WorldWideScience

Sample records for expression analysis applied

  1. August Dvorak (1894-1975): Early expressions of applied behavior analysis and precision teaching

    Science.gov (United States)

    Joyce, Bonnie; Moxley, Roy A.

    1988-01-01

    August Dvorak is best known for his development of the Dvorak keyboard. However, Dvorak also adapted and applied many behavioral and scientific management techniques to the field of education. Taken collectively, these techniques are representative of many of the procedures currently used in applied behavior analysis, in general, and especially in precision teaching. The failure to consider Dvorak's instructional methods may explain some of the discrepant findings in studies which compare the efficiency of the Dvorak to the standard keyboard. This article presents a brief background on the development of the standard (QWERTY) and Dvorak keyboards, describes parallels between Dvorak's teaching procedures and those used in precision teaching, reviews some of the comparative research on the Dvorak keyboard, and suggests some implications for further research in applying the principles of behavior analysis. PMID:22477993

  2. Handbook of Applied Analysis

    CERN Document Server

    Papageorgiou, Nikolaos S

    2009-01-01

    Offers an examination of important theoretical methods and procedures in applied analysis. This book details the important theoretical trends in nonlinear analysis and applications to different fields. It is suitable for those working on nonlinear analysis.

  3. Applied longitudinal analysis

    CERN Document Server

    Fitzmaurice, Garrett M; Ware, James H

    2012-01-01

    Praise for the First Edition "". . . [this book] should be on the shelf of everyone interested in . . . longitudinal data analysis.""-Journal of the American Statistical Association   Features newly developed topics and applications of the analysis of longitudinal data Applied Longitudinal Analysis, Second Edition presents modern methods for analyzing data from longitudinal studies and now features the latest state-of-the-art techniques. The book emphasizes practical, rather than theoretical, aspects of methods for the analysis of diverse types of lo

  4. Applied Behavior Analysis

    Science.gov (United States)

    Szapacs, Cindy

    2006-01-01

    Teaching strategies that work for typically developing children often do not work for those diagnosed with an autism spectrum disorder. However, teaching strategies that work for children with autism do work for typically developing children. In this article, the author explains how the principles and concepts of Applied Behavior Analysis can be…

  5. Applied multivariate statistical analysis

    CERN Document Server

    Härdle, Wolfgang Karl

    2015-01-01

    Focusing on high-dimensional applications, this 4th edition presents the tools and concepts used in multivariate data analysis in a style that is also accessible for non-mathematicians and practitioners.  It surveys the basic principles and emphasizes both exploratory and inferential statistics; a new chapter on Variable Selection (Lasso, SCAD and Elastic Net) has also been added.  All chapters include practical exercises that highlight applications in different multivariate data analysis fields: in quantitative financial studies, where the joint dynamics of assets are observed; in medicine, where recorded observations of subjects in different locations form the basis for reliable diagnoses and medication; and in quantitative marketing, where consumers’ preferences are collected in order to construct models of consumer behavior.  All of these examples involve high to ultra-high dimensions and represent a number of major fields in big data analysis. The fourth edition of this book on Applied Multivariate ...

  6. 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.

  7. Applied functional analysis

    CERN Document Server

    Oden, J Tinsley

    2010-01-01

    The textbook is designed to drive a crash course for beginning graduate students majoring in something besides mathematics, introducing mathematical foundations that lead to classical results in functional analysis. More specifically, Oden and Demkowicz want to prepare students to learn the variational theory of partial differential equations, distributions, and Sobolev spaces and numerical analysis with an emphasis on finite element methods. The 1996 first edition has been used in a rather intensive two-semester course. -Book News, June 2010

  8. Applied functional analysis

    CERN Document Server

    Griffel, DH

    2002-01-01

    A stimulating introductory text, this volume examines many important applications of functional analysis to mechanics, fluid mechanics, diffusive growth, and approximation. Detailed enough to impart a thorough understanding, the text is also sufficiently straightforward for those unfamiliar with abstract analysis. Its four-part treatment begins with distribution theory and discussions of Green's functions. Essentially independent of the preceding material, the second and third parts deal with Banach spaces, Hilbert space, spectral theory, and variational techniques. The final part outlines the

  9. Conversation Analysis in Applied Linguistics

    DEFF Research Database (Denmark)

    Kasper, Gabriele; Wagner, Johannes

    2014-01-01

    on applied CA, the application of basic CA's principles, methods, and findings to the study of social domains and practices that are interactionally constituted. We consider three strands—foundational, social problem oriented, and institutional applied CA—before turning to recent developments in CA research...... on learning and development. In conclusion, we address some emerging themes in the relationship of CA and applied linguistics, including the role of multilingualism, standard social science methods as research objects, CA's potential for direct social intervention, and increasing efforts to complement CA......For the last decade, conversation analysis (CA) has increasingly contributed to several established fields in applied linguistics. In this article, we will discuss its methodological contributions. The article distinguishes between basic and applied CA. Basic CA is a sociological endeavor concerned...

  10. Applied analysis and differential equations

    CERN Document Server

    Cârj, Ovidiu

    2007-01-01

    This volume contains refereed research articles written by experts in the field of applied analysis, differential equations and related topics. Well-known leading mathematicians worldwide and prominent young scientists cover a diverse range of topics, including the most exciting recent developments. A broad range of topics of recent interest are treated: existence, uniqueness, viability, asymptotic stability, viscosity solutions, controllability and numerical analysis for ODE, PDE and stochastic equations. The scope of the book is wide, ranging from pure mathematics to various applied fields such as classical mechanics, biomedicine, and population dynamics.

  11. Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery.

    Science.gov (United States)

    Jia, Zhilong; Liu, Ying; Guan, Naiyang; Bo, Xiaochen; Luo, Zhigang; Barnes, Michael R

    2016-05-27

    Drug repositioning, finding new indications for existing drugs, has gained much recent attention as a potentially efficient and economical strategy for accelerating new therapies into the clinic. Although improvement in the sensitivity of computational drug repositioning methods has identified numerous credible repositioning opportunities, few have been progressed. Arguably the "black box" nature of drug action in a new indication is one of the main blocks to progression, highlighting the need for methods that inform on the broader target mechanism in the disease context. We demonstrate that the analysis of co-expressed genes may be a critical first step towards illumination of both disease pathology and mode of drug action. We achieve this using a novel framework, co-expressed gene-set enrichment analysis (cogena) for co-expression analysis of gene expression signatures and gene set enrichment analysis of co-expressed genes. The cogena framework enables simultaneous, pathway driven, disease and drug repositioning analysis. Cogena can be used to illuminate coordinated changes within disease transcriptomes and identify drugs acting mechanistically within this framework. We illustrate this using a psoriatic skin transcriptome, as an exemplar, and recover two widely used Psoriasis drugs (Methotrexate and Ciclosporin) with distinct modes of action. Cogena out-performs the results of Connectivity Map and NFFinder webservers in similar disease transcriptome analyses. Furthermore, we investigated the literature support for the other top-ranked compounds to treat psoriasis and showed how the outputs of cogena analysis can contribute new insight to support the progression of drugs into the clinic. We have made cogena freely available within Bioconductor or https://github.com/zhilongjia/cogena . In conclusion, by targeting co-expressed genes within disease transcriptomes, cogena offers novel biological insight, which can be effectively harnessed for drug discovery and

  12. Applied survival analysis using R

    CERN Document Server

    Moore, Dirk F

    2016-01-01

    Applied Survival Analysis Using R covers the main principles of survival analysis, gives examples of how it is applied, and teaches how to put those principles to use to analyze data using R as a vehicle. Survival data, where the primary outcome is time to a specific event, arise in many areas of biomedical research, including clinical trials, epidemiological studies, and studies of animals. Many survival methods are extensions of techniques used in linear regression and categorical data, while other aspects of this field are unique to survival data. This text employs numerous actual examples to illustrate survival curve estimation, comparison of survivals of different groups, proper accounting for censoring and truncation, model variable selection, and residual analysis. Because explaining survival analysis requires more advanced mathematics than many other statistical topics, this book is organized with basic concepts and most frequently used procedures covered in earlier chapters, with more advanced topics...

  13. Modern problems in applied analysis

    CERN Document Server

    Rogosin, Sergei

    2018-01-01

    This book features a collection of recent findings in Applied Real and Complex Analysis that were presented at the 3rd International Conference “Boundary Value Problems, Functional Equations and Applications” (BAF-3), held in Rzeszow, Poland on 20-23 April 2016. The contributions presented here develop a technique related to the scope of the workshop and touching on the fields of differential and functional equations, complex and real analysis, with a special emphasis on topics related to boundary value problems. Further, the papers discuss various applications of the technique, mainly in solid mechanics (crack propagation, conductivity of composite materials), biomechanics (viscoelastic behavior of the periodontal ligament, modeling of swarms) and fluid dynamics (Stokes and Brinkman type flows, Hele-Shaw type flows). The book is addressed to all readers who are interested in the development and application of innovative research results that can help solve theoretical and real-world problems.

