to comparative analysis of the PCA3 expression in urine sediments and exosomes for the determination of the biomaterial, which allows detecting the PCA3 expression in more efficient manner.Materials and methods. The 12 patients with different stages of PCa and 8 control samples were examined.Results. The diagnostic accuracy of the PCA3 gene expression analysis in this cohort exceeded 90 %. We had not obtained significant differences in the sensitivity and specificity of the PCA3 hyperexpression in the urine sediments compared with exosomes. This result indicates in favor to using urine sediment for the PCA3 analysis as a biomaterial with less time-consuming sample preparation, although the possible advantage of exosomes for the analysis of the expression marker panels requires further studies.

Advanced Connectivity Analysis (ACA): a Large Scale Functional Connectivity Data Mining Environment.

Science.gov (United States)

Chen, Rong; Nixon, Erika; Herskovits, Edward

2016-04-01

Using resting-state functional magnetic resonance imaging (rs-fMRI) to study functional connectivity is of great importance to understand normal development and function as well as a host of neurological and psychiatric disorders. Seed-based analysis is one of the most widely used rs-fMRI analysis methods. Here we describe a freely available large scale functional connectivity data mining software package called Advanced Connectivity Analysis (ACA). ACA enables large-scale seed-based analysis and brain-behavior analysis. It can seamlessly examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables. We demonstrate applications of ACA to rs-fMRI data sets from a study of autism.

Analysis of multiplex gene expression maps obtained by voxelation

Directory of Open Access Journals (Sweden)

Smith Desmond J

2009-04-01

Full Text Available Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. Results To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in

Analysis of multiplex gene expression maps obtained by voxelation.

Science.gov (United States)

An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

2009-04-29

Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental

Scaling analysis and instantons for thermally assisted tunneling and quantum Monte Carlo simulations

Science.gov (United States)

Jiang, Zhang; Smelyanskiy, Vadim N.; Isakov, Sergei V.; Boixo, Sergio; Mazzola, Guglielmo; Troyer, Matthias; Neven, Hartmut

2017-01-01

We develop an instantonic calculus to derive an analytical expression for the thermally assisted tunneling decay rate of a metastable state in a fully connected quantum spin model. The tunneling decay problem can be mapped onto the Kramers escape problem of a classical random dynamical field. This dynamical field is simulated efficiently by path-integral quantum Monte Carlo (QMC). We show analytically that the exponential scaling with the number of spins of the thermally assisted quantum tunneling rate and the escape rate of the QMC process are identical. We relate this effect to the existence of a dominant instantonic tunneling path. The instanton trajectory is described by nonlinear dynamical mean-field theory equations for a single-site magnetization vector, which we solve exactly. Finally, we derive scaling relations for the "spiky" barrier shape when the spin tunneling and QMC rates scale polynomially with the number of spins N while a purely classical over-the-barrier activation rate scales exponentially with N .

Multi-Scale Factor Analysis of High-Dimensional Brain Signals

KAUST Repository

Ting, Chee-Ming; Ombao, Hernando; Salleh, Sh-Hussain

2017-01-01

In this paper, we develop an approach to modeling high-dimensional networks with a large number of nodes arranged in a hierarchical and modular structure. We propose a novel multi-scale factor analysis (MSFA) model which partitions the massive

Asians' Facial Responsiveness to Basic Tastes by Automated Facial Expression Analysis System.

Science.gov (United States)

Zhi, Ruicong; Cao, Lianyu; Cao, Gang

2017-03-01

Growing evidence shows that consumer choices in real life are mostly driven by unconscious mechanisms rather than conscious. The unconscious process could be measured by behavioral measurements. This study aims to apply automatic facial expression analysis technique for consumers' emotion representation, and explore the relationships between sensory perception and facial responses. Basic taste solutions (sourness, sweetness, bitterness, umami, and saltiness) with 6 levels plus water were used, which could cover most of the tastes found in food and drink. The other contribution of this study is to analyze the characteristics of facial expressions and correlation between facial expressions and perceptive hedonic liking for Asian consumers. Up until now, the facial expression application researches only reported for western consumers, while few related researches investigated the facial responses during food consuming for Asian consumers. Experimental results indicated that facial expressions could identify different stimuli with various concentrations and different hedonic levels. The perceived liking increased at lower concentrations and decreased at higher concentrations, while samples with medium concentrations were perceived as the most pleasant except sweetness and bitterness. High correlations were founded between perceived intensities of bitterness, umami, saltiness, and facial reactions of disgust and fear. Facial expression disgust and anger could characterize emotion "dislike," and happiness could characterize emotion "like," while neutral could represent "neither like nor dislike." The identified facial expressions agree with the perceived sensory emotions elicited by basic taste solutions. The correlation analysis between hedonic levels and facial expression intensities obtained in this study are in accordance with that discussed for western consumers. © 2017 Institute of Food Technologists®.

Scaling of mode shapes from operational modal analysis using harmonic forces

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Brandt, A.; Berardengo, M.; Manzoni, S.; Cigada, A.

2017-10-01

This paper presents a new method for scaling mode shapes obtained by means of operational modal analysis. The method is capable of scaling mode shapes on any structure, also structures with closely coupled modes, and the method can be used in the presence of ambient vibration from traffic or wind loads, etc. Harmonic excitation can be relatively easily accomplished by using general-purpose actuators, also for force levels necessary for driving large structures such as bridges and highrise buildings. The signal processing necessary for mode shape scaling by the proposed method is simple and the method can easily be implemented in most measurement systems capable of generating a sine wave output. The tests necessary to scale the modes are short compared to typical operational modal analysis test time. The proposed method is thus easy to apply and inexpensive relative to some other methods for scaling mode shapes that are available in literature. Although it is not necessary per se, we propose to excite the structure at, or close to, the eigenfrequencies of the modes to be scaled, since this provides better signal-to-noise ratio in the response sensors, thus permitting the use of smaller actuators. An extensive experimental activity on a real structure was carried out and the results reported demonstrate the feasibility and accuracy of the proposed method. Since the method utilizes harmonic excitation for the mode shape scaling, we propose to call the method OMAH.

Expression analysis of dihydroflavonol 4-reductase genes in Petunia hybrida.

Science.gov (United States)

Chu, Y X; Chen, H R; Wu, A Z; Cai, R; Pan, J S

2015-05-12

Dihydroflavonol 4-reductase (DFR) genes from Rosa chinensis (Asn type) and Calibrachoa hybrida (Asp type), driven by a CaMV 35S promoter, were integrated into the petunia (Petunia hybrida) cultivar 9702. Exogenous DFR gene expression characteristics were similar to flower-color changes, and effects on anthocyanin concentration were observed in both types of DFR gene transformants. Expression analysis showed that exogenous DFR genes were expressed in all of the tissues, but the expression levels were significantly different. However, both of them exhibited a high expression level in petals that were starting to open. The introgression of DFR genes may significantly change DFR enzyme activity. Anthocyanin ultra-performance liquid chromatography results showed that anthocyanin concentrations changed according to DFR enzyme activity. Therefore, the change in flower color was probably the result of a DFR enzyme change. Pelargonidin 3-O-glucoside was found in two different transgenic petunias, indicating that both CaDFR and RoDFR could catalyze dihydrokaempferol. Our results also suggest that transgenic petunias with DFR gene of Asp type could biosynthesize pelargonidin 3-O-glucoside.

Rasch Analysis of the Fullerton Advanced Balance (FAB) Scale

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Fiedler, Roger C.; Rose, Debra J.

2011-01-01

ABSTRACT Purpose: This cross-sectional study explores the psychometric properties and dimensionality of the Fullerton Advanced Balance (FAB) Scale, a multi-item balance test for higher-functioning older adults. Methods: Participants (n=480) were community-dwelling adults able to ambulate independently. Data gathering consisted of survey and balance performance assessment. Psychometric properties were assessed using Rasch analysis. Results: Mean age of participants was 76.4 (SD=7.1) years. Mean FAB Scale scores were 24.7/40 (SD=7.5). Analyses for scale dimensionality showed that 9 of the 10 items fit a unidimensional measure of balance. Item 10 (Reactive Postural Control) did not fit the model. The reliability of the scale to separate persons was 0.81 out of 1.00; the reliability of the scale to separate items in terms of their difficulty was 0.99 out of 1.00. Cronbach's alpha for a 10-item model was 0.805. Items of differing difficulties formed a useful ordinal hierarchy for scaling patterns of expected balance ability scoring for a normative population. Conclusion: The FAB Scale appears to be a reliable and valid tool to assess balance function in higher-functioning older adults. The test was found to discriminate among participants of varying balance abilities. Further exploration of concurrent validity of Rasch-generated expected item scoring patterns should be undertaken to determine the test's diagnostic and prescriptive utility. PMID:22210989

Rasch Analysis of the Fullerton Advanced Balance (FAB) Scale.

Science.gov (United States)

Klein, Penelope J; Fiedler, Roger C; Rose, Debra J

2011-01-01

This cross-sectional study explores the psychometric properties and dimensionality of the Fullerton Advanced Balance (FAB) Scale, a multi-item balance test for higher-functioning older adults. Participants (n=480) were community-dwelling adults able to ambulate independently. Data gathering consisted of survey and balance performance assessment. Psychometric properties were assessed using Rasch analysis. Mean age of participants was 76.4 (SD=7.1) years. Mean FAB Scale scores were 24.7/40 (SD=7.5). Analyses for scale dimensionality showed that 9 of the 10 items fit a unidimensional measure of balance. Item 10 (Reactive Postural Control) did not fit the model. The reliability of the scale to separate persons was 0.81 out of 1.00; the reliability of the scale to separate items in terms of their difficulty was 0.99 out of 1.00. Cronbach's alpha for a 10-item model was 0.805. Items of differing difficulties formed a useful ordinal hierarchy for scaling patterns of expected balance ability scoring for a normative population. The FAB Scale appears to be a reliable and valid tool to assess balance function in higher-functioning older adults. The test was found to discriminate among participants of varying balance abilities. Further exploration of concurrent validity of Rasch-generated expected item scoring patterns should be undertaken to determine the test's diagnostic and prescriptive utility.