  14. Conversation Analysis and Applied Linguistics.

    Science.gov (United States)

    Schegloff, Emanuel A.; Koshik, Irene; Jacoby, Sally; Olsher, David

    2002-01-01

    Offers biographical guidance on several major areas of conversation-analytic work--turn-taking, repair, and word selection--and indicates past or potential points of contact with applied linguistics. Also discusses areas of applied linguistic work. (Author/VWL)

  15. Applying critical analysis - main methods

    Directory of Open Access Journals (Sweden)

    Miguel Araujo Alonso

    2012-02-01

    Full Text Available What is the usefulness of critical appraisal of literature? Critical analysis is a fundamental condition for the correct interpretation of any study that is subject to review. In epidemiology, in order to learn how to read a publication, we must be able to analyze it critically. Critical analysis allows us to check whether a study fulfills certain previously established methodological inclusion and exclusion criteria. This is frequently used in conducting systematic reviews although eligibility criteria are generally limited to the study design. Critical analysis of literature and be done implicitly while reading an article, as in reading for personal interest, or can be conducted in a structured manner, using explicit and previously established criteria. The latter is done when formally reviewing a topic.

  16. 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

  17. Essentials of applied dynamic analysis

    CERN Document Server

    Jia, Junbo

    2014-01-01

    This book presents up-to-date knowledge of dynamic analysis in engineering world. To facilitate the understanding of the topics by readers with various backgrounds, general principles are linked to their applications from different angles. Special interesting topics such as statistics of motions and loading, damping modeling and measurement, nonlinear dynamics, fatigue assessment, vibration and buckling under axial loading, structural health monitoring, human body vibrations, and vehicle-structure interactions etc., are also presented. The target readers include industry professionals in civil, marine and mechanical engineering, as well as researchers and students in this area.

  18. Applied systems analysis. No. 22

    International Nuclear Information System (INIS)

    1980-12-01

    Based on a detailed analysis of demands in the area Cologne/Frankfurt, the amount of the system products for this region were ascertained, which under consideration of technical conditions and entrepreneurial aspects seemed to be disposable at cost equality with competative energy supplies. Based on these data, the technical components of the system, location and piping were fixed and first- and operating costs were determined. For a judgement of the economics, the key numbers, cash value, internal rate of interest and cost recovery rate were determined from the difference of costs between the nuclear long distance energy system and alternative facilities. Furthermore specific production cost, associated prices and contribution margin were presented for each product. (orig.) [de

  19. 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...

  20. Applied Behavior Analysis and Statistical Process Control?

    Science.gov (United States)

    Hopkins, B. L.

    1995-01-01

    Incorporating statistical process control (SPC) methods into applied behavior analysis is discussed. It is claimed that SPC methods would likely reduce applied behavior analysts' intimate contacts with problems and would likely yield poor treatment and research decisions. Cases and data presented by Pfadt and Wheeler (1995) are cited as examples.…

  1. Concept analysis of culture applied to nursing.

    Science.gov (United States)

    Marzilli, Colleen

    2014-01-01

    Culture is an important concept, especially when applied to nursing. A concept analysis of culture is essential to understanding the meaning of the word. This article applies Rodgers' (2000) concept analysis template and provides a definition of the word culture as it applies to nursing practice. This article supplies examples of the concept of culture to aid the reader in understanding its application to nursing and includes a case study demonstrating components of culture that must be respected and included when providing health care.

  2. Caldwell University's Department of Applied Behavior Analysis.

    Science.gov (United States)

    Reeve, Kenneth F; Reeve, Sharon A

    2016-05-01

    Since 2004, faculty members at Caldwell University have developed three successful graduate programs in Applied Behavior Analysis (i.e., PhD, MA, non-degree programs), increased program faculty from two to six members, developed and operated an on-campus autism center, and begun a stand-alone Applied Behavior Analysis Department. This paper outlines a number of strategies used to advance these initiatives, including those associated with an extensive public relations campaign. We also outline challenges that have limited our programs' growth. These strategies, along with a consideration of potential challenges, might prove useful in guiding academicians who are interested in starting their own programs in behavior analysis.

  3. Applied regression analysis a research tool

    CERN Document Server

    Pantula, Sastry; Dickey, David

    1998-01-01

    Least squares estimation, when used appropriately, is a powerful research tool. A deeper understanding of the regression concepts is essential for achieving optimal benefits from a least squares analysis. This book builds on the fundamentals of statistical methods and provides appropriate concepts that will allow a scientist to use least squares as an effective research tool. Applied Regression Analysis is aimed at the scientist who wishes to gain a working knowledge of regression analysis. The basic purpose of this book is to develop an understanding of least squares and related statistical methods without becoming excessively mathematical. It is the outgrowth of more than 30 years of consulting experience with scientists and many years of teaching an applied regression course to graduate students. Applied Regression Analysis serves as an excellent text for a service course on regression for non-statisticians and as a reference for researchers. It also provides a bridge between a two-semester introduction to...

  4. Building an applied activation analysis centre

    International Nuclear Information System (INIS)

    Bartosek, J.; Kasparec, I.; Masek, J.

    1972-01-01

    Requirements are defined and all available background material is reported and discussed for the building up of a centre of applied activation analysis in Czechoslovakia. A detailed analysis of potential users and the centre's envisaged availability is also presented as part of the submitted study. A brief economic analysis is annexed. The study covers the situation up to the end of 1972. (J.K.)

  5. Lessons learned in applying function analysis

    International Nuclear Information System (INIS)

    Mitchel, G.R.; Davey, E.; Basso, R.

    2001-01-01

    This paper summarizes the lessons learned in undertaking and applying function analysis based on the recent experience of utility, AECL and international design and assessment projects. Function analysis is an analytical technique that can be used to characterize and asses the functions of a system and is widely recognized as an essential component of a 'systematic' approach to design, on that integrated operational and user requirements into the standard design process. (author)

  6. Positive Behavior Support and Applied Behavior Analysis

    Science.gov (United States)

    Johnston, J. M.; Foxx, R. M.; Jacobson, J. W.; Green, G.; Mulick, J. A.

    2006-01-01

    This article reviews the origins and characteristics of the positive behavior support (PBS) movement and examines those features in the context of the field of applied behavior analysis (ABA). We raise a number of concerns about PBS as an approach to delivery of behavioral services and its impact on how ABA is viewed by those in human services. We…

  7. Applied Behavior Analysis: Beyond Discrete Trial Teaching

    Science.gov (United States)

    Steege, Mark W.; Mace, F. Charles; Perry, Lora; Longenecker, Harold

    2007-01-01

    We discuss the problem of autism-specific special education programs representing themselves as Applied Behavior Analysis (ABA) programs when the only ABA intervention employed is Discrete Trial Teaching (DTT), and often for limited portions of the school day. Although DTT has many advantages to recommend its use, it is not well suited to teach…

  8. Applied decision analysis and risk evaluation

    International Nuclear Information System (INIS)

    Ferse, W.; Kruber, S.

    1995-01-01

    During 1994 the workgroup 'Applied Decision Analysis and Risk Evaluation; continued the work on the knowledge based decision support system XUMA-GEFA for the evaluation of the hazard potential of contaminated sites. Additionally a new research direction was started which aims at the support of a later stage of the treatment of contaminated sites: The clean-up decision. For the support of decisions arising at this stage, the methods of decision analysis will be used. Computational aids for evaluation and decision support were implemented and a case study at a waste disposal site in Saxony which turns out to be a danger for the surrounding groundwater ressource was initiated. (orig.)

  9. Applied research in uncertainty modeling and analysis

    CERN Document Server

    Ayyub, Bilal

    2005-01-01

    Uncertainty has been a concern to engineers, managers, and scientists for many years. For a long time uncertainty has been considered synonymous with random, stochastic, statistic, or probabilistic. Since the early sixties views on uncertainty have become more heterogeneous. In the past forty years numerous tools that model uncertainty, above and beyond statistics, have been proposed by several engineers and scientists. The tool/method to model uncertainty in a specific context should really be chosen by considering the features of the phenomenon under consideration, not independent of what is known about the system and what causes uncertainty. In this fascinating overview of the field, the authors provide broad coverage of uncertainty analysis/modeling and its application. Applied Research in Uncertainty Modeling and Analysis presents the perspectives of various researchers and practitioners on uncertainty analysis and modeling outside their own fields and domain expertise. Rather than focusing explicitly on...

  10. Strategic decision analysis applied to borehole seismology

    International Nuclear Information System (INIS)

    Menke, M.M.; Paulsson, B.N.P.

    1994-01-01

    Strategic Decision Analysis (SDA) is the evolving body of knowledge on how to achieve high quality in the decision that shapes an organization's future. SDA comprises philosophy, process concepts, methodology, and tools for making good decisions. It specifically incorporates many concepts and tools from economic evaluation and risk analysis. Chevron Petroleum Technology Company (CPTC) has applied SDA to evaluate and prioritize a number of its most important and most uncertain R and D projects, including borehole seismology. Before SDA, there were significant issues and concerns about the value to CPTC of continuing to work on borehole seismology. The SDA process created a cross-functional team of experts to structure and evaluate this project. A credible economic model was developed, discrete risks and continuous uncertainties were assessed, and an extensive sensitivity analysis was performed. The results, even applied to a very restricted drilling program for a few years, were good enough to demonstrate the value of continuing the project. This paper explains the SDA philosophy concepts, and process and demonstrates the methodology and tools using the borehole seismology project example. SDA is useful in the upstream industry not just in the R and D/technology decisions, but also in major exploration and production decisions. Since a major challenge for upstream companies today is to create and realize value, the SDA approach should have a very broad applicability

  11. Functional Data Analysis Applied in Chemometrics

    DEFF Research Database (Denmark)

    Muller, Martha

    nutritional status and metabolic phenotype. We want to understand how metabolomic spectra can be analysed using functional data analysis to detect the in uence of dierent factors on specic metabolites. These factors can include, for example, gender, diet culture or dietary intervention. In Paper I we apply...... representation of each spectrum. Subset selection of wavelet coecients generates the input to mixed models. Mixed-model methodology enables us to take the study design into account while modelling covariates. Bootstrap-based inference preserves the correlation structure between curves and enables the estimation...

  12. Applied spectrophotometry: analysis of a biochemical mixture.

    Science.gov (United States)

    Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software. Copyright © 2013 Wiley Periodicals, Inc.

  13. Tissue Microarray Analysis Applied to Bone Diagenesis.

    Science.gov (United States)

    Mello, Rafael Barrios; Silva, Maria Regina Regis; Alves, Maria Teresa Seixas; Evison, Martin Paul; Guimarães, Marco Aurelio; Francisco, Rafaella Arrabaca; Astolphi, Rafael Dias; Iwamura, Edna Sadayo Miazato

    2017-01-04

    Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens. Standard hematoxylin and eosin, periodic acid-Schiff and silver methenamine, and picrosirius red staining, and CD31 and CD34 immunohistochemistry were applied to TMA sections. Osteocyte and osteocyte lacuna counts, percent bone matrix loss, and fungal spheroid element counts could be measured and collagen fibre bundles observed in all specimens. Decalcification with 7% nitric acid proceeded more rapidly than with 0.5 M EDTA and may offer better preservation of histological and cellular structure. No endothelial cells could be detected using CD31 and CD34 immunohistochemistry. Correlation between osteocytes per lacuna and age at death may reflect reported age-related responses to microdamage. Methodological limitations and caveats, and results of the TMA analysis of post mortem diagenesis in bone are discussed, and implications for DNA survival and recovery considered.

  14. Applied linear algebra and matrix analysis

    CERN Document Server

    Shores, Thomas S

    2018-01-01

    In its second edition, this textbook offers a fresh approach to matrix and linear algebra. Its blend of theory, computational exercises, and analytical writing projects is designed to highlight the interplay between these aspects of an application. This approach places special emphasis on linear algebra as an experimental science that provides tools for solving concrete problems. The second edition’s revised text discusses applications of linear algebra like graph theory and network modeling methods used in Google’s PageRank algorithm. Other new materials include modeling examples of diffusive processes, linear programming, image processing, digital signal processing, and Fourier analysis. These topics are woven into the core material of Gaussian elimination and other matrix operations; eigenvalues, eigenvectors, and discrete dynamical systems; and the geometrical aspects of vector spaces. Intended for a one-semester undergraduate course without a strict calculus prerequisite, Applied Linear Algebra and M...

  15. A Classification Framework Applied to Cancer Gene Expression Profiles

    Directory of Open Access Journals (Sweden)

    Hussein Hijazi

    2013-01-01

    Full Text Available Classification of cancer based on gene expression has provided insight into possible treatment strategies. Thus, developing machine learning methods that can successfully distinguish among cancer subtypes or normal versus cancer samples is important. This work discusses supervised learning techniques that have been employed to classify cancers. Furthermore, a two-step feature selection method based on an attribute estimation method (e.g., ReliefF and a genetic algorithm was employed to find a set of genes that can best differentiate between cancer subtypes or normal versus cancer samples. The application of different classification methods (e.g., decision tree, k-nearest neighbor, support vector machine (SVM, bagging, and random forest on 5 cancer datasets shows that no classification method universally outperforms all the others. However, k-nearest neighbor and linear SVM generally improve the classification performance over other classifiers. Finally, incorporating diverse types of genomic data (e.g., protein-protein interaction data and gene expression increase the prediction accuracy as compared to using gene expression alone.

  16. Epithermal neutron activation analysis in applied microbiology

    International Nuclear Information System (INIS)

    Marina Frontasyeva

    2012-01-01

    Some results from applying epithermal neutron activation analysis at FLNP JINR, Dubna, Russia, in medical biotechnology, environmental biotechnology and industrial biotechnology are reviewed. In the biomedical experiments biomass from the blue-green alga Spirulina platensis (S. platensis) has been used as a matrix for the development of pharmaceutical substances containing such essential trace elements as selenium, chromium and iodine. The feasibility of target-oriented introduction of these elements into S. platensis biocomplexes retaining its protein composition and natural beneficial properties was shown. The absorption of mercury on growth dynamics of S. platensis and other bacterial strains was observed. Detoxification of Cr and Hg by Arthrobacter globiformis 151B was demonstrated. Microbial synthesis of technologically important silver nanoparticles by the novel actinomycete strain Streptomyces glaucus 71 MD and blue-green alga S. platensis were characterized by a combined use of transmission electron microscopy, scanning electron microscopy and energy-dispersive analysis of X-rays. It was established that the tested actinomycete S. glaucus 71 MD produces silver nanoparticles extracellularly when acted upon by the silver nitrate solution, which offers a great advantage over an intracellular process of synthesis from the point of view of applications. The synthesis of silver nanoparticles by S. platensis proceeded differently under the short-term and long-term silver action. (author)

  17. 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.

  18. Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells.

    Science.gov (United States)

    Wu, Liang; Zhang, Xiaolong; Zhao, Zhikun; Wang, Ling; Li, Bo; Li, Guibo; Dean, Michael; Yu, Qichao; Wang, Yanhui; Lin, Xinxin; Rao, Weijian; Mei, Zhanlong; Li, Yang; Jiang, Runze; Yang, Huan; Li, Fuqiang; Xie, Guoyun; Xu, Liqin; Wu, Kui; Zhang, Jie; Chen, Jianghao; Wang, Ting; Kristiansen, Karsten; Zhang, Xiuqing; Li, Yingrui; Yang, Huanming; Wang, Jian; Hou, Yong; Xu, Xun

    2015-01-01

    Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas. Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied. HeLa is a well characterized HPV+ cervical cancer cell line. We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip. Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing. Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions. Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level. By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins. Our results reveal the heterogeneity of a virus-infected cell line. It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers.

  19. Analysis of the interaction between experimental and applied behavior analysis.

    Science.gov (United States)

    Virues-Ortega, Javier; Hurtado-Parrado, Camilo; Cox, Alison D; Pear, Joseph J

    2014-01-01

    To study the influences between basic and applied research in behavior analysis, we analyzed the coauthorship interactions of authors who published in JABA and JEAB from 1980 to 2010. We paid particular attention to authors who published in both JABA and JEAB (dual authors) as potential agents of cross-field interactions. We present a comprehensive analysis of dual authors' coauthorship interactions using social networks methodology and key word analysis. The number of dual authors more than doubled (26 to 67) and their productivity tripled (7% to 26% of JABA and JEAB articles) between 1980 and 2010. Dual authors stood out in terms of number of collaborators, number of publications, and ability to interact with multiple groups within the field. The steady increase in JEAB and JABA interactions through coauthors and the increasing range of topics covered by dual authors provide a basis for optimism regarding the progressive integration of basic and applied behavior analysis. © Society for the Experimental Analysis of Behavior.

  20. Social network analysis applied to team sports analysis

    CERN Document Server

    Clemente, Filipe Manuel; Mendes, Rui Sousa

    2016-01-01

    Explaining how graph theory and social network analysis can be applied to team sports analysis, This book presents useful approaches, models and methods that can be used to characterise the overall properties of team networks and identify the prominence of each team player. Exploring the different possible network metrics that can be utilised in sports analysis, their possible applications and variances from situation to situation, the respective chapters present an array of illustrative case studies. Identifying the general concepts of social network analysis and network centrality metrics, readers are shown how to generate a methodological protocol for data collection. As such, the book provides a valuable resource for students of the sport sciences, sports engineering, applied computation and the social sciences.