Comprehensive analysis of gene expression patterns of hedgehog-related genes

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Baillie David

2006-10-01

Full Text Available Abstract Background The Caenorhabditis elegans genome encodes ten proteins that share sequence similarity with the Hedgehog signaling molecule through their C-terminal autoprocessing Hint/Hog domain. These proteins contain novel N-terminal domains, and C. elegans encodes dozens of additional proteins containing only these N-terminal domains. These gene families are called warthog, groundhog, ground-like and quahog, collectively called hedgehog (hh-related genes. Previously, the expression pattern of seventeen genes was examined, which showed that they are primarily expressed in the ectoderm. Results With the completion of the C. elegans genome sequence in November 2002, we reexamined and identified 61 hh-related ORFs. Further, we identified 49 hh-related ORFs in C. briggsae. ORF analysis revealed that 30% of the genes still had errors in their predictions and we improved these predictions here. We performed a comprehensive expression analysis using GFP fusions of the putative intergenic regulatory sequence with one or two transgenic lines for most genes. The hh-related genes are expressed in one or a few of the following tissues: hypodermis, seam cells, excretory duct and pore cells, vulval epithelial cells, rectal epithelial cells, pharyngeal muscle or marginal cells, arcade cells, support cells of sensory organs, and neuronal cells. Using time-lapse recordings, we discovered that some hh-related genes are expressed in a cyclical fashion in phase with molting during larval development. We also generated several translational GFP fusions, but they did not show any subcellular localization. In addition, we also studied the expression patterns of two genes with similarity to Drosophila frizzled, T23D8.1 and F27E11.3A, and the ortholog of the Drosophila gene dally-like, gpn-1, which is a heparan sulfate proteoglycan. The two frizzled homologs are expressed in a few neurons in the head, and gpn-1 is expressed in the pharynx. Finally, we compare the

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer

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Halabi, Najeeb M.; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G.; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A.; Malek, Joel A.; Rafii, Arash

2016-01-01

Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

Cloning, characterization and expression analysis of porcine microRNAs

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Desilva Udaya

2009-02-01

Full Text Available Abstract Background MicroRNAs (miRNAs are small ~22-nt regulatory RNAs that can silence target genes, by blocking their protein production or degrading the mRNAs. Pig is an important animal in the agriculture industry because of its utility in the meat production. Besides, pig has tremendous biomedical importance as a model organism because of its closer proximity to humans than the mouse model. Several hundreds of miRNAs have been identified from mammals, humans, mice and rats, but little is known about the miRNA component in the pig genome. Here, we adopted an experimental approach to identify conserved and unique miRNAs and characterize their expression patterns in diverse tissues of pig. Results By sequencing a small RNA library generated using pooled RNA from the pig heart, liver and thymus; we identified a total of 120 conserved miRNA homologs in pig. Expression analysis of conserved miRNAs in 14 different tissue types revealed heart-specific expression of miR-499 and miR-208 and liver-specific expression of miR-122. Additionally, miR-1 and miR-133 in the heart, miR-181a and miR-142-3p in the thymus, miR-194 in the liver, and miR-143 in the stomach showed the highest levels of expression. miR-22, miR-26b, miR-29c and miR-30c showed ubiquitous expression in diverse tissues. The expression patterns of pig-specific miRNAs also varied among the tissues examined. Conclusion Identification of 120 miRNAs and determination of the spatial expression patterns of a sub-set of these in the pig is a valuable resource for molecular biologists, breeders, and biomedical investigators interested in post-transcriptional gene regulation in pig and in related mammals, including humans.

Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation.

Science.gov (United States)

Li, Jian-Feng; Bush, Jenifer; Xiong, Yan; Li, Lei; McCormack, Matthew

2011-01-01

Protein-protein interactions (PPIs) constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been successfully used for large-scale surveys of PPIs in plants, each having advantages and disadvantages. Here we present split firefly luciferase complementation (SFLC) as a highly sensitive and noninvasive technique for in planta PPI investigation. In this assay, the separate halves of a firefly luciferase can come into close proximity and transiently restore its catalytic activity only when their fusion partners, namely the two proteins of interest, interact with each other. This assay was conferred with quantitativeness and high throughput potential when the Arabidopsis mesophyll protoplast system and a microplate luminometer were employed for protein expression and luciferase measurement, respectively. Using the SFLC assay, we could monitor the dynamics of rapamycin-induced and ascomycin-disrupted interaction between Arabidopsis FRB and human FKBP proteins in a near real-time manner. As a proof of concept for large-scale PPI survey, we further applied the SFLC assay to testing 132 binary PPIs among 8 auxin response factors (ARFs) and 12 Aux/IAA proteins from Arabidopsis. Our results demonstrated that the SFLC assay is ideal for in vivo quantitative PPI analysis in plant cells and is particularly powerful for large-scale binary PPI screens.

Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation.

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Jian-Feng Li

Full Text Available Protein-protein interactions (PPIs constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been successfully used for large-scale surveys of PPIs in plants, each having advantages and disadvantages. Here we present split firefly luciferase complementation (SFLC as a highly sensitive and noninvasive technique for in planta PPI investigation. In this assay, the separate halves of a firefly luciferase can come into close proximity and transiently restore its catalytic activity only when their fusion partners, namely the two proteins of interest, interact with each other. This assay was conferred with quantitativeness and high throughput potential when the Arabidopsis mesophyll protoplast system and a microplate luminometer were employed for protein expression and luciferase measurement, respectively. Using the SFLC assay, we could monitor the dynamics of rapamycin-induced and ascomycin-disrupted interaction between Arabidopsis FRB and human FKBP proteins in a near real-time manner. As a proof of concept for large-scale PPI survey, we further applied the SFLC assay to testing 132 binary PPIs among 8 auxin response factors (ARFs and 12 Aux/IAA proteins from Arabidopsis. Our results demonstrated that the SFLC assay is ideal for in vivo quantitative PPI analysis in plant cells and is particularly powerful for large-scale binary PPI screens.

Long SAGE analysis of genes differentially expressed in the midgut ...

African Journals Online (AJOL)

Long SAGE analysis of genes differentially expressed in the midgut and silk gland between the sexes of the silkwormBombyx mori. Liping Gan, Ying Wang, Jian Xi, Yanshan Niu, Hongyou Qin, Yanghu Sima, Shiqing Xu ...

A constructive approach to gene expression dynamics

International Nuclear Information System (INIS)

Ochiai, T.; Nacher, J.C.; Akutsu, T.

2004-01-01

Recently, experiments on mRNA abundance (gene expression) have revealed that gene expression shows a stationary organization described by a scale-free distribution. Here we propose a constructive approach to gene expression dynamics which restores the scale-free exponent and describes the intermediate state dynamics. This approach requires only one assumption: Markov property

Analysis of gene expression profile microarray data in complex regional pain syndrome.

Science.gov (United States)

Tan, Wulin; Song, Yiyan; Mo, Chengqiang; Jiang, Shuangjian; Wang, Zhongxing

2017-09-01

The aim of the present study was to predict key genes and proteins associated with complex regional pain syndrome (CRPS) using bioinformatics analysis. The gene expression profiling microarray data, GSE47603, which included peripheral blood samples from 4 patients with CRPS and 5 healthy controls, was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in CRPS patients compared with healthy controls were identified using the GEO2R online tool. Functional enrichment analysis was then performed using The Database for Annotation Visualization and Integrated Discovery online tool. Protein‑protein interaction (PPI) network analysis was subsequently performed using Search Tool for the Retrieval of Interaction Genes database and analyzed with Cytoscape software. A total of 257 DEGs were identified, including 243 upregulated genes and 14 downregulated ones. Genes in the human leukocyte antigen (HLA) family were most significantly differentially expressed. Enrichment analysis demonstrated that signaling pathways, including immune response, cell motion, adhesion and angiogenesis were associated with CRPS. PPI network analysis revealed that key genes, including early region 1A binding protein p300 (EP300), CREB‑binding protein (CREBBP), signal transducer and activator of transcription (STAT)3, STAT5A and integrin α M were associated with CRPS. The results suggest that the immune response may therefore serve an important role in CRPS development. In addition, genes in the HLA family, such as HLA‑DQB1 and HLA‑DRB1, may present potential biomarkers for the diagnosis of CRPS. Furthermore, EP300, its paralog CREBBP, and the STAT family genes, STAT3 and STAT5 may be important in the development of CRPS.

Expression analysis of the Theileria parva subtelomere-encoded variable secreted protein gene family.

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Jacqueline Schmuckli-Maurer

Full Text Available The intracellular protozoan parasite Theileria parva transforms bovine lymphocytes inducing uncontrolled proliferation. Proteins released from the parasite are assumed to contribute to phenotypic changes of the host cell and parasite persistence. With 85 members, genes encoding subtelomeric variable secreted proteins (SVSPs form the largest gene family in T. parva. The majority of SVSPs contain predicted signal peptides, suggesting secretion into the host cell cytoplasm.We analysed SVSP expression in T. parva-transformed cell lines established in vitro by infection of T or B lymphocytes with cloned T. parva parasites. Microarray and quantitative real-time PCR analysis revealed mRNA expression for a wide range of SVSP genes. The pattern of mRNA expression was largely defined by the parasite genotype and not by host background or cell type, and found to be relatively stable in vitro over a period of two months. Interestingly, immunofluorescence analysis carried out on cell lines established from a cloned parasite showed that expression of a single SVSP encoded by TP03_0882 is limited to only a small percentage of parasites. Epitope-tagged TP03_0882 expressed in mammalian cells was found to translocate into the nucleus, a process that could be attributed to two different nuclear localisation signals.Our analysis reveals a complex pattern of Theileria SVSP mRNA expression, which depends on the parasite genotype. Whereas in cell lines established from a cloned parasite transcripts can be found corresponding to a wide range of SVSP genes, only a minority of parasites appear to express a particular SVSP protein. The fact that a number of SVSPs contain functional nuclear localisation signals suggests that proteins released from the parasite could contribute to phenotypic changes of the host cell. This initial characterisation will facilitate future studies on the regulation of SVSP gene expression and the potential biological role of these enigmatic

Multi-scaling allometric analysis for urban and regional development

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Chen, Yanguang

2017-01-01

The concept of allometric growth is based on scaling relations, and it has been applied to urban and regional analysis for a long time. However, most allometric analyses were devoted to the single proportional relation between two elements of a geographical system. Few researches focus on the allometric scaling of multielements. In this paper, a process of multiscaling allometric analysis is developed for the studies on spatio-temporal evolution of complex systems. By means of linear algebra, general system theory, and by analogy with the analytical hierarchy process, the concepts of allometric growth can be integrated with the ideas from fractal dimension. Thus a new methodology of geo-spatial analysis and the related theoretical models emerge. Based on the least squares regression and matrix operations, a simple algorithm is proposed to solve the multiscaling allometric equation. Applying the analytical method of multielement allometry to Chinese cities and regions yields satisfying results. A conclusion is reached that the multiscaling allometric analysis can be employed to make a comprehensive evaluation for the relative levels of urban and regional development, and explain spatial heterogeneity. The notion of multiscaling allometry may enrich the current theory and methodology of spatial analyses of urban and regional evolution.

Serial analysis of gene expression in the silkworm, Bombyx mori.

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Huang, Jianhua; Miao, Xuexia; Jin, Weirong; Couble, Pierre; Mita, Kasuei; Zhang, Yong; Liu, Wenbin; Zhuang, Leijun; Shen, Yan; Keime, Celine; Gandrillon, Olivier; Brouilly, Patrick; Briolay, Jerome; Zhao, Guoping; Huang, Yongping

2005-08-01

The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmental life cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, of which 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, and adult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes.

Partial Least Squares Based Gene Expression Analysis in EBV- Positive and EBV-Negative Posttransplant Lymphoproliferative Disorders.

Science.gov (United States)

Wu, Sa; Zhang, Xin; Li, Zhi-Ming; Shi, Yan-Xia; Huang, Jia-Jia; Xia, Yi; Yang, Hang; Jiang, Wen-Qi

2013-01-01

Post-transplant lymphoproliferative disorder (PTLD) is a common complication of therapeutic immunosuppression after organ transplantation. Gene expression profile facilitates the identification of biological difference between Epstein-Barr virus (EBV) positive and negative PTLDs. Previous studies mainly implemented variance/regression analysis without considering unaccounted array specific factors. The aim of this study is to investigate the gene expression difference between EBV positive and negative PTLDs through partial least squares (PLS) based analysis. With a microarray data set from the Gene Expression Omnibus database, we performed PLS based analysis. We acquired 1188 differentially expressed genes. Pathway and Gene Ontology enrichment analysis identified significantly over-representation of dysregulated genes in immune response and cancer related biological processes. Network analysis identified three hub genes with degrees higher than 15, including CREBBP, ATXN1, and PML. Proteins encoded by CREBBP and PML have been reported to be interact with EBV before. Our findings shed light on expression distinction of EBV positive and negative PTLDs with the hope to offer theoretical support for future therapeutic study.