  1. 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.

  2. Colilert® applied to food analysis

    Directory of Open Access Journals (Sweden)

    Maria José Rodrigues

    2014-06-01

    Full Text Available Colilert® (IDEXX was originally developed for the simultaneous enumeration of coliforms and E. coli in water samples and has been used for the quality control routine of drinking, swimming pools, fresh, coastal and waste waters (Grossi et al., 2013. The Colilert® culture medium contains the indicator nutrient 4-Methylumbelliferyl-β-D-Glucuronide (MUG. MUG acts as a substrate for the E. coli enzyme β-glucuronidase, from which a fluorescent compound is produced. A positive MUG result produces fluorescence when viewed under an ultraviolet lamp. If the test fluorescence is equal to or greater than that of the control, the presence of E. coli has been confirmed (Lopez-Roldan et al., 2013. The present work aimed to apply Colilert® to the enumeration of E. coli in different foods, through the comparison of results against the reference method (ISO 16649-2, 2001 for E. coli food analysis. The study was divided in two stages. During the first stage ten different types of foods were analyzed with Colilert®, these included pastry, raw meat, ready to eat meals, yogurt, raw seabream and salmon, and cooked shrimp. From these it were approved the following: pastry with custard; raw minced pork; soup "caldo-verde"; raw vegetable salad (lettuce and carrots and solid yogurt. The approved foods presented a better insertion in the tray, the colour of the wells was lighter and the UV reading was easier. In the second stage the foods were artificially contaminated with 2 log/g of E. coli (ATCC 25922 and analyzed. Colilert® proved to be an accurate method and the counts were similar to the ones obtained with the reference method. In the present study, the Colilert® method did not reveal neither false-positive or false-negative results, however sometimes the results were difficult to read due to the presence of green fluorescence in some wells. Generally Colilert® was an easy and rapid method, but less objective and more expensive than the reference method.

  3. Moving Forward: Positive Behavior Support and Applied Behavior Analysis

    Science.gov (United States)

    Tincani, Matt

    2007-01-01

    A controversy has emerged about the relationship between positive behavior support and applied behavior analysis. Some behavior analysts suggest that positive behavior support and applied behavior analysis are the same (e.g., Carr & Sidener, 2002). Others argue that positive behavior support is harmful to applied behavior analysis (e.g., Johnston,…

  4. Introduction: Conversation Analysis in Applied Linguistics

    Science.gov (United States)

    Sert, Olcay; Seedhouse, Paul

    2011-01-01

    This short, introductory paper presents an up-to-date account of works within the field of Applied Linguistics which have been influenced by a Conversation Analytic paradigm. The article reviews recent studies in classroom interaction, materials development, proficiency assessment and language teacher education. We believe that the publication of…

  5. Applied time series analysis and innovative computing

    CERN Document Server

    Ao, Sio-Iong

    2010-01-01

    This text is a systematic, state-of-the-art introduction to the use of innovative computing paradigms as an investigative tool for applications in time series analysis. It includes frontier case studies based on recent research.

  6. Tissue Microarray Analysis Applied to Bone Diagenesis

    OpenAIRE

    Barrios Mello, Rafael; Regis Silva, Maria Regina; Seixas Alves, Maria Teresa; Evison, Martin; Guimarães, Marco Aurélio; Francisco, Rafaella Arrabaça; Dias Astolphi, Rafael; Miazato Iwamura, Edna Sadayo

    2017-01-01

    Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens....

  7. Meta-analysis in applied ecology.

    Science.gov (United States)

    Stewart, Gavin

    2010-02-23

    This overview examines research synthesis in applied ecology and conservation. Vote counting and pooling unweighted averages are widespread despite the superiority of syntheses based on weighted combination of effects. Such analyses allow exploration of methodological uncertainty in addition to consistency of effects across species, space and time, but exploring heterogeneity remains controversial. Meta-analyses are required to generalize in ecology, and to inform evidence-based decision-making, but the more sophisticated statistical techniques and registers of research used in other disciplines must be employed in ecology to fully realize their benefits.

  8. Applied surface analysis of metal materials

    International Nuclear Information System (INIS)

    Weiss, Z.

    1987-01-01

    The applications of surface analytical techniques in the solution of technological problems in metalurgy and engineering are reviewed. Some important application areas such as corrosion, grain boundary segregation and metallurgical coatings are presented together with specific requirements for the type of information which is necessary for solving particular problems. The techniques discussed include: electron spectroscopies (Auger Electron Spectroscopy, Electron Spectroscopy for Chemical Analysis), ion spectroscopies (Secondary Ion Mass Spectrometry, Ion Scattering Spectroscopy), Rutherford Back-Scattering, nuclear reaction analysis, optical methods (Glow Discharge Optical Emission Spectrometry), ellipsometry, infrared and Raman spectroscopy, the Moessbauer spectroscopy and methods of consumptive depth profile analysis. Principles and analytical features of these methods are demonstrated and examples of their applications to metallurgy are taken from recent literature. (author). 4 figs., 2 tabs., 112 refs

  9. Applied modal analysis of wind turbine blades

    DEFF Research Database (Denmark)

    Pedersen, H.B.; Kristensen, O.J.D.

    2003-01-01

    In this project modal analysis has been used to determine the natural frequencies, damping and the mode shapes for wind turbine blades. Different methods to measure the position and adjust the direction of the measuring points are discussed. Differentequipment for mounting the accelerometers...... is investigated by repeated measurement on the same wind turbine blade. Furthermore the flexibility of the test set-up is investigated, by use ofaccelerometers mounted on the flexible adapter plate during the measurement campaign. One experimental campaign investigated the results obtained from a loaded...... and unloaded wind turbine blade. During this campaign the modal analysis are performed on ablade mounted in a horizontal and a vertical position respectively. Finally the results obtained from modal analysis carried out on a wind turbine blade are compared with results obtained from the Stig Øyes blade_EV1...

  10. Applied quantitative analysis in the social sciences

    CERN Document Server

    Petscher, Yaacov; Compton, Donald L

    2013-01-01

    To say that complex data analyses are ubiquitous in the education and social sciences might be an understatement. Funding agencies and peer-review journals alike require that researchers use the most appropriate models and methods for explaining phenomena. Univariate and multivariate data structures often require the application of more rigorous methods than basic correlational or analysis of variance models. Additionally, though a vast set of resources may exist on how to run analysis, difficulties may be encountered when explicit direction is not provided as to how one should run a model

  11. Applied Spectrophotometry: Analysis of a Biochemical Mixture

    Science.gov (United States)

    Trumbo, Toni A.; Schultz, Emeric; Borland, Michael G.; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the…

  12. Emerald Express '95: Analysis Report

    National Research Council Canada - National Science Library

    Newett, Sandra

    1996-01-01

    The purpose of Emerald Express was to bring together senior representatives from military, relief, political, and diplomatic communities to address issues that arise during Humanitarian Assistance and Peace Operations (HA/POs...

  13. Thermal analysis applied to irradiated propolis

    Energy Technology Data Exchange (ETDEWEB)

    Matsuda, Andrea Harumi; Machado, Luci Brocardo; Mastro, N.L. del E-mail: nelida@usp.br

    2002-03-01

    Propolis is a resinous hive product, collected by bees. Raw propolis requires a decontamination procedure and irradiation appears as a promising technique for this purpose. The valuable properties of propolis for food and pharmaceutical industries have led to increasing interest in its technological behavior. Thermal analysis is a chemical analysis that gives information about changes on heating of great importance for technological applications. Ground propolis samples were {sup 60}Co gamma irradiated with 0 and 10 kGy. Thermogravimetry curves shown a similar multi-stage decomposition pattern for both irradiated and unirradiated samples up to 600 deg. C. Similarly, through differential scanning calorimetry , a coincidence of melting point of irradiated and unirradiated samples was found. The results suggest that the irradiation process do not interfere on the thermal properties of propolis when irradiated up to 10 kGy.

  14. Applied modal analysis of wind turbine blades

    Energy Technology Data Exchange (ETDEWEB)

    Broen Pedersen, H.; Dahl Kristensen, O.J.

    2003-02-01

    In this project modal analysis has been used to determine the natural frequencies, damping and the mode shapes for wind turbine blades. Different methods to measure the position and adjust the direction of the measuring points are discussed. Different equipment for mounting the accelerometers are investigated and the most suitable are chosen. Different excitation techniques are tried during experimental campaigns. After a discussion the pendulum hammer were chosen, and a new improved hammer was manufactured. Some measurement errors are investigated. The ability to repeat the measured results is investigated by repeated measurement on the same wind turbine blade. Furthermore the flexibility of the test set-up is investigated, by use of accelerometers mounted on the flexible adapter plate during the measurement campaign. One experimental campaign investigated the results obtained from a loaded and unloaded wind turbine blade. During this campaign the modal analysis are performed on a blade mounted in a horizontal and a vertical position respectively. Finally the results obtained from modal analysis carried out on a wind turbine blade are compared with results obtained from the Stig Oeyes blade{sub E}V1 program. (au)

  15. Reliability analysis applied to structural tests

    Science.gov (United States)

    Diamond, P.; Payne, A. O.