Application of Trait Anger and Anger Expression Styles Scale New Modelling on University Students from Various Social and Cultural Environments

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Arslan, Fethi

2016-01-01

The purpose of this study is to investigate the differences in anger traits of university students and teacher candidates studying in various social and cultural regions, of Batman and Denizli, Turkey. Modelling anger and anger expression style scale according to some variables such as age, gender, education level, number of siblings, parents'…

Expressing Anger Is More Dangerous than Feeling Angry when Driving.

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Weina Qu

Full Text Available Anger is an emotion that drivers often feel and express while driving, and it is believed by researchers to be an important cause of dangerous driving behavior. In this study, the relationships between driving trait anger, driving anger expression, and dangerous driving behaviors were analyzed. The Driving Anger Scale (DAS was used to measure driving trait anger, whereas the Driving Anger Expression (DAX Inventory was used to measure expressions of driving anger. A sample of 38 drivers completed the DAS, DAX, and a driving simulation session on a simulator where their driving behaviors were recorded. Correlation analysis showed that the higher scores on the DAS were associated with longer durations of speeding in the simulator. The more participants expressed their anger in verbal and physical ways, the more likely they were to crash the virtual vehicle during the simulation. Regression analyses illustrated the same pattern. The findings suggest that, although trait anger is related to speeding, the passive expression of anger is the real factor underling traffic accidents. This study extends findings about the predictive effects of self-report scales of driving behaviors to behaviors recorded on a simulator. Thus, if in traffic safety propaganda, guiding drivers to use positive ways to cope with driving anger is recommended by our findings.

Expressing Anger Is More Dangerous than Feeling Angry when Driving.

Science.gov (United States)

Qu, Weina; Dai, Mengnuo; Zhao, Wenguo; Zhang, Kan; Ge, Yan

2016-01-01

Anger is an emotion that drivers often feel and express while driving, and it is believed by researchers to be an important cause of dangerous driving behavior. In this study, the relationships between driving trait anger, driving anger expression, and dangerous driving behaviors were analyzed. The Driving Anger Scale (DAS) was used to measure driving trait anger, whereas the Driving Anger Expression (DAX) Inventory was used to measure expressions of driving anger. A sample of 38 drivers completed the DAS, DAX, and a driving simulation session on a simulator where their driving behaviors were recorded. Correlation analysis showed that the higher scores on the DAS were associated with longer durations of speeding in the simulator. The more participants expressed their anger in verbal and physical ways, the more likely they were to crash the virtual vehicle during the simulation. Regression analyses illustrated the same pattern. The findings suggest that, although trait anger is related to speeding, the passive expression of anger is the real factor underling traffic accidents. This study extends findings about the predictive effects of self-report scales of driving behaviors to behaviors recorded on a simulator. Thus, if in traffic safety propaganda, guiding drivers to use positive ways to cope with driving anger is recommended by our findings.

Analysis of image versus position, scale and direction reveals pattern texture anisotropy

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Roland eLehoucq

2015-01-01

Full Text Available Pattern heterogeneities and anisotropies often carry significant physical information. We provide a toolbox which: (i cumulates analysis in terms of position, direction and scale; (ii is as general as possible; (iii is simple and fast to understand, implement, execute and exploit.It consists in dividing the image into analysis boxes at a chosen scale; in each box an ellipse (the inertia tensor is fitted to the signal and thus determines the direction in which the signal is more present. This tensor can be averaged in position and/or be used to study the dependence with scale. This choice is formally linked with Leray transforms and anisotropic wavelet analysis. Such protocol is intutively interpreted and consistent with what the eye detects: relevant scales, local variations in space, priviledged directions. It is fast and parallelizable.Its several variants are adaptable to the user's data and needs. It is useful to statistically characterize anisotropies of 2D or 3D patterns in which individual objects are not easily distinguished, with only minimal pre-processing of the raw image, and more generally applies to data in higher dimensions.It is less sensitive to edge effects, and thus better adapted for a multiscale analysis down to small scale boxes, than pair correlation function or Fourier transform.Easy to understand and implement,it complements more sophisticated methods such as Hough transform or diffusion tensor imaging.We use it on various fracture patterns (sea ice cover, thin sections of granite, granular materials, to pinpoint the maximal anisotropy scales. The results are robust to noise and to user choices. This toolbox could turn also useful for granular materials, hard condensed matter, geophysics, thin films, statistical mechanics, characterisation of networks, fluctuating amorphous systems, inhomogeneous and disordered systems, or medical imaging, among others.

A scaling analysis of alloy solidification in presence of electromagnetic stirring

International Nuclear Information System (INIS)

Kumar, Arvind; Dutta, Pradip

2006-01-01

Application of electromagnetic stirring (EMS) during continuous casting shears off the dendrites from the solidification front to produce billets with a non-dendritic microstructure. In the present study, a systematic approach to the scaling analysis of momentum, energy and species conservation equations pertaining to the case of the solidification of a binary alloy in the presence of EMS is outlined. With suitable choices of non-dimensionalizing parameters, the governing equations coupled with appropriate boundary conditions are first scaled, and then the relative significance of various terms appearing in them are analysed. In the physical domain two regions are identified, one where the electromagnetic forces play a dominant role in the momentum equations, and the other where the inertia and viscous effects play major roles. Using the scaling predictions, the influence of various processing parameters on the system variables can be utilized for the selection of appropriate electromagnetic forces to shear off the dendrites from the solidification area. For the sake of assessment of the scaling analysis, the predictions are validated against corresponding computational results

Dynamics analysis of the fast-slow hydro-turbine governing system with different time-scale coupling

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Zhang, Hao; Chen, Diyi; Wu, Changzhi; Wang, Xiangyu

2018-01-01

Multi-time scales modeling of hydro-turbine governing system is crucial in precise modeling of hydropower plant and provides support for the stability analysis of the system. Considering the inertia and response time of the hydraulic servo system, the hydro-turbine governing system is transformed into the fast-slow hydro-turbine governing system. The effects of the time-scale on the dynamical behavior of the system are analyzed and the fast-slow dynamical behaviors of the system are investigated with different time-scale. Furthermore, the theoretical analysis of the stable regions is presented. The influences of the time-scale on the stable region are analyzed by simulation. The simulation results prove the correctness of the theoretical analysis. More importantly, the methods and results of this paper provide a perspective to multi-time scales modeling of hydro-turbine governing system and contribute to the optimization analysis and control of the system.

Of mice and men: divergence of gene expression patterns in kidney.

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Lydie Cheval

Full Text Available Since the development of methods for homologous gene recombination, mouse models have played a central role in research in renal pathophysiology. However, many published and unpublished results show that mice with genetic changes mimicking human pathogenic mutations do not display the human phenotype. These functional differences may stem from differences in gene expression between mouse and human kidneys. However, large scale comparison of gene expression networks revealed conservation of gene expression among a large panel of human and mouse tissues including kidneys. Because renal functions result from the spatial integration of elementary processes originating in the glomerulus and the successive segments constituting the nephron, we hypothesized that differences in gene expression profiles along the human and mouse nephron might account for different behaviors. Analysis of SAGE libraries generated from the glomerulus and seven anatomically defined nephron segments from human and mouse kidneys allowed us to identify 4644 pairs of gene orthologs expressed in either one or both species. Quantitative analysis shows that many transcripts are present at different levels in the two species. It also shows poor conservation of gene expression profiles, with less than 10% of the 4644 gene orthologs displaying a higher conservation of expression profiles than the neutral expectation (p<0.05. Accordingly, hierarchical clustering reveals a higher degree of conservation of gene expression patterns between functionally unrelated kidney structures within a given species than between cognate structures from the two species. Similar findings were obtained for sub-groups of genes with either kidney-specific or housekeeping functions. Conservation of gene expression at the scale of the whole organ and divergence at the level of its constituting sub-structures likely account for the fact that although kidneys assume the same global function in the two species

Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI.

Science.gov (United States)

Wang, Weijing; Jiang, Wenjie; Hou, Lin; Duan, Haiping; Wu, Yili; Xu, Chunsheng; Tan, Qihua; Li, Shuxia; Zhang, Dongfeng

2017-11-13

The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins. In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database and NF-kappa B signaling pathway within KEGG database. DEGs of NAMPT, TLR9, PTGS2, HBD, and PCSK1N might be associated with obesity. In the WGCNA, among the total 20 distinct co-expression modules identified, coral1 module (68 genes) had the strongest positive correlation with BMI (r = 0.56, P = 0.04) and disease status (r = 0.56, P = 0.04). Categories of positive regulation of phospholipase activity, high-density lipoprotein particle clearance, chylomicron remnant clearance, reverse cholesterol transport, intermediate-density lipoprotein particle, chylomicron, low-density lipoprotein particle, very-low-density lipoprotein particle, voltage-gated potassium channel complex, cholesterol transporter activity, and neuropeptide hormone activity were significantly enriched within GO database for this module. And alcoholism and cell adhesion molecules pathways were significantly enriched within KEGG database. Several hub genes, such as GAL, ASB9, NPPB, TBX2, IL17C, APOE, ABCG4, and APOC2 were also identified. The module eigengene of saddlebrown module (212 genes) was also significantly

Clinical Omics Analysis of Colorectal Cancer Incorporating Copy Number Aberrations and Gene Expression Data

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Tsuyoshi Yoshida

2010-07-01

Full Text Available Background: Colorectal cancer (CRC is one of the most frequently occurring cancers in Japan, and thus a wide range of methods have been deployed to study the molecular mechanisms of CRC. In this study, we performed a comprehensive analysis of CRC, incorporating copy number aberration (CRC and gene expression data. For the last four years, we have been collecting data from CRC cases and organizing the information as an “omics” study by integrating many kinds of analysis into a single comprehensive investigation. In our previous studies, we had experienced difficulty in finding genes related to CRC, as we observed higher noise levels in the expression data than in the data for other cancers. Because chromosomal aberrations are often observed in CRC, here, we have performed a combination of CNA analysis and expression analysis in order to identify some new genes responsible for CRC. This study was performed as part of the Clinical Omics Database Project at Tokyo Medical and Dental University. The purpose of this study was to investigate the mechanism of genetic instability in CRC by this combination of expression analysis and CNA, and to establish a new method for the diagnosis and treatment of CRC. Materials and methods: Comprehensive gene expression analysis was performed on 79 CRC cases using an Affymetrix Gene Chip, and comprehensive CNA analysis was performed using an Affymetrix DNA Sty array. To avoid the contamination of cancer tissue with normal cells, laser micro-dissection was performed before DNA/RNA extraction. Data analysis was performed using original software written in the R language. Result: We observed a high percentage of CNA in colorectal cancer, including copy number gains at 7, 8q, 13 and 20q, and copy number losses at 8p, 17p and 18. Gene expression analysis provided many candidates for CRC-related genes, but their association with CRC did not reach the level of statistical significance. The combination of CNA and gene

Can Automated Facial Expression Analysis Show Differences Between Autism and Typical Functioning?

Science.gov (United States)

Borsos, Zsófia; Gyori, Miklos

2017-01-01

Exploratory analyses of emotional expressions using a commercially available facial expression recognition software are reported, from the context of a serious game for screening purposes. Our results are based on a comparative analysis of two matched groups of kindergarten-age children (high-functioning children with autism spectrum condition: n=13; typically developing children: n=13). Results indicate that this technology has the potential to identify autism-specific emotion expression features, and may play a role in affective diagnostic and assistive technologies.

Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

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Henry D Priest

Full Text Available Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes

International Nuclear Information System (INIS)

Warnat, Patrick; Oberthuer, André; Fischer, Matthias; Westermann, Frank; Eils, Roland; Brors, Benedikt

2007-01-01

Neuroblastoma patients show heterogeneous clinical courses ranging from life-threatening progression to spontaneous regression. Recently, gene expression profiles of neuroblastoma tumours were associated with clinically different phenotypes. However, such data is still rare for important patient subgroups, such as patients with MYCN non-amplified advanced stage disease. Prediction of the individual course of disease and optimal therapy selection in this cohort is challenging. Additional research effort is needed to describe the patterns of gene expression in this cohort and to identify reliable prognostic markers for this subset of patients. We combined gene expression data from two studies in a meta-analysis in order to investigate differences in gene expression of advanced stage (3 or 4) tumours without MYCN amplification that show contrasting outcomes (alive or dead) at five years after initial diagnosis. In addition, a predictive model for outcome was generated. Gene expression profiles from 66 patients were included from two studies using different microarray platforms. In the combined data set, 72 genes were identified as differentially expressed by meta-analysis at a false discovery rate (FDR) of 8.33%. Meta-analysis detected 34 differentially expressed genes that were not found as significant in either single study. Outcome prediction based on data of both studies resulted in a predictive accuracy of 77%. Moreover, the genes that were differentially expressed in subgroups of advanced stage patients without MYCN amplification accurately separated MYCN amplified tumours from low stage tumours without MYCN amplification. Our findings support the hypothesis that neuroblastoma consists of two biologically distinct subgroups that differ by characteristic gene expression patterns, which are associated with divergent clinical outcome

Serial Analysis of Gene Expression: Applications in Human Studies

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Tuteja Renu

2004-01-01

Full Text Available Serial analysis of gene expression (SAGE is a powerful tool, which provides quantitative and comprehensive expression profile of genes in a given cell population. It works by isolating short fragments of genetic information from the expressed genes that are present in the cell being studied. These short sequences, called SAGE tags, are linked together for efficient sequencing. The frequency of each SAGE tag in the cloned multimers directly reflects the transcript abundance. Therefore, SAGE results in an accurate picture of gene expression at both the qualitative and the quantitative levels. It does not require a hybridization probe for each transcript and allows new genes to be discovered. This technique has been applied widely in human studies and various SAGE tags/SAGE libraries have been generated from different cells/tissues such as dendritic cells, lung fibroblast cells, oocytes, thyroid tissue, B-cell lymphoma, cultured keratinocytes, muscles, brain tissues, sciatic nerve, cultured Schwann cells, cord blood-derived mast cells, retina, macula, retinal pigment epithelial cells, skin cells, and so forth. In this review we present the updated information on the applications of SAGE technology mainly to human studies.

Cloning and expression analysis of a new anther-specific gene ...

Indian Academy of Sciences (India)

sequencing gene differential expression analysis (Chen et al. ... DNase digestion (Takara, Shiga, Japan), so that any remain- ..... ing the early moments of pollen germination (Guyon et al. 2000). The steady-state transcript level of PGPS/D3 ...

Gene expression analysis of early stage endometrial cancersreveals unique transcripts associated with grade and histologybut not depth of invasion

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John eRisinger

2013-06-01

Full Text Available Endometrial cancer is the most common gynecologic malignancy in the United States but it remains poorly understood at the molecular level. This investigation was conducted to specifically assess whether gene expression changes underlie the clinical and pathologic factors traditionally used for determining treatment regimens in women with stage I endometrial cancer. These include the effect of tumor grade, depth of myometrial invasion and histotype. We utilized oligonucleotide microarrays to assess the transcript expression profile in epithelial glandular cells laser microdissected from 79 endometrioid and 12 serous stage I endometrial cancers with a heterogeneous distribution of grade and depth of myometrial invasion, along with 12 normal post-menopausal endometrial samples. Unsupervised multidimensional scaling analyses revealed that serous and endometrioid stage I cancers have similar transcript expression patterns when compared to normal controls where 900 transcripts were identified to be differentially expressed by at least 4-fold (univariate t-test, p <0.001 between the cancers and normal endometrium. This analysis also identified transcript expression differences between serous and endometrioid cancers and tumor grade, but no apparent differences were identified as a function of depth of myometrial invasion. Four genes were validated by quantitative PCR on an independent set of cancer and normal endometrium samples. These findings indicate that unique gene expression profiles are associated with histologic type and grade, but not myometrial invasion among early stage endometrial cancers. These data provide a comprehensive perspective on the molecular alterations associated with stage I endometrial cancer, particularly those subtypes that have the worst prognosis.

Analysis of gene expression in prostate cancer epithelial and interstitial stromal cells using laser capture microdissection

International Nuclear Information System (INIS)

Gregg, Jennifer L; Brown, Kathleen E; Mintz, Eric M; Piontkivska, Helen; Fraizer, Gail C

2010-01-01

The prostate gland represents a multifaceted system in which prostate epithelia and stroma have distinct physiological roles. To understand the interaction between stroma and glandular epithelia, it is essential to delineate the gene expression profiles of these two tissue types in prostate cancer. Most studies have compared tumor and normal samples by performing global expression analysis using a mixture of cell populations. This report presents the first study of prostate tumor tissue that examines patterns of differential expression between specific cell types using laser capture microdissection (LCM). LCM was used to isolate distinct cell-type populations and identify their gene expression differences using oligonucleotide microarrays. Ten differentially expressed genes were then analyzed in paired tumor and non-neoplastic prostate tissues by quantitative real-time PCR. Expression patterns of the transcription factors, WT1 and EGR1, were further compared in established prostate cell lines. WT1 protein expression was also examined in prostate tissue microarrays using immunohistochemistry. The two-step method of laser capture and microarray analysis identified nearly 500 genes whose expression levels were significantly different in prostate epithelial versus stromal tissues. Several genes expressed in epithelial cells (WT1, GATA2, and FGFR-3) were more highly expressed in neoplastic than in non-neoplastic tissues; conversely several genes expressed in stromal cells (CCL5, CXCL13, IGF-1, FGF-2, and IGFBP3) were more highly expressed in non-neoplastic than in neoplastic tissues. Notably, EGR1 was also differentially expressed between epithelial and stromal tissues. Expression of WT1 and EGR1 in cell lines was consistent with these patterns of differential expression. Importantly, WT1 protein expression was demonstrated in tumor tissues and was absent in normal and benign tissues. The prostate represents a complex mix of cell types and there is a need to analyze

Effect of vibration on osteoblastic and osteoclastic activities: Analysis of bone metabolism using goldfish scale as a model for bone

Science.gov (United States)

Suzuki, N.; Kitamura, K.; Nemoto, T.; Shimizu, N.; Wada, S.; Kondo, T.; Tabata, M. J.; Sodeyama, F.; Ijiri, K.; Hattori, A.

In osteoclastic activity during space flight as well as hind limb unloading by tail suspension, inconsistent results have been reported in an in vivo study. The bone matrix plays an important role in the response to physical stress. However, there is no suitable in vitro co-culture system of osteoblasts and osteoclasts including bone matrix. On the other hand, fish scale is a calcified tissue that contains osteoblasts, osteoclasts, and bone matrix, all of which are similar to those found in human bones. Recently, we developed a new in vitro model system using goldfish scale. This system can detect the activities of osteoclasts and osteoblasts with tartrate-resistant acid phosphatase and alkaline phosphatase as the respective markers and precisely analyze the co-relationship between osteoblasts and osteoclasts. Using this system, we analyzed the bone metabolism under various degrees of acceleration (0.5-, 1-, 2-, 4-, and 6-G) by vibration with a G-load apparatus. After loading for 5 and 10 min, the scales were incubated for 6 and 24 h. The osteoblastic and osteoclastic activities were then measured. The osteoblastic activities gradually increased corresponding to 1-G to 6-G acceleration. In addition, ER mRNA expression was the highest under 6-G acceleration. On the other hand, the osteoclastic activity decreased at 24 h of incubation under low acceleration (0.5- and 1-G). This change coincided with TRAP mRNA expression. Under 2-G acceleration, the strength of suppression in osteoclastic activity was the highest. The strength of the inhibitory action under 4- and 6-G acceleration was lower than that under 2-G acceleration. In our co-culture system, osteoblasts and osteoclasts in the scale sensitively responded to several degrees of acceleration. Therefore, we strongly believe that our in vitro co-culture system is useful for the analysis of bone metabolism under loading or unloading.

Quantitative analysis of geomorphic processes using satellite image data at different scales

Science.gov (United States)

Williams, R. S., Jr.

1985-01-01

When aerial and satellite photographs and images are used in the quantitative analysis of geomorphic processes, either through direct observation of active processes or by analysis of landforms resulting from inferred active or dormant processes, a number of limitations in the use of such data must be considered. Active geomorphic processes work at different scales and rates. Therefore, the capability of imaging an active or dormant process depends primarily on the scale of the process and the spatial-resolution characteristic of the imaging system. Scale is an important factor in recording continuous and discontinuous active geomorphic processes, because what is not recorded will not be considered or even suspected in the analysis of orbital images. If the geomorphic process of landform change caused by the process is less than 200 m in x to y dimension, then it will not be recorded. Although the scale factor is critical, in the recording of discontinuous active geomorphic processes, the repeat interval of orbital-image acquisition of a planetary surface also is a consideration in order to capture a recurring short-lived geomorphic process or to record changes caused by either a continuous or a discontinuous geomorphic process.

HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.

Science.gov (United States)

Bryan, Kenneth; Jarboui, Mohamed-Ali; Raso, Cinzia; Bernal-Llinares, Manuel; McCann, Brendan; Rauch, Jens; Boldt, Karsten; Lynn, David J

2016-06-03

Recent advances in mass-spectrometry-based proteomics are now facilitating ambitious large-scale investigations of the spatial and temporal dynamics of the proteome; however, the increasing size and complexity of these data sets is overwhelming current downstream computational methods, specifically those that support the postquantification analysis pipeline. Here we present HiQuant, a novel application that enables the design and execution of a postquantification workflow, including common data-processing steps, such as assay normalization and grouping, and experimental replicate quality control and statistical analysis. HiQuant also enables the interpretation of results generated from large-scale data sets by supporting interactive heatmap analysis and also the direct export to Cytoscape and Gephi, two leading network analysis platforms. HiQuant may be run via a user-friendly graphical interface and also supports complete one-touch automation via a command-line mode. We evaluate HiQuant's performance by analyzing a large-scale, complex interactome mapping data set and demonstrate a 200-fold improvement in the execution time over current methods. We also demonstrate HiQuant's general utility by analyzing proteome-wide quantification data generated from both a large-scale public tyrosine kinase siRNA knock-down study and an in-house investigation into the temporal dynamics of the KSR1 and KSR2 interactomes. Download HiQuant, sample data sets, and supporting documentation at http://hiquant.primesdb.eu .