    1972-01-01

    The application of reliability theory to predict, from structural fatigue test data, the risk of failure of a structure under service conditions because its load-carrying capability is progressively reduced by the extension of a fatigue crack, is considered. The procedure is applicable to both safe-life and fail-safe structures and, for a prescribed safety level, it will enable an inspection procedure to be planned or, if inspection is not feasible, it will evaluate the life to replacement. The theory has been further developed to cope with the case of structures with initial cracks, such as can occur in modern high-strength materials which are susceptible to the formation of small flaws during the production process. The method has been applied to a structure of high-strength steel and the results are compared with those obtained by the current life estimation procedures. This has shown that the conventional methods can be unconservative in certain cases, depending on the characteristics of the structure and the design operating conditions. The suitability of the probabilistic approach to the interpretation of the results from full-scale fatigue testing of aircraft structures is discussed and the assumptions involved are examined.

  16. Artificial intelligence applied to process signal analysis

    Science.gov (United States)

    Corsberg, Dan

    1988-01-01

    Many space station processes are highly complex systems subject to sudden, major transients. In any complex process control system, a critical aspect of the human/machine interface is the analysis and display of process information. Human operators can be overwhelmed by large clusters of alarms that inhibit their ability to diagnose and respond to a disturbance. Using artificial intelligence techniques and a knowledge base approach to this problem, the power of the computer can be used to filter and analyze plant sensor data. This will provide operators with a better description of the process state. Once a process state is recognized, automatic action could be initiated and proper system response monitored.

  17. Thermal transient analysis applied to horizontal wells

    Energy Technology Data Exchange (ETDEWEB)

    Duong, A.N. [Society of Petroleum Engineers, Canadian Section, Calgary, AB (Canada)]|[ConocoPhillips Canada Resources Corp., Calgary, AB (Canada)

    2008-10-15

    Steam assisted gravity drainage (SAGD) is a thermal recovery process used to recover bitumen and heavy oil. This paper presented a newly developed model to estimate cooling time and formation thermal diffusivity by using a thermal transient analysis along the horizontal wellbore under a steam heating process. This radial conduction heating model provides information on the heat influx distribution along a horizontal wellbore or elongated steam chamber, and is therefore important for determining the effectiveness of the heating process in the start-up phase in SAGD. Net heat flux estimation in the target formation during start-up can be difficult to measure because of uncertainties regarding heat loss in the vertical section; steam quality along the horizontal segment; distribution of steam along the wellbore; operational conditions; and additional effects of convection heating. The newly presented model can be considered analogous to pressure transient analysis of a buildup after a constant pressure drawdown. The model is based on an assumption of an infinite-acting system. This paper also proposed a new concept of a heating ring to measure the heat storage in the heated bitumen at the time of testing. Field observations were used to demonstrate how the model can be used to save heat energy, conserve steam and enhance bitumen recovery. 18 refs., 14 figs., 2 appendices.

  18. Photometric analysis applied in determining facial type

    Directory of Open Access Journals (Sweden)

    Luciana Flaquer Martins

    2012-10-01

    Full Text Available INTRODUCTION: In orthodontics, determining the facial type is a key element in the prescription of a correct diagnosis. In the early days of our specialty, observation and measurement of craniofacial structures were done directly on the face, in photographs or plaster casts. With the development of radiographic methods, cephalometric analysis replaced the direct facial analysis. Seeking to validate the analysis of facial soft tissues, this work compares two different methods used to determining the facial types, the anthropometric and the cephalometric methods. METHODS: The sample consisted of sixty-four Brazilian individuals, adults, Caucasian, of both genders, who agreed to participate in this research. All individuals had lateral cephalograms and facial frontal photographs. The facial types were determined by the Vert Index (cephalometric and the Facial Index (photographs. RESULTS: The agreement analysis (Kappa, made for both types of analysis, found an agreement of 76.5%. CONCLUSIONS: We concluded that the Facial Index can be used as an adjunct to orthodontic diagnosis, or as an alternative method for pre-selection of a sample, avoiding that research subjects have to undergo unnecessary tests.INTRODUÇÃO: em Ortodontia, a determinação do tipo facial é um elemento-chave na prescrição de um diagnóstico correto. Nos primórdios de nossa especialidade, a observação e a medição das estruturas craniofaciais eram feitas diretamente na face, em fotografias ou em modelos de gesso. Com o desenvolvimento dos métodos radiográficos, a análise cefalométrica foi substituindo a análise facial direta. Visando legitimar o estudo dos tecidos moles faciais, esse trabalho comparou a determinação do tipo facial pelos métodos antropométrico e cefalométrico. MÉTODOS: a amostra constou de sessenta e quatro indivíduos brasileiros, adultos, leucodermas, de ambos os sexos, que aceitaram participar da pesquisa. De todos os indivíduos da amostra

  19. Gradient pattern analysis applied to galaxy morphology

    Science.gov (United States)

    Rosa, R. R.; de Carvalho, R. R.; Sautter, R. A.; Barchi, P. H.; Stalder, D. H.; Moura, T. C.; Rembold, S. B.; Morell, D. R. F.; Ferreira, N. C.

    2018-06-01

    Gradient pattern analysis (GPA) is a well-established technique for measuring gradient bilateral asymmetries of a square numerical lattice. This paper introduces an improved version of GPA designed for galaxy morphometry. We show the performance of the new method on a selected sample of 54 896 objects from the SDSS-DR7 in common with Galaxy Zoo 1 catalogue. The results suggest that the second gradient moment, G2, has the potential to dramatically improve over more conventional morphometric parameters. It separates early- from late-type galaxies better (˜ 90 per cent) than the CAS system (C˜ 79 per cent, A˜ 50 per cent, S˜ 43 per cent) and a benchmark test shows that it is applicable to hundreds of thousands of galaxies using typical processing systems.

  20. Energy analysis applied to uranium resource estimation

    International Nuclear Information System (INIS)

    Mortimer, N.D.

    1980-01-01

    It is pointed out that fuel prices and ore costs are interdependent, and that in estimating ore costs (involving the cost of fuels used to mine and process the uranium) it is necessary to take into account the total use of energy by the entire fuel system, through the technique of energy analysis. The subject is discussed, and illustrated with diagrams, under the following heads: estimate of how total workable resources would depend on production costs; sensitivity of nuclear electricity prices to ore costs; variation of net energy requirement with ore grade for a typical PWR reactor design; variation of average fundamental cost of nuclear electricity with ore grade; variation of cumulative uranium resources with current maximum ore costs. (U.K.)

  1. Toward applied behavior analysis of life aloft

    Science.gov (United States)

    Brady, J. V.

    1990-01-01

    This article deals with systems at multiple levels, at least from cell to organization. It also deals with learning, decision making, and other behavior at multiple levels. Technological development of a human behavioral ecosystem appropriate to space environments requires an analytic and synthetic orientation, explicitly experimental in nature, dictated by scientific and pragmatic considerations, and closely approximating procedures of established effectiveness in other areas of natural science. The conceptual basis of such an approach has its roots in environmentalism which has two main features: (1) knowledge comes from experience rather than from innate ideas, divine revelation, or other obscure sources; and (2) action is governed by consequences rather than by instinct, reason, will, beliefs, attitudes or even the currently fashionable cognitions. Without an experimentally derived data base founded upon such a functional analysis of human behavior, the overgenerality of "ecological systems" approaches render them incapable of ensuring the successful establishment of enduring space habitats. Without an experimentally derived function account of individual behavioral variability, a natural science of behavior cannot exist. And without a natural science of behavior, the social sciences will necessarily remain in their current status as disciplines of less than optimal precision or utility. Such a functional analysis of human performance should provide an operational account of behavior change in a manner similar to the way in which Darwin's approach to natural selection accounted for the evolution of phylogenetic lines (i.e., in descriptive, nonteleological terms). Similarly, as Darwin's account has subsequently been shown to be consonant with information obtained at the cellular level, so too should behavior principles ultimately prove to be in accord with an account of ontogenetic adaptation at a biochemical level. It would thus seem obvious that the most

  2. Probabilistic safety analysis applied to RBMK reactors

    International Nuclear Information System (INIS)

    Gerez Martin, L.; Fernandez Ramos, P.

    1995-01-01

    The project financed by the European Union ''Revision of RBMK Reactor Safety was divided into nine Topic Groups dealing with different aspects of safety. The area covered by Topic Group 9 was Probabilistic Safety Analysis. TG9 will have touched on some of the problems discussed by other groups, although in terms of the systematic quantification of the impact of design characteristics and RBMK reactor operating practices on the risk of core damage. On account of the reduced time scale and the resources available for the project, the analysis was made using a simplified method based on the results of PSAs conducted in Western countries and on the judgement of the group members. The simplifies method is based on the concepts of Qualification, Redundancy and Automatic Actuation of the systems considered. PSA experience shows that systems complying with the above-mentioned concepts have a failure probability of 1.0E-3 when redundancy is simple, ie two similar equipment items capable of carrying out the same function. In general terms, this value can be considered to be dominated by potential common cause failures. The value considered above changes according to factors that have a positive effect upon it, such as an additional redundancy with a different equipment item (eg a turbo pumps and a motor pump), individual trains with good separations, etc, or a negative effect, such as the absence of suitable periodical tests, the need for operators to perform manual operations, etc. Similarly, possible actions required by the operator during accident sequences are assigned failure probability values between 1 and 1.0E-4, according to the complexity of the action (including local actions to be performed outside the control room) and the time available

  3. Digital photoelastic analysis applied to implant dentistry

    Science.gov (United States)

    Ramesh, K.; Hariprasad, M. P.; Bhuvanewari, S.

    2016-12-01

    Development of improved designs of implant systems in dentistry have necessitated the study of stress fields in the implant regions of the mandible/maxilla for better understanding of the biomechanics involved. Photoelasticity has been used for various studies related to dental implants in view of whole field visualization of maximum shear stress in the form of isochromatic contours. The potential of digital photoelasticity has not been fully exploited in the field of implant dentistry. In this paper, the fringe field in the vicinity of the connected implants (All-On-Four® concept) is analyzed using recent advances in digital photoelasticity. Initially, a novel 3-D photoelastic model making procedure, to closely mimic all the anatomical features of the human mandible is proposed. By choosing appropriate orientation of the model with respect to the light path, the essential region of interest were sought to be analysed while keeping the model under live loading conditions. Need for a sophisticated software module to carefully identify the model domain has been brought out. For data extraction, five-step method is used and isochromatics are evaluated by twelve fringe photoelasticity. In addition to the isochromatic fringe field, whole field isoclinic data is also obtained for the first time in implant dentistry, which could throw important information in improving the structural stability of the implant systems. Analysis is carried out for the implant in the molar as well as the incisor region. In addition, the interaction effects of loaded molar implant on the incisor area are also studied.

  4. Matrix suites applying when making the commercial-company-activity-andfinancial-risks-express-diagnostics

    Directory of Open Access Journals (Sweden)

    Valentina Petrovn Neganova

    2011-09-01

    Full Text Available This paper describes an original technique and peculiarities of its use for the express diagnostics of a company and analysis of financial risks. The feature of this technique is potential Russian reality accountance of optimizational transformations of statements in order to minimize taxation and refract the information field of a business system for the apperception. It is based on the conceptual principle of studies of the University of Ghent, according to which, these three cycles affect stability of the companies to the important risk - the risk of bankruptcy. It is noted that the use of matrix analysis can become an additional powerful tool for solving the conceptual verification problem of financial permanence of business systems operation in the marketplace because it allows to determine the internal nature of the underlying processes that occur within an atomic business system and to make every effort to minimize potential and actual manifestations of instability of the external and internal environment of the business system. This method satisfies the multiple set of conditions-equations: apperceptive, asymptotic and simplificational functions that form the basis of calculations for model creation. The technique can be applied by commercial banks in the analysis of the elements of their loan portfolio. Application of this technique allows analyzing the performance of a commercial company in the features of Russian life with minimal iterations.

  5. 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.

  6. Applied research of environmental monitoring using instrumental neutron activation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Young Sam; Moon, Jong Hwa; Chung, Young Ju

    1997-08-01

    This technical report is written as a guide book for applied research of environmental monitoring using Instrumental Neutron Activation Analysis. The contents are as followings; sampling and sample preparation as a airborne particulate matter, analytical methodologies, data evaluation and interpretation, basic statistical methods of data analysis applied in environmental pollution studies. (author). 23 refs., 7 tabs., 9 figs.

  7. Multiscale Embedded Gene Co-expression Network Analysis.

    Directory of Open Access Journals (Sweden)

    Won-Min Song

    2015-11-01

    Full Text Available Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3, the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA by: i introducing quality control of co-expression similarities, ii parallelizing embedded network construction, and iii developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs. We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA. MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

  8. Multiscale Embedded Gene Co-expression Network Analysis.

    Science.gov (United States)

    Song, Won-Min; Zhang, Bin

    2015-11-01

    Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG) has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3), the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA) by: i) introducing quality control of co-expression similarities, ii) parallelizing embedded network construction, and iii) developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs). We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA). MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

  9. Applying homotopy analysis method for solving differential-difference equation

    International Nuclear Information System (INIS)

    Wang Zhen; Zou Li; Zhang Hongqing

    2007-01-01

    In this Letter, we apply the homotopy analysis method to solving the differential-difference equations. A simple but typical example is applied to illustrate the validity and the great potential of the generalized homotopy analysis method in solving differential-difference equation. Comparisons are made between the results of the proposed method and exact solutions. The results show that the homotopy analysis method is an attractive method in solving the differential-difference equations

  10. Sensitivity analysis approaches applied to systems biology models.

    Science.gov (United States)

    Zi, Z

    2011-11-01

    With the rising application of systems biology, sensitivity analysis methods have been widely applied to study the biological systems, including metabolic networks, signalling pathways and genetic circuits. Sensitivity analysis can provide valuable insights about how robust the biological responses are with respect to the changes of biological parameters and which model inputs are the key factors that affect the model outputs. In addition, sensitivity analysis is valuable for guiding experimental analysis, model reduction and parameter estimation. Local and global sensitivity analysis approaches are the two types of sensitivity analysis that are commonly applied in systems biology. Local sensitivity analysis is a classic method that studies the impact of small perturbations on the model outputs. On the other hand, global sensitivity analysis approaches have been applied to understand how the model outputs are affected by large variations of the model input parameters. In this review, the author introduces the basic concepts of sensitivity analysis approaches applied to systems biology models. Moreover, the author discusses the advantages and disadvantages of different sensitivity analysis methods, how to choose a proper sensitivity analysis approach, the available sensitivity analysis tools for systems biology models and the caveats in the interpretation of sensitivity analysis results.

  11. 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.

  12. Animal Research in the "Journal of Applied Behavior Analysis"

    Science.gov (United States)

    Edwards, Timothy L.; Poling, Alan

    2011-01-01

    This review summarizes the 6 studies with nonhuman animal subjects that have appeared in the "Journal of Applied Behavior Analysis" and offers suggestions for future research in this area. Two of the reviewed articles described translational research in which pigeons were used to illustrate and examine behavioral phenomena of applied significance…

  13. Dimensional Analysis with space discrimination applied to Fickian difussion phenomena

    International Nuclear Information System (INIS)

    Diaz Sanchidrian, C.; Castans, M.

    1989-01-01

    Dimensional Analysis with space discrimination is applied to Fickian difussion phenomena in order to transform its partial differen-tial equations into ordinary ones, and also to obtain in a dimensionl-ess fom the Ficks second law. (Author)

  14. The Roles of Age and Gender in Applying Proverbs and Expressions in Daily Conversations of Shirazians

    Directory of Open Access Journals (Sweden)

    Mohammad Saber Khaghaninejad

    2017-01-01

    Full Text Available Change and transformation are the basic characteristics of languages. Each community incorporates different generations with different ideologies toward life and obviously use different dialects. The difference in dialects among different generations in Iran is so drastic that it seems people speak different languages. This research has attempted to study the amount of applying proverbs and expressions in different age-groups of the society. Therefore, two groups of 24 respondents were randomly selected from both male and female as the statistical population so that investigating age and sex factors in the type and amount of applying proverbs and expressions in the daily conversations become possible. All participants were interviewed individually and their sentences were transcribed accurately. By counting the number of proverbs and expressions in the sentences of Middle-aged and teenager groups, and also by counting the male and female participants, and considering their Expression Density; i.e., the proportion of the number of proverbs and expressions to the total number of the words of each sentence, and by using the method of inferential non-parametric statistics, these results have been achieved: 1.The Middle-aged Group use more proverbs and expressions than teenagers. Perhaps, because they are more familiar with the culture and literature, and they are much more aware of the delicacies of language and literature. 2.Teenagers also use proverbs and expressions; however, these are of the type of words which were inserted suddenly into the lexicon of the society through printed matters or media and cyber networks. 3.Moreover, men totally use more proverbs and expressions than women in their daily conversations.