Decentral gene expression analysis: analytical validation of the Endopredict genomic multianalyte breast cancer prognosis test

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Kronenwett Ralf

2012-10-01

Full Text Available Abstract Background EndoPredict (EP is a clinically validated multianalyte gene expression test to predict distant metastasis in ER-positive, HER2-negative breast cancer treated with endocrine therapy alone. The test is based on the combined analysis of 12 genes in formalin-fixed, paraffin-embedded (FFPE tissue by reverse transcription-quantitative real-time PCR (RT-qPCR. Recently, it was shown that EP is feasible for reliable decentralized assessment of gene expression. The aim of this study was the analytical validation of the performance characteristics of the assay and its verification in a molecular-pathological routine laboratory. Methods Gene expression values to calculate the EP score were assayed by one-step RT-qPCR using RNA from FFPE tumor tissue. Limit of blank, limit of detection, linear range, and PCR efficiency were assessed for each of the 12 PCR assays using serial samples dilutions. Different breast cancer samples were used to evaluate RNA input range, precision and inter-laboratory variability. Results PCR assays were linear up to Cq values between 35.1 and 37.2. Amplification efficiencies ranged from 75% to 101%. The RNA input range without considerable change of the EP score was between 0.16 and 18.5 ng/μl. Analysis of precision (variation of day, day time, instrument, operator, reagent lots resulted in a total noise (standard deviation of 0.16 EP score units on a scale from 0 to 15. The major part of the total noise (SD 0.14 was caused by the replicate-to-replicate noise of the PCR assays (repeatability and was not associated with different operating conditions (reproducibility. Performance characteristics established in the manufacturer’s laboratory were verified in a routine molecular pathology laboratory. Comparison of 10 tumor samples analyzed in two different laboratories showed a Pearson coefficient of 0.995 and a mean deviation of 0.15 score units. Conclusions The EP test showed reproducible performance

Decentral gene expression analysis: analytical validation of the Endopredict genomic multianalyte breast cancer prognosis test

International Nuclear Information System (INIS)

Kronenwett, Ralf; Brase, Jan C; Weber, Karsten E; Fisch, Karin; Müller, Berit M; Schmidt, Marcus; Filipits, Martin; Dubsky, Peter; Petry, Christoph; Dietel, Manfred; Denkert, Carsten; Bohmann, Kerstin; Prinzler, Judith; Sinn, Bruno V; Haufe, Franziska; Roth, Claudia; Averdick, Manuela; Ropers, Tanja; Windbergs, Claudia

2012-01-01

EndoPredict (EP) is a clinically validated multianalyte gene expression test to predict distant metastasis in ER-positive, HER2-negative breast cancer treated with endocrine therapy alone. The test is based on the combined analysis of 12 genes in formalin-fixed, paraffin-embedded (FFPE) tissue by reverse transcription-quantitative real-time PCR (RT-qPCR). Recently, it was shown that EP is feasible for reliable decentralized assessment of gene expression. The aim of this study was the analytical validation of the performance characteristics of the assay and its verification in a molecular-pathological routine laboratory. Gene expression values to calculate the EP score were assayed by one-step RT-qPCR using RNA from FFPE tumor tissue. Limit of blank, limit of detection, linear range, and PCR efficiency were assessed for each of the 12 PCR assays using serial samples dilutions. Different breast cancer samples were used to evaluate RNA input range, precision and inter-laboratory variability. PCR assays were linear up to C q values between 35.1 and 37.2. Amplification efficiencies ranged from 75% to 101%. The RNA input range without considerable change of the EP score was between 0.16 and 18.5 ng/μl. Analysis of precision (variation of day, day time, instrument, operator, reagent lots) resulted in a total noise (standard deviation) of 0.16 EP score units on a scale from 0 to 15. The major part of the total noise (SD 0.14) was caused by the replicate-to-replicate noise of the PCR assays (repeatability) and was not associated with different operating conditions (reproducibility). Performance characteristics established in the manufacturer’s laboratory were verified in a routine molecular pathology laboratory. Comparison of 10 tumor samples analyzed in two different laboratories showed a Pearson coefficient of 0.995 and a mean deviation of 0.15 score units. The EP test showed reproducible performance characteristics with good precision and negligible laboratory

A large-scale electrophoresis- and chromatography-based determination of gene expression profiles in bovine brain capillary endothelial cells after the re-induction of blood-brain barrier properties

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Duban-Deweer Sophie

2010-11-01

Full Text Available Abstract Background Brain capillary endothelial cells (BCECs form the physiological basis of the blood-brain barrier (BBB. The barrier function is (at least in part due to well-known proteins such as transporters, tight junctions and metabolic barrier proteins (e.g. monoamine oxidase, gamma glutamyltranspeptidase and P-glycoprotein. Our previous 2-dimensional gel proteome analysis had identified a large number of proteins and revealed the major role of dynamic cytoskeletal remodelling in the differentiation of bovine BCECs. The aim of the present study was to elaborate a reference proteome of Triton X-100-soluble species from bovine BCECs cultured in the well-established in vitro BBB model developed in our laboratory. Results A total of 215 protein spots (corresponding to 130 distinct proteins were identified by 2-dimensional gel electrophoresis, whereas over 350 proteins were identified by a shotgun approach. We classified around 430 distinct proteins expressed by bovine BCECs. Our large-scale gene expression analysis enabled the correction of mistakes referenced into protein databases (e.g. bovine vinculin and constitutes valuable evidence for predictions based on genome annotation. Conclusions Elaboration of a reference proteome constitutes the first step in creating a gene expression database dedicated to capillary endothelial cells displaying BBB characteristics. It improves of our knowledge of the BBB and the key proteins in cell structures, cytoskeleton organization, metabolism, detoxification and drug resistance. Moreover, our results emphasize the need for both appropriate experimental design and correct interpretation of proteome datasets.

Psychometric properties of a scale to measure alexithymia.

Science.gov (United States)

Blanchard, E B; Arena, J G; Pallmeyer, T P

1981-01-01

Four studies were conducted on a sample of 230 undergraduates to determine the psychometric properties of a measure of alexithymia, the Schalling-Sifneos Scale. In the first study it was found that scores on the scale are approximately normally distributed for each sex with 8.2% of males and 1.8% of females in the alexithymia range. In the second study a factor analysis of the scale revealed three distinct factors: (1) 'difficulty in expression of feelings'; (2) 'the importance of feelings especially about people'; (3) 'day-dreaming or introspection'. In the second factor analytic study, scores from several standard psychological tests on the same subjects were introduced with the scale items. Two factors in this analysis were comprised almost entirely of the other test scores: a 'general psychological distress factor' and a 'concerns about physical symptoms factor'. The other two factors were similar to factors 1 and 2 above in terms of items. The Rathus Assertiveness Scale loaded positively on the equivalent of factor 1. In the lst study, it was shown that Schalling-Sifneos Scale score is relatively orthogonal to other psychological tests with the exception of a Psychosomatic Symptom Checklist and thus is measuring something other than depression, anxiety, etc.

Characterization of the global profile of genes expressed in cervical epithelium by Serial Analysis of Gene Expression (SAGE

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Piña-Sanchez Patricia

2005-09-01

Full Text Available Abstract Background Serial Analysis of Gene Expression (SAGE is a new technique that allows a detailed and profound quantitative and qualitative knowledge of gene expression profile, without previous knowledge of sequence of analyzed genes. We carried out a modification of SAGE methodology (microSAGE, useful for the analysis of limited quantities of tissue samples, on normal human cervical tissue obtained from a donor without histopathological lesions. Cervical epithelium is constituted mainly by cervical keratinocytes which are the targets of human papilloma virus (HPV, where persistent HPV infection of cervical epithelium is associated with an increase risk for developing cervical carcinomas (CC. Results We report here a transcriptome analysis of cervical tissue by SAGE, derived from 30,418 sequenced tags that provide a wealth of information about the gene products involved in normal cervical epithelium physiology, as well as genes not previously found in uterine cervix tissue involved in the process of epidermal differentiation. Conclusion This first comprehensive and profound analysis of uterine cervix transcriptome, should be useful for the identification of genes involved in normal cervix uterine function, and candidate genes associated with cervical carcinoma.

Temporal scaling and spatial statistical analyses of groundwater level fluctuations

Science.gov (United States)

Sun, H.; Yuan, L., Sr.; Zhang, Y.

2017-12-01

Natural dynamics such as groundwater level fluctuations can exhibit multifractionality and/or multifractality due likely to multi-scale aquifer heterogeneity and controlling factors, whose statistics requires efficient quantification methods. This study explores multifractionality and non-Gaussian properties in groundwater dynamics expressed by time series of daily level fluctuation at three wells located in the lower Mississippi valley, after removing the seasonal cycle in the temporal scaling and spatial statistical analysis. First, using the time-scale multifractional analysis, a systematic statistical method is developed to analyze groundwater level fluctuations quantified by the time-scale local Hurst exponent (TS-LHE). Results show that the TS-LHE does not remain constant, implying the fractal-scaling behavior changing with time and location. Hence, we can distinguish the potentially location-dependent scaling feature, which may characterize the hydrology dynamic system. Second, spatial statistical analysis shows that the increment of groundwater level fluctuations exhibits a heavy tailed, non-Gaussian distribution, which can be better quantified by a Lévy stable distribution. Monte Carlo simulations of the fluctuation process also show that the linear fractional stable motion model can well depict the transient dynamics (i.e., fractal non-Gaussian property) of groundwater level, while fractional Brownian motion is inadequate to describe natural processes with anomalous dynamics. Analysis of temporal scaling and spatial statistics therefore may provide useful information and quantification to understand further the nature of complex dynamics in hydrology.

Comprehensive comparison of large-scale tissue expression datasets

DEFF Research Database (Denmark)

Santos Delgado, Alberto; Tsafou, Kalliopi; Stolte, Christian

2015-01-01

a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining. We further found that most datasets support the assumed but not demonstrated distinction between......For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present......://tissues.jensenlab.org), which makes all the scored and integrated data available through a single user-friendly web interface....

New Developments in Mokken Scale Analysis in R

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L. Andries van der Ark

2012-05-01

Full Text Available Mokken (1971 developed a scaling procedure for both dichotomous and polytomous items that was later coined Mokken scale analysis (MSA. MSA has been developed ever since, and the developments until 2000 have been implemented in the software package MSP (Molenaar and Sijtsma 2000 and the R package mokken (Van der Ark 2007. This paper describes the new developments in MSA since 2000 that have been implemented in mokken since its first release in 2007. These new developments pertain to invariant item ordering, a new automated item selection procedure based on a genetic algorithm, inclusion of reliability coefficients, and the computation of standard errors for the scalability coefficients. We demonstrate all new applications using data obtained with a transitive reasoning test and a personality test.

Dimensional analysis, scaling and fractals

International Nuclear Information System (INIS)

Timm, L.C.; Reichardt, K.; Oliveira Santos Bacchi, O.