  15. 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.

  16. The Significance of Regional Analysis in Applied Geography.

    Science.gov (United States)

    Sommers, Lawrence M.

    Regional analysis is central to applied geographic research, contributing to better planning and policy development for a variety of societal problems facing the United States. The development of energy policy serves as an illustration of the capabilities of this type of analysis. The United States has had little success in formulating a national…

  17. 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

  18. Applied data analysis and modeling for energy engineers and scientists

    CERN Document Server

    Reddy, T Agami

    2011-01-01

    ""Applied Data Analysis and Modeling for Energy Engineers and Scientists"" discusses mathematical models, data analysis, and decision analysis in modeling. The approach taken in this volume focuses on the modeling and analysis of thermal systems in an engineering environment, while also covering a number of other critical areas. Other material covered includes the tools that researchers and engineering professionals will need in order to explore different analysis methods, use critical assessment skills and reach sound engineering conclusions. The book also covers process and system design and

  19. 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.

  20. 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/.

  1. Fourier convergence analysis applied to neutron diffusion Eigenvalue problem

    International Nuclear Information System (INIS)

    Lee, Hyun Chul; Noh, Jae Man; Joo, Hyung Kook

    2004-01-01

    Fourier error analysis has been a standard technique for the stability and convergence analysis of linear and nonlinear iterative methods. Though the methods can be applied to Eigenvalue problems too, all the Fourier convergence analyses have been performed only for fixed source problems and a Fourier convergence analysis for Eigenvalue problem has never been reported. Lee et al proposed new 2-D/1-D coupling methods and they showed that the new ones are unconditionally stable while one of the two existing ones is unstable at a small mesh size and that the new ones are better than the existing ones in terms of the convergence rate. In this paper the convergence of method A in reference 4 for the diffusion Eigenvalue problem was analyzed by the Fourier analysis. The Fourier convergence analysis presented in this paper is the first one applied to a neutronics eigenvalue problem to the best of our knowledge

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

    Science.gov (United States)

    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

  3. Spectral analysis and filter theory in applied geophysics

    CERN Document Server

    Buttkus, Burkhard

    2000-01-01

    This book is intended to be an introduction to the fundamentals and methods of spectral analysis and filter theory and their appli­ cations in geophysics. The principles and theoretical basis of the various methods are described, their efficiency and effectiveness eval­ uated, and instructions provided for their practical application. Be­ sides the conventional methods, newer methods arediscussed, such as the spectral analysis ofrandom processes by fitting models to the ob­ served data, maximum-entropy spectral analysis and maximum-like­ lihood spectral analysis, the Wiener and Kalman filtering methods, homomorphic deconvolution, and adaptive methods for nonstation­ ary processes. Multidimensional spectral analysis and filtering, as well as multichannel filters, are given extensive treatment. The book provides a survey of the state-of-the-art of spectral analysis and fil­ ter theory. The importance and possibilities ofspectral analysis and filter theory in geophysics for data acquisition, processing an...

  4. Animal research in the Journal of Applied Behavior Analysis.

    Science.gov (United States)

    Edwards, Timothy L; Poling, Alan

    2011-01-01

    This review summarizes the 6 studies with nonhuman animal subjects that have appeared in the Journal of Applied Behavior Analysis and offers suggestions for future research in this area. Two of the reviewed articles described translational research in which pigeons were used to illustrate and examine behavioral phenomena of applied significance (say-do correspondence and fluency), 3 described interventions that changed animals' behavior (self-injury by a baboon, feces throwing and spitting by a chimpanzee, and unsafe trailer entry by horses) in ways that benefited the animals and the people in charge of them, and 1 described the use of trained rats that performed a service to humans (land-mine detection). We suggest that each of these general research areas merits further attention and that the Journal of Applied Behavior Analysis is an appropriate outlet for some of these publications.

  5. Applied Behavior Analysis Is a Science And, Therefore, Progressive

    Science.gov (United States)

    Leaf, Justin B.; Leaf, Ronald; McEachin, John; Taubman, Mitchell; Ala'i-Rosales, Shahla; Ross, Robert K.; Smith, Tristram; Weiss, Mary Jane

    2016-01-01

    Applied behavior analysis (ABA) is a science and, therefore, involves progressive approaches and outcomes. In this commentary we argue that the spirit and the method of science should be maintained in order to avoid reductionist procedures, stifled innovation, and rote, unresponsive protocols that become increasingly removed from meaningful…

  6. X-ray fluorescence spectrometry applied to soil analysis

    International Nuclear Information System (INIS)

    Salvador, Vera Lucia Ribeiro; Sato, Ivone Mulako; Scapin Junior, Wilson Santo; Scapin, Marcos Antonio; Imakima, Kengo

    1997-01-01

    This paper studies the X-ray fluorescence spectrometry applied to the soil analysis. A comparative study of the WD-XRFS and ED-XRFS techniques was carried out by using the following soil samples: SL-1, SOIL-7 and marine sediment SD-M-2/TM, from IAEA, and clay, JG-1a from Geological Survey of Japan (GSJ)

  7. Progressive-Ratio Schedules and Applied Behavior Analysis

    Science.gov (United States)

    Poling, Alan

    2010-01-01

    Establishing appropriate relations between the basic and applied areas of behavior analysis has been of long and persistent interest to the author. In this article, the author illustrates that there is a direct relation between how hard an organism will work for access to an object or activity, as indexed by the largest ratio completed under a…

  8. B. F. Skinner's Contributions to Applied Behavior Analysis

    Science.gov (United States)

    Morris, Edward K.; Smith, Nathaniel G.; Altus, Deborah E.

    2005-01-01

    Our paper reviews and analyzes B. F. Skinner's contributions to applied behavior analysis in order to assess his role as the field's originator and founder. We found, first, that his contributions fall into five categorizes: the style and content of his science, his interpretations of typical and atypical human behavior, the implications he drew…

  9. Applied Behavior Analysis: Current Myths in Public Education

    Science.gov (United States)

    Fielding, Cheryl; Lowdermilk, John; Lanier, Lauren L.; Fannin, Abigail G.; Schkade, Jennifer L.; Rose, Chad A.; Simpson, Cynthia G.

    2013-01-01

    The effective use of behavior management strategies and related policies continues to be a debated issue in public education. Despite overwhelming evidence espousing the benefits of the implementation of procedures derived from principles based on the science of applied behavior analysis (ABA), educators often indicate many common misconceptions…

  10. Positive Behavior Support and Applied Behavior Analysis: A Familial Alliance

    Science.gov (United States)

    Dunlap, Glen; Carr, Edward G.; Horner, Robert H.; Zarcone, Jennifer R.; Schwartz, Ilene

    2008-01-01

    Positive behavior support (PBS) emerged in the mid-1980s as an approach for understanding and addressing problem behaviors. PBS was derived primarily from applied behavior analysis (ABA). Over time, however, PBS research and practice has incorporated evaluative methods, assessment and intervention procedures, and conceptual perspectives associated…

  11. Neutron activation analysis applied to energy and environment

    International Nuclear Information System (INIS)

    Lyon, W.S.

    1975-01-01

    Neutron activation analysis was applied to a number of problems concerned with energy production and the environment. Burning of fossil fuel, the search for new sources of uranium, possible presence of toxic elements in food and water, and the relationship of trace elements to cardiovascular disease are some of the problems in which neutron activation was used. (auth)

  12. Structural reliability analysis applied to pipeline risk analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gardiner, M. [GL Industrial Services, Loughborough (United Kingdom); Mendes, Renato F.; Donato, Guilherme V.P. [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil)

    2009-07-01

    Quantitative Risk Assessment (QRA) of pipelines requires two main components to be provided. These are models of the consequences that follow from some loss of containment incident, and models for the likelihood of such incidents occurring. This paper describes how PETROBRAS have used Structural Reliability Analysis for the second of these, to provide pipeline- and location-specific predictions of failure frequency for a number of pipeline assets. This paper presents an approach to estimating failure rates for liquid and gas pipelines, using Structural Reliability Analysis (SRA) to analyze the credible basic mechanisms of failure such as corrosion and mechanical damage. SRA is a probabilistic limit state method: for a given failure mechanism it quantifies the uncertainty in parameters to mathematical models of the load-resistance state of a structure and then evaluates the probability of load exceeding resistance. SRA can be used to benefit the pipeline risk management process by optimizing in-line inspection schedules, and as part of the design process for new construction in pipeline rights of way that already contain multiple lines. A case study is presented to show how the SRA approach has recently been used on PETROBRAS pipelines and the benefits obtained from it. (author)

  13. 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

  14. Gene expression analysis of flax seed development

    Directory of Open Access Journals (Sweden)

    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

  15. Research in applied mathematics, numerical analysis, and computer science

    Science.gov (United States)

    1984-01-01

    Research conducted at the Institute for Computer Applications in Science and Engineering (ICASE) in applied mathematics, numerical analysis, and computer science is summarized and abstracts of published reports are presented. The major categories of the ICASE research program are: (1) numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; (2) control and parameter identification; (3) computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, and structural analysis; and (4) computer systems and software, especially vector and parallel computers.