2004-01-01

Dimensional analysis refers to the study of the dimensions that characterize physical entities, like mass, force and energy. Classical mechanics is based on three fundamental entities, with dimensions MLT, the mass M, the length L and the time T. The combination of these entities gives rise to derived entities, like volume, speed and force, of dimensions L 3 , LT -1 , MLT -2 , respectively. In other areas of physics, four other fundamental entities are defined, among them the temperature θ and the electrical current I. The parameters that characterize physical phenomena are related among themselves by laws, in general of quantitative nature, in which they appear as measures of the considered physical entities. The measure of an entity is the result of its comparison with another one, of the same type, called unit. Maps are also drawn in scale, for example, in a scale of 1:10,000, 1 cm 2 of paper can represent 10,000 m 2 in the field. Entities that differ in scale cannot be compared in a simple way. Fractal geometry, in contrast to the Euclidean geometry, admits fractional dimensions. The term fractal is defined in Mandelbrot (1982) as coming from the Latin fractus, derived from frangere which signifies to break, to form irregular fragments. The term fractal is opposite to the term algebra (from the Arabic: jabara) which means to join, to put together the parts. For Mandelbrot, fractals are non topologic objects, that is, objects which have as their dimension a real, non integer number, which exceeds the topologic dimension. For the topologic objects, or Euclidean forms, the dimension is an integer (0 for the point, 1 for a line, 2 for a surface, and 3 for a volume). The fractal dimension of Mandelbrot is a measure of the degree of irregularity of the object under consideration. It is related to the speed by which the estimate of the measure of an object increases as the measurement scale decreases. An object normally taken as uni-dimensional, like a piece of a

Cloning and expression analysis of chalcone synthase gene from ...

Indian Academy of Sciences (India)

Expression analysis of CfCHS in different tissues and elicitor treatments showed that methyl jasmonate ... Journal of Genetics, DOI 10.1007/s12041-016-0680-8, Vol. 95, No. ... leaf of C. forskohlii. Quantitative real time RT-PCR was used ..... SGG acknowledges the financial support for this work from CSIR. 12th FYP project ...

Most experiments done so far with limited plants. Large-scale testing ...

Indian Academy of Sciences (India)

First page Back Continue Last page Graphics. Most experiments done so far with limited plants. Large-scale testing needs to be done with objectives such as: Apart from primary transformants, their progenies must be tested. Experiments on segregation, production of homozygous lines, analysis of expression levels in ...

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.

Science.gov (United States)

Theodosiou, Theodosios; Efstathiou, Georgios; Papanikolaou, Nikolas; Kyrpides, Nikos C; Bagos, Pantelis G; Iliopoulos, Ioannis; Pavlopoulos, Georgios A

2017-07-14

Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks. Network Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .

Development and analysis of prognostic equations for mesoscale kinetic energy and mesoscale (subgrid scale) fluxes for large-scale atmospheric models

Science.gov (United States)

Avissar, Roni; Chen, Fei

1993-01-01

Generated by landscape discontinuities (e.g., sea breezes) mesoscale circulation processes are not represented in large-scale atmospheric models (e.g., general circulation models), which have an inappropiate grid-scale resolution. With the assumption that atmospheric variables can be separated into large scale, mesoscale, and turbulent scale, a set of prognostic equations applicable in large-scale atmospheric models for momentum, temperature, moisture, and any other gaseous or aerosol material, which includes both mesoscale and turbulent fluxes is developed. Prognostic equations are also developed for these mesoscale fluxes, which indicate a closure problem and, therefore, require a parameterization. For this purpose, the mean mesoscale kinetic energy (MKE) per unit of mass is used, defined as E-tilde = 0.5 (the mean value of u'(sub i exp 2), where u'(sub i) represents the three Cartesian components of a mesoscale circulation (the angle bracket symbol is the grid-scale, horizontal averaging operator in the large-scale model, and a tilde indicates a corresponding large-scale mean value). A prognostic equation is developed for E-tilde, and an analysis of the different terms of this equation indicates that the mesoscale vertical heat flux, the mesoscale pressure correlation, and the interaction between turbulence and mesoscale perturbations are the major terms that affect the time tendency of E-tilde. A-state-of-the-art mesoscale atmospheric model is used to investigate the relationship between MKE, landscape discontinuities (as characterized by the spatial distribution of heat fluxes at the earth's surface), and mesoscale sensible and latent heat fluxes in the atmosphere. MKE is compared with turbulence kinetic energy to illustrate the importance of mesoscale processes as compared to turbulent processes. This analysis emphasizes the potential use of MKE to bridge between landscape discontinuities and mesoscale fluxes and, therefore, to parameterize mesoscale fluxes

Assessing social isolation in motor neurone disease: a Rasch analysis of the MND Social Withdrawal Scale.

Science.gov (United States)

Gibbons, Chris J; Thornton, Everard W; Ealing, John; Shaw, Pamela J; Talbot, Kevin; Tennant, Alan; Young, Carolyn A

2013-11-15

Social withdrawal is described as the condition in which an individual experiences a desire to make social contact, but is unable to satisfy that desire. It is an important issue for patients with motor neurone disease who are likely to experience severe physical impairment. This study aims to reassess the psychometric and scaling properties of the MND Social Withdrawal Scale (MND-SWS) domains and examine the feasibility of a summary scale, by applying scale data to the Rasch model. The MND Social Withdrawal Scale was administered to 298 patients with a diagnosis of MND, alongside the Hospital Anxiety and Depression Scale. The factor structure of the MND Social Withdrawal Scale was assessed using confirmatory factor analysis. Model fit, category threshold analysis, differential item functioning (DIF), dimensionality and local dependency were evaluated. Factor analysis confirmed the suitability of the four-factor solution suggested by the original authors. Mokken scale analysis suggested the removal of item five. Rasch analysis removed a further three items; from the Community (one item) and Emotional (two items) withdrawal subscales. Following item reduction, each scale exhibited excellent fit to the Rasch model. A 14-item Summary scale was shown to fit the Rasch model after subtesting the items into three subtests corresponding to the Community, Family and Emotional subscales, indicating that items from these three subscales could be summed together to create a total measure for social withdrawal. Removal of four items from the Social Withdrawal Scale led to a four factor solution with a 14-item hierarchical Summary scale that were all unidimensional, free for DIF and well fitted to the Rasch model. The scale is reliable and allows clinicians and researchers to measure social withdrawal in MND along a unidimensional construct. © 2013. Published by Elsevier B.V. All rights reserved.

Gene expression profile of pulpitis.

Science.gov (United States)

Galicia, J C; Henson, B R; Parker, J S; Khan, A A

2016-06-01

The cost, prevalence and pain associated with endodontic disease necessitate an understanding of the fundamental molecular aspects of its pathogenesis. This study was aimed to identify the genetic contributors to pulpal pain and inflammation. Inflamed pulps were collected from patients diagnosed with irreversible pulpitis (n=20). Normal pulps from teeth extracted for various reasons served as controls (n=20). Pain level was assessed using a visual analog scale (VAS). Genome-wide microarray analysis was performed using Affymetrix GeneTitan Multichannel Instrument. The difference in gene expression levels were determined by the significance analysis of microarray program using a false discovery rate (q-value) of 5%. Genes involved in immune response, cytokine-cytokine receptor interaction and signaling, integrin cell surface interactions, and others were expressed at relatively higher levels in the pulpitis group. Moreover, several genes known to modulate pain and inflammation showed differential expression in asymptomatic and mild pain patients (⩾30 mm on VAS) compared with those with moderate to severe pain. This exploratory study provides a molecular basis for the clinical diagnosis of pulpitis. With an enhanced understanding of pulpal inflammation, future studies on treatment and management of pulpitis and on pain associated with it can have a biological reference to bridge treatment strategies with pulpal biology.

dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder.

Science.gov (United States)

Zhang, Shuyun; Deng, Libin; Jia, Qiyue; Huang, Shaoting; Gu, Junwang; Zhou, Fankun; Gao, Meng; Sun, Xinyi; Feng, Chang; Fan, Guangqin

2017-11-16

Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. Therefore, a systematic review to synthesize the current findings from brain tissues and a search tool to share the meta-analysis results are urgently needed. Here, we conducted a meta-analysis of brain gene expression profiles in the current reported human ASD expression datasets (with 84 frozen male cortex samples, 17 female cortex samples, 32 cerebellum samples and 4 formalin fixed samples) and knock-out mouse ASD model expression datasets (with 80 collective brain samples). Then, we applied R language software and developed an interactive shared and updated database (dbMDEGA) displaying the results of meta-analysis of data from ASD studies regarding differentially expressed genes (DEGs) in the brain. This database, dbMDEGA ( https://dbmdega.shinyapps.io/dbMDEGA/ ), is a publicly available web-portal for manual annotation and visualization of DEGs in the brain from data from ASD studies. This database uniquely presents meta-analysis values and homologous forest plots of DEGs in brain tissues. Gene entries are annotated with meta-values, statistical values and forest plots of DEGs in brain samples. This database aims to provide searchable meta-analysis results based on the current reported brain gene expression datasets of ASD to help detect candidate genes underlying this disorder. This new analytical tool may provide valuable assistance in the discovery of DEGs and the elucidation of the molecular pathogenicity of ASD. This database model may be replicated to study other disorders.

A Confirmatory Factor Analysis on the Attitude Scale of Constructivist Approach for Science Teachers

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E. Evrekli

2010-11-01

Full Text Available Underlining the importance of teachers for the constructivist approach, the present study attempts to develop “Attitude Scale of Construc¬tivist Approach for Science Teachers (ASCAST”. The pre-applications of the scale were administered to a total of 210 science teachers; however, the data obtained from 5 teachers were excluded from the analysis. As a result of the analysis of the data obtained from the pre-applications, it was found that the scale could have a single factor structure, which was tested using the confir¬matory factor analysis. As a result of the initial confirmatory factor analysis, the values of fit were examined and found to be low. Subsequently, by exam¬ining the modification indices, error covariance was added between items 23 and 24 and the model was tested once again. The added error covariance led to a significant improvement in the model, producing values of fit suitable for limit values. Thus, it was concluded that the scale could be employed with a single factor. The explained variance value for the scale developed with a sin¬gle factor structure was calculated to be 50.43% and its reliability was found to be .93. The results obtained suggest that the scale possesses reliable-valid characteristics and could be used in further studies.

Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration

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Kelemen Arpad

2008-08-01

Full Text Available Abstract Background This paper addresses key biological problems and statistical issues in the analysis of large gene expression data sets that describe systemic temporal response cascades to therapeutic doses in multiple tissues such as liver, skeletal muscle, and kidney from the same animals. Affymetrix time course gene expression data U34A are obtained from three different tissues including kidney, liver and muscle. Our goal is not only to find the concordance of gene in different tissues, identify the common differentially expressed genes over time and also examine the reproducibility of the findings by integrating the results through meta analysis from multiple tissues in order to gain a significant increase in the power of detecting differentially expressed genes over time and to find the differential differences of three tissues responding to the drug. Results and conclusion Bayesian categorical model for estimating the proportion of the 'call' are used for pre-screening genes. Hierarchical Bayesian Mixture Model is further developed for the identifications of differentially expressed genes across time and dynamic clusters. Deviance information criterion is applied to determine the number of components for model comparisons and selections. Bayesian mixture model produces the gene-specific posterior probability of differential/non-differential expression and the 95% credible interval, which is the basis for our further Bayesian meta-inference. Meta-analysis is performed in order to identify commonly expressed genes from multiple tissues that may serve as ideal targets for novel treatment strategies and to integrate the results across separate studies. We have found the common expressed genes in the three tissues. However, the up/down/no regulations of these common genes are different at different time points. Moreover, the most differentially expressed genes were found in the liver, then in kidney, and then in muscle.

Equivalent Gene Expression Profiles between Glatopa™ and Copaxone®.

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Josephine S D'Alessandro

Full Text Available Glatopa™ is a generic glatiramer acetate recently approved for the treatment of patients with relapsing forms of multiple sclerosis. Gene expression profiling was performed as a means to evaluate equivalence of Glatopa and Copaxone®. Microarray analysis containing 39,429 unique probes across the entire genome was performed in murine glatiramer acetate--responsive Th2-polarized T cells, a test system highly relevant to the biology of glatiramer acetate. A closely related but nonequivalent glatiramoid molecule was used as a control to establish assay sensitivity. Multiple probe-level (Student's t-test and sample-level (principal component analysis, multidimensional scaling, and hierarchical clustering statistical analyses were utilized to look for differences in gene expression induced by the test articles. The analyses were conducted across all genes measured, as well as across a subset of genes that were shown to be modulated by Copaxone. The following observations were made across multiple statistical analyses: the expression of numerous genes was significantly changed by treatment with Copaxone when compared against media-only control; gene expression profiles induced by Copaxone and Glatopa were not significantly different; and gene expression profiles induced by Copaxone and the nonequivalent glatiramoid were significantly different, underscoring the sensitivity of the test system and the multiple analysis methods. Comparative analysis was also performed on sets of transcripts relevant to T-cell biology and antigen presentation, among others that are known to be modulated by glatiramer acetate. No statistically significant differences were observed between Copaxone and Glatopa in the expression levels (magnitude and direction of these glatiramer acetate-regulated genes. In conclusion, multiple methods consistently supported equivalent gene expression profiles between Copaxone and Glatopa.

Cost analysis of enzymatic biodiesel production in small-scaled packed-bed reactors

NARCIS (Netherlands)

Budzaki, S.; Miljic, G.; Sundaram, S.; Tisma, M.; Hessel, V.

2017-01-01

A cost analysis of enzymatic biodiesel production in small-scaled packed-bed reactors using refined sunflower oil is performed in this work. A few enzymatic micro-flow reactors have so far reached a performance close to gram-scale, which might be sufficient for the pharmaceutical industry. This

Prognostic significance of p53 expression in patients with esophageal cancer: a meta-analysis

International Nuclear Information System (INIS)

Wang, Lianghai; Yu, Xiaodan; Li, Jing; Zhang, Zhiyu; Hou, Jun; Li, Feng

2016-01-01

The prognostic value of p53 protein expression in esophageal cancer has been evaluated, but the results remain inconclusive and no consensus has yet been achieved. This meta-analysis was conducted to quantitatively assess the prognostic significance of p53 expression in esophageal cancer. Publications that assessed the clinical or prognostic significance of p53 expression in esophageal cancer and were published before July 1, 2015 were identified by searching the PubMed and EMBASE databases. A meta-analysis was performed to clarify the association between p53 expression and the clinical outcomes. A total of 36 publications met the criteria and included 4577 cases. Analysis of these data showed that p53 expression in esophageal cancer was significantly associated with poorer 5-year survival (RR = 1.30, 95 % CI: 1.11–1.51, P = 0.0008). Subgroup analyses according to histological type, continent of the patients, and cut-off value revealed the similar results. The results also indicated that p53 expression was highly associated with advanced TNM stages (I/II vs. III/IV, OR = 0.74, 95 % CI: 0.55–0.99, P = 0.04), lymph node metastasis (OR = 0.77, 95 % CI: 0.66–0.90, P = 0.001), and distant metastasis (OR = 0.46, 95 % CI: 0.26–0.80, P = 0.006). However, p53 expression in the included studies was not significantly associated with tumor size (≤ 5 cm vs. > 5 cm, OR = 1.13, 95 % CI: 0.92–1.40, P = 0.24), tumor location (upper + middle vs. lower, OR = 0.91, 95 % CI: 0.70–1.17, P = 0.45), grade of differentiation (well + moderate vs. poor, OR = 1.10, 95 % CI: 0.90–1.34, P = 0.35), and the depth of invasion (T1/T2 vs. T3/T4, OR = 0.86, 95 % CI: 0.71–1.03, P = 0.09). This meta-analysis showed that p53 expression may be a useful biomarker for predicting poorer prognosis in patients with esophageal cancer

Analysis of Mel-18 expression in prostate cancer tissues and correlation with clinicopathologic features.

Science.gov (United States)

Wang, Wei; Lin, Tianxin; Huang, Jian; Hu, Weilie; Xu, Kewei; Liu, Jun

2011-01-01

Mel-18 is a member of the polycomb group (PcG) of proteins, which are chromatin regulatory factors that play an important role in development and oncogenesis. This study was designed to investigate the clinical and prognostic significance of Mel-18 in the patients with prostate cancer. Immunostaining with Mel-18 specific antibodies was performed on paraffin sections from 202 patients. Correlations between Mel-18 and the Gleason grading system, clinical stage, serum prostate-specific antigen (PSA) levels, and age were evaluated. PSA recurrence in 76 patients who underwent radical prostatectomy and survival in 59 patients with metastases at diagnosis were analyzed to evaluate the influence of Mel-18 expression in cancer progression using Kaplan-Meier analysis and multivariate Cox regression analysis. Staining was seen in all prostatic tissues. Mel-18 expression was significantly reduced in the prostate cancer patients with PSA levels over 100 ng/ml (P=0.009), advanced clinical stage (>T4, N1, or M1 disease, P=0.029), higher Gleason grade or with a higher Gleason score (P=0.018) than in those with other clinicopathologic features. Negative expression of Mel-18 was associated with significantly higher rates of PSA recurrence after radical prostatectomy than with positive expression of Mel-18 (P = 0.029), and was an independent predictor of PSA recurrence (P=0.034, HR=2.143) in multivariate analysis. Similarly, metastatic prostate cancer patients with negative expression of Mel-18 showed significantly worse survival compared with the positive expression of Mel-18 (P=0.025). In multivariate analysis, negative expression of Mel-18 was an independent predictor of cancer-specific survival (P=0.024, HR=2.365). Our study provides important evidence for the recognition of Mel-18 as a tumor suppressor. The expression of Mel-18 showed potential as a prognostic marker for human prostate cancer. Copyright © 2011 Elsevier Inc. All rights reserved.

Domain-oriented functional analysis based on expression profiling

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Greene Jonathan

2002-10-01

Full Text Available Abstract Background Co-regulation of genes may imply involvement in similar biological processes or related function. Many clusters of co-regulated genes have been identified using microarray experiments. In this study, we examined co-regulated gene families using large-scale cDNA microarray experiments on the human transcriptome. Results We present a simple model, which, for each probe pair, distills expression changes into binary digits and summarizes the expression of multiple members of a gene family as the Family Regulation Ratio. The set of Family Regulation Ratios for each protein family across multiple experiments is called a Family Regulation Profile. We analyzed these Family Regulation Profiles using Pearson Correlation Coefficients and derived a network diagram portraying relationships between the Family Regulation Profiles of gene families that are well represented on the microarrays. Our strategy was cross-validated with two randomly chosen data subsets and was proven to be a reliable approach. Conclusion This work will help us to understand and identify the functional relationships between gene families and the regulatory pathways in which each family is involved. Concepts presented here may be useful for objective clustering of protein functions and deriving a comprehensive protein interaction map. Functional genomic approaches such as this may also be applicable to the elucidation of complex genetic regulatory networks.

CHESS (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome.

Science.gov (United States)

Lee, Mikyung; Kim, Yangseok

2009-12-16

Genomic alterations frequently occur in many cancer patients and play important mechanistic roles in the pathogenesis of cancer. Furthermore, they can modify the expression level of genes due to altered copy number in the corresponding region of the chromosome. An accumulating body of evidence supports the possibility that strong genome-wide correlation exists between DNA content and gene expression. Therefore, more comprehensive analysis is needed to quantify the relationship between genomic alteration and gene expression. A well-designed bioinformatics tool is essential to perform this kind of integrative analysis. A few programs have already been introduced for integrative analysis. However, there are many limitations in their performance of comprehensive integrated analysis using published software because of limitations in implemented algorithms and visualization modules. To address this issue, we have implemented the Java-based program CHESS to allow integrative analysis of two experimental data sets: genomic alteration and genome-wide expression profile. CHESS is composed of a genomic alteration analysis module and an integrative analysis module. The genomic alteration analysis module detects genomic alteration by applying a threshold based method or SW-ARRAY algorithm and investigates whether the detected alteration is phenotype specific or not. On the other hand, the integrative analysis module measures the genomic alteration's influence on gene expression. It is divided into two separate parts. The first part calculates overall correlation between comparative genomic hybridization ratio and gene expression level by applying following three statistical methods: simple linear regression, Spearman rank correlation and Pearson's correlation. In the second part, CHESS detects the genes that are differentially expressed according to the genomic alteration pattern with three alternative statistical approaches: Student's t-test, Fisher's exact test and Chi square

GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

Science.gov (United States)

Cumbie, Jason S; Kimbrel, Jeffrey A; Di, Yanming; Schafer, Daniel W; Wilhelm, Larry J; Fox, Samuel E; Sullivan, Christopher M; Curzon, Aron D; Carrington, James C; Mockler, Todd C; Chang, Jeff H

2011-01-01

GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM)-compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO) terms. Results are transparent and data are systematically stored in a MySQL relational database to facilitate additional analyses as well as quality assessment. We used next generation sequencing to generate a small-scale RNA-Seq dataset derived from the heavily studied defense response of Arabidopsis thaliana and used GENE-counter to process the data. Collectively, the support from analysis of microarrays as well as the observed and substantial overlap in results from each of the three statistics packages demonstrates that GENE-counter is well suited for handling the unique characteristics of small sample sizes and high variability in gene counts.

GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

Directory of Open Access Journals (Sweden)

Jason S Cumbie

Full Text Available GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM-compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO terms. Results are transparent and data are systematically stored in a MySQL relational database to facilitate additional analyses as well as quality assessment. We used next generation sequencing to generate a small-scale RNA-Seq dataset derived from the heavily studied defense response of Arabidopsis thaliana and used GENE-counter to process the data. Collectively, the support from analysis of microarrays as well as the observed and substantial overlap in results from each of the three statistics packages demonstrates that GENE-counter is well suited for handling the unique characteristics of small sample sizes and high variability in gene counts.

FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data.

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Takeru Uchiyama

Full Text Available Exponential growth of high-throughput data and the increasing complexity of omics information have been making processing and interpreting biological data an extremely difficult and daunting task. Here we developed FuncTree (http://bioviz.tokyo/functree, a web-based application for analyzing and visualizing large-scale omics data, including but not limited to genomic, metagenomic, and transcriptomic data. FuncTree allows user to map their omics data onto the "Functional Tree map", a predefined circular dendrogram, which represents the hierarchical relationship of all known biological functions defined in the KEGG database. This novel visualization method allows user to overview the broad functionality of their data, thus allowing a more accurate and comprehensive understanding of the omics information. FuncTree provides extensive customization and calculation methods to not only allow user to directly map their omics data to identify the functionality of their data, but also to compute statistically enriched functions by comparing it to other predefined omics data. We have validated FuncTree's analysis and visualization capability by mapping pan-genomic data of three different types of bacterial genera, metagenomic data of the human gut, and transcriptomic data of two different types of human cell expression. All three mapping strongly confirms FuncTree's capability to analyze and visually represent key functional feature of the omics data. We believe that FuncTree's capability to conduct various functional calculations and visualizing the result into a holistic overview of biological function, would make it an integral analysis/visualization tool for extensive omics base research.

Serial analysis of gene expression (SAGE) in rat liver regeneration

International Nuclear Information System (INIS)

Cimica, Velasco; Batusic, Danko; Haralanova-Ilieva, Borislava; Chen, Yonglong; Hollemann, Thomas; Pieler, Tomas; Ramadori, Giuliano

2007-01-01

We have applied serial analysis of gene expression for studying the molecular mechanism of the rat liver regeneration in the model of 70% partial hepatectomy. We generated three SAGE libraries from a normal control liver (NL library: 52,343 tags), from a sham control operated liver (Sham library: 51,028 tags), and from a regenerating liver (PH library: 53,061 tags). By SAGE bioinformatics analysis we identified 40 induced genes and 20 repressed genes during the liver regeneration. We verified temporal expression of such genes by real time PCR during the regeneration process and we characterized 13 induced genes and 3 repressed genes. We found connective tissue growth factor transcript and protein induced very early at 4 h after PH operation before hepatocytes proliferation is triggered. Our study suggests CTGF as a growth factor signaling mediator that could be involved directly in the mechanism of liver regeneration induction

Self-Compassion Scale: IRT Psychometric Analysis, Validation, and Factor Structure – Slovak Translation

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Júlia Halamová

2018-01-01

Full Text Available The present study verifies the psychometric properties of the Slovak version of the Self-Compassion Scale through item response theory, factor-analysis, validity analyses and norm development. The surveyed sample consisted of 1,181 participants (34% men and 66% women with a mean age of 30.30 years (SD = 12.40. Two general factors (Self-compassionate responding and Self-uncompassionate responding were identified, whereas there was no support for a single general factor of the scale and six subscales. The results of the factor analysis were supported by an independent sample of 676 participants. Therefore, the use of total score for the whole scale would be inappropriate. In Slovak language the Self-Compassion Scale should be used in the form of two general subscales (Self-compassionate responding and Self-uncompassionate responding. In line with our theoretical assumptions, we obtained relatively high Spearman’s correlation coefficients between the Self-Compassion Scale and related external variables, demonstrating construct validity for the scale. To sum up, the Slovak translation of The Self-Compassion Scale is a reliable and valid instrument that measures Self-compassionate responding and Self-uncompassionate responding.

Secondary Analysis of Large-Scale Assessment Data: An Alternative to Variable-Centred Analysis

Science.gov (United States)

Chow, Kui Foon; Kennedy, Kerry John

2014-01-01

International large-scale assessments are now part of the educational landscape in many countries and often feed into major policy decisions. Yet, such assessments also provide data sets for secondary analysis that can address key issues of concern to educators and policymakers alike. Traditionally, such secondary analyses have been based on a…

DEXTER: Disease-Expression Relation Extraction from Text.

Science.gov (United States)

Gupta, Samir; Dingerdissen, Hayley; Ross, Karen E; Hu, Yu; Wu, Cathy H; Mazumder, Raja; Vijay-Shanker, K

2018-01-01

Gene expression levels affect biological processes and play a key role in many diseases. Characterizing expression profiles is useful for clinical research, and diagnostics and prognostics of diseases. There are currently several high-quality databases that capture gene expression information, obtained mostly from large-scale studies, such as microarray and next-generation sequencing technologies, in the context of disease. The scientific literature is another rich source of information on gene expression-disease relationships that not only have been captured from large-scale studies but have also been observed in thousands of small-scale studies. Expression information obtained from literature through manual curation can extend expression databases. While many of the existing databases include information from literature, they are limited by the time-consuming nature of manual curation and have difficulty keeping up with the explosion of publications in the biomedical field. In this work, we describe an automated text-mining tool, Disease-Expression Relation Extraction from Text (DEXTER) to extract information from literature on gene and microRNA expression in the context of disease. One of the motivations in developing DEXTER was to extend the BioXpress database, a cancer-focused gene expression database that includes data derived from large-scale experiments and manual curation of publications. The literature-based portion of BioXpress lags behind significantly compared to expression information obtained from large-scale studies and can benefit from our text-mined results. We have conducted two different evaluations to measure the accuracy of our text-mining tool and achieved average F-scores of 88.51 and 81.81% for the two evaluations, respectively. Also, to demonstrate the ability to extract rich expression information in different disease-related scenarios, we used DEXTER to extract information on differential expression information for 2024 genes in lung

Gene Expression Signature in Endemic Osteoarthritis by Microarray Analysis

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Xi Wang

2015-05-01

Full Text Available Kashin-Beck Disease (KBD is an endemic osteochondropathy with an unknown pathogenesis. Diagnosis of KBD is effective only in advanced cases, which eliminates the possibility of early treatment and leads to an inevitable exacerbation of symptoms. Therefore, we aim to identify an accurate blood-based gene signature for the detection of KBD. Previously published gene expression profile data on cartilage and peripheral blood mononuclear cells (PBMCs from adults with KBD were compared to select potential target genes. Microarray analysis was conducted to evaluate the expression of the target genes in a cohort of 100 KBD patients and 100 healthy controls. A gene expression signature was identified using a training set, which was subsequently validated using an independent test set with a minimum redundancy maximum relevance (mRMR algorithm and support vector machine (SVM algorithm. Fifty unique genes were differentially expressed between KBD patients and healthy controls. A 20-gene signature was identified that distinguished between KBD patients and controls with 90% accuracy, 85% sensitivity, and 95% specificity. This study identified a 20-gene signature that accurately distinguishes between patients with KBD and controls using peripheral blood samples. These results promote the further development of blood-based genetic biomarkers for detection of KBD.

The utility of optical detection system (qPCR) and bioinformatics methods in reference gene expression analysis

Science.gov (United States)

Skarzyńska, Agnieszka; Pawełkowicz, Magdalena; PlÄ der, Wojciech; Przybecki, Zbigniew

2016-09-01

Real-time quantitative polymerase chain reaction is consider as the most reliable method for gene expression studies. However, the expression of target gene could be misinterpreted due to improper normalization. Therefore, the crucial step for analysing of qPCR data is selection of suitable reference genes, which should be validated experimentally. In order to choice the gene with stable expression in the designed experiment, we performed reference gene expression analysis. In this study genes described in the literature and novel genes predicted as control genes, based on the in silico analysis of transcriptome data were used. Analysis with geNorm and NormFinder algorithms allow to create the ranking of candidate genes and indicate the best reference for flower morphogenesis study. According to the results, genes CACS and CYCL were characterised the most stable expression, but the least suitable genes were TUA and EF.

Analysis of the Determinants of Small-Scale Farmers' Grain Market ...

African Journals Online (AJOL)

In some cases, farmers may sell at low price when they face financial constraints, especially ... Analysis of the Determinants of Small-Scale Farmers' Grain Market Participations. [76] ...... An MSc Thesis Presented to the School of Graduate.

Genomewide identification and expression analysis of the ARF gene ...

Indian Academy of Sciences (India)

Figure 1. Phylogenetic relation of apple ARF genes. The phylogenetic tree was constructed based on a complete protein sequence align- ment of MdARFs by the neighbour-joining method with bootstrapping analysis (1000 replicates). The scale bar represents 0.05 amino acid substitutions per site. Paralogous gene pairs ...

Selection of reference genes for expression analysis in the entomophthoralean fungus Pandora neoaphidis.

Science.gov (United States)

Chen, Chun; Xie, Tingna; Ye, Sudan; Jensen, Annette Bruun; Eilenberg, Jørgen

2016-01-01

The selection of suitable reference genes is crucial for accurate quantification of gene expression and can add to our understanding of host-pathogen interactions. To identify suitable reference genes in Pandora neoaphidis, an obligate aphid pathogenic fungus, the expression of three traditional candidate genes including 18S rRNA(18S), 28S rRNA(28S) and elongation factor 1 alpha-like protein (EF1), were measured by quantitative polymerase chain reaction at different developmental stages (conidia, conidia with germ tubes, short hyphae and elongated hyphae), and under different nutritional conditions. We calculated the expression stability of candidate reference genes using four algorithms including geNorm, NormFinder, BestKeeper and Delta Ct. The analysis results revealed that the comprehensive ranking of candidate reference genes from the most stable to the least stable was 18S (1.189), 28S (1.414) and EF1 (3). The 18S was, therefore, the most suitable reference gene for real-time RT-PCR analysis of gene expression under all conditions. These results will support further studies on gene expression in P. neoaphidis. Copyright © 2015 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Selection of reference genes for expression analysis in the entomophthoralean fungus Pandora neoaphidis

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Chun Chen

2016-03-01

Full Text Available Abstract The selection of suitable reference genes is crucial for accurate quantification of gene expression and can add to our understanding of host–pathogen interactions. To identify suitable reference genes in Pandora neoaphidis, an obligate aphid pathogenic fungus, the expression of three traditional candidate genes including 18S rRNA(18S, 28S rRNA(28S and elongation factor 1 alpha-like protein (EF1, were measured by quantitative polymerase chain reaction at different developmental stages (conidia, conidia with germ tubes, short hyphae and elongated hyphae, and under different nutritional conditions. We calculated the expression stability of candidate reference genes using four algorithms including geNorm, NormFinder, BestKeeper and Delta Ct. The analysis results revealed that the comprehensive ranking of candidate reference genes from the most stable to the least stable was 18S (1.189, 28S (1.414 and EF1 (3. The 18S was, therefore, the most suitable reference gene for real-time RT-PCR analysis of gene expression under all conditions. These results will support further studies on gene expression in P. neoaphidis.

Cross-cultural validity of the scale for interpersonal behavior.

Science.gov (United States)

Nota, Laura; Arrindell, Willem A; Soresi, Salvatore; van der Ende, Jan; Sanavio, Ezio

2011-01-01

The Scale for Interpersonal Behavior (SIB) is a 50-item multidimensional measure of difficulty and distress in assertiveness. The SIB assesses negative assertion, expression of and dealing with personal limitations, initiating assertiveness and positive assertion. The SIB was originally developed in the Netherlands. The present study attempted to replicate the original factors with an Italian student sample (n = 995). The four distress and four performance factors were replicable across two methods of analysis (the multiple group method of confirmatory analysis and Tucker's coefficient of congruence (phi). The corresponding scales were internally consistent and showed predicted patterns of correlations with a measure of self-efficacy. Sex and age differences in assertiveness were generally negligible. Italian students had higher positive assertion-performance scores than the Dutch and comparable scores on other performance scales; by contrast, the Italian subjects had significantly higher scores on all SIB distress scales than their Dutch equivalents. This was ascribed to the stronger pressure on people in Italian society to behave assertively (Hofstede's National Masculinity score = 70) as opposed to the Dutch society (National Masculinity score = 14).

Basic dimensions of experience of architectural objects’ expressiveness: Effect of expertise

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Marković Slobodan

2015-01-01

Full Text Available The purpose of the present study was to compare the structure of experience of architectural expressiveness of architects and non-architects. Twenty architects and twenty non-architects rated twenty photographs of architectural objects on thirty expressiveness scales. Principal components analysis revealed four factors for both groups of participants: Aggressiveness, Regularity, Color and Aesthetics. In a cluster analysis two clusters of architectural objects were obtained: Choleric (high Aggressiveness and Color and Phlegmatic (low Aggressiveness and Color, and high Regularity. All objects were highly rated on Aesthetics. Analysis of variance has shown that architects rated both clusters as less aggressive than non-architects. Also, experts rated the Phlegmatic cluster as more aesthetic, while nonexperts rated the Choleric cluster as more aesthetic. These results supported the Processing Fluency model: compared to non-architects, architects processed the expressive information of minimalistic objects (Phlegmatic cluster with ease, which led towards positive hedonic reactions and higher. [Projekat Ministarstva nauke Republike Srbije, br. 179033

SCALE system cross-section validation for criticality safety analysis