  16. Applied Fourier analysis from signal processing to medical imaging

    CERN Document Server

    Olson, Tim

    2017-01-01

    The first of its kind, this focused textbook serves as a self-contained resource for teaching from scratch the fundamental mathematics of Fourier analysis and illustrating some of its most current, interesting applications, including medical imaging and radar processing. Developed by the author from extensive classroom teaching experience, it provides a breadth of theory that allows students to appreciate the utility of the subject, but at as accessible a depth as possible. With myriad applications included, this book can be adapted to a one or two semester course in Fourier Analysis or serve as the basis for independent study. Applied Fourier Analysis assumes no prior knowledge of analysis from its readers, and begins by making the transition from linear algebra to functional analysis. It goes on to cover basic Fourier series and Fourier transforms before delving into applications in sampling and interpolation theory, digital communications, radar processing, medical i maging, and heat and wave equations. Fo...

  17. 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

  18. 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

  19. A Study of Applied Strategies in Translating Idiomatic Expressions in Two Movie Subtitles: Bring It On & Mean Girls

    Directory of Open Access Journals (Sweden)

    Mahmood Hashemian

    2017-10-01

    Full Text Available Idiomatic expressions are considered as a part of everyday language. In other words, they are the essence of each language and one of the most problematic parts to cope with, especially in the process of interlingual translation. Furthermore, there is sometimes no one-to-one equivalent for the idioms of the source language (SL in the target language (TL. This study aimed at investigating the applied strategies in the translation of idiomatic expressions in 2 American subtitled movies, namely Mean Girls (2004 and Bring It On! (2009, through using Baker’s (1992 proposed procedures in translating idiomatic expressions in translation studies. To this aim, the idiomatic expressions were extracted from the original versions of the movies and compared with the subtitled translations in Persian. Analysis of the relevant data indicated that the chi-square results were not significant at χ2 (3, N = 2 = 1.188, p = 0, considering p ˂ 0.05. Therefore, Baker’s (1992 strategies were not distributed equally between these two movies. Moreover, the “omission” strategy with the frequency of 40 was the topmost used strategy in these movies.

  20. 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.

  1. International publication trends in the Journal of Applied Behavior Analysis: 2000-2014.

    Science.gov (United States)

    Martin, Neil T; Nosik, Melissa R; Carr, James E

    2016-06-01

    Dymond, Clarke, Dunlap, and Steiner's (2000) analysis of international publication trends in the Journal of Applied Behavior Analysis (JABA) from 1970 to 1999 revealed low numbers of publications from outside North America, leading the authors to express concern about the lack of international involvement in applied behavior analysis. They suggested that a future review would be necessary to evaluate any changes in international authorship in the journal. As a follow-up, we analyzed non-U.S. publication trends in the most recent 15 years of JABA and found similar results. We discuss potential reasons for the relative paucity of international authors and suggest potential strategies for increasing non-U.S. contributions to the advancement of behavior analysis. © 2015 Society for the Experimental Analysis of Behavior.

  2. 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

  3. Analysis of musical expression in audio signals

    Science.gov (United States)

    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.

  4. Applying DEA sensitivity analysis to efficiency measurement of Vietnamese universities

    Directory of Open Access Journals (Sweden)

    Thi Thanh Huyen Nguyen

    2015-11-01

    Full Text Available The primary purpose of this study is to measure the technical efficiency of 30 doctorate-granting universities, the universities or the higher education institutes with PhD training programs, in Vietnam, applying the sensitivity analysis of data envelopment analysis (DEA. The study uses eight sets of input-output specifications using the replacement as well as aggregation/disaggregation of variables. The measurement results allow us to examine the sensitivity of the efficiency of these universities with the sets of variables. The findings also show the impact of variables on their efficiency and its “sustainability”.

  5. 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

  6. Analysis of concrete beams using applied element method

    Science.gov (United States)

    Lincy Christy, D.; Madhavan Pillai, T. M.; Nagarajan, Praveen

    2018-03-01

    The Applied Element Method (AEM) is a displacement based method of structural analysis. Some of its features are similar to that of Finite Element Method (FEM). In AEM, the structure is analysed by dividing it into several elements similar to FEM. But, in AEM, elements are connected by springs instead of nodes as in the case of FEM. In this paper, background to AEM is discussed and necessary equations are derived. For illustrating the application of AEM, it has been used to analyse plain concrete beam of fixed support condition. The analysis is limited to the analysis of 2-dimensional structures. It was found that the number of springs has no much influence on the results. AEM could predict deflection and reactions with reasonable degree of accuracy.

  7. Apply Functional Modelling to Consequence Analysis in Supervision Systems

    DEFF Research Database (Denmark)

    Zhang, Xinxin; Lind, Morten; Gola, Giulio

    2013-01-01

    This paper will first present the purpose and goals of applying functional modelling approach to consequence analysis by adopting Multilevel Flow Modelling (MFM). MFM Models describe a complex system in multiple abstraction levels in both means-end dimension and whole-part dimension. It contains...... consequence analysis to practical or online applications in supervision systems. It will also suggest a multiagent solution as the integration architecture for developing tools to facilitate the utilization results of functional consequence analysis. Finally a prototype of the multiagent reasoning system...... causal relations between functions and goals. A rule base system can be developed to trace the causal relations and perform consequence propagations. This paper will illustrate how to use MFM for consequence reasoning by using rule base technology and describe the challenges for integrating functional...

  8. Analysis of Brick Masonry Wall using Applied Element Method

    Science.gov (United States)

    Lincy Christy, D.; Madhavan Pillai, T. M.; Nagarajan, Praveen

    2018-03-01

    The Applied Element Method (AEM) is a versatile tool for structural analysis. Analysis is done by discretising the structure as in the case of Finite Element Method (FEM). In AEM, elements are connected by a set of normal and shear springs instead of nodes. AEM is extensively used for the analysis of brittle materials. Brick masonry wall can be effectively analyzed in the frame of AEM. The composite nature of masonry wall can be easily modelled using springs. The brick springs and mortar springs are assumed to be connected in series. The brick masonry wall is analyzed and failure load is determined for different loading cases. The results were used to find the best aspect ratio of brick to strengthen brick masonry wall.

  9. 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...

  10. Applied research and development of neutron activation analysis

    International Nuclear Information System (INIS)

    Chung, Yong Sam; Moon, Jong Hwa; Kim, Sun Ha; Baek, Sung Ryel; Kim, Young Gi; Jung, Hwan Sung; Park, Kwang Won; Kang, Sang Hun; Lim, Jong Myoung

    2003-05-01

    The aims of this project are to establish the quality control system of Neutron Activation Analysis(NAA) due to increase of industrial needs for standard analytical method and to prepare and identify the standard operation procedure of NAA through practical testing for different analytical items. R and D implementations of analytical quality system using neutron irradiation facility and gamma-ray measurement system and automation of NAA facility in HANARO research reactor are as following ; 1) Establishment of NAA quality control system for the maintenance of best measurement capability and the promotion of utilization of HANARO research reactor 2) Improvement of analytical sensitivity for industrial applied technologies and establishment of certified standard procedures 3) Standardization and development of Prompt Gamma-ray Activation Analysis (PGAA) technology

  11. Automated SEM Modal Analysis Applied to the Diogenites

    Science.gov (United States)

    Bowman, L. E.; Spilde, M. N.; Papike, James J.

    1996-01-01

    Analysis of volume proportions of minerals, or modal analysis, is routinely accomplished by point counting on an optical microscope, but the process, particularly on brecciated samples such as the diogenite meteorites, is tedious and prone to error by misidentification of very small fragments, which may make up a significant volume of the sample. Precise volume percentage data can be gathered on a scanning electron microscope (SEM) utilizing digital imaging and an energy dispersive spectrometer (EDS). This form of automated phase analysis reduces error, and at the same time provides more information than could be gathered using simple point counting alone, such as particle morphology statistics and chemical analyses. We have previously studied major, minor, and trace-element chemistry of orthopyroxene from a suite of diogenites. This abstract describes the method applied to determine the modes on this same suite of meteorites and the results of that research. The modal abundances thus determined add additional information on the petrogenesis of the diogenites. In addition, low-abundance phases such as spinels were located for further analysis by this method.

  12. Sports dance artistic expression culture analysis

    Directory of Open Access Journals (Sweden)

    Chen Zegang

    2017-01-01

    Full Text Available 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, form, music, shape of the expressive force. In this paper, the study will be more in-depth excavation of the cultural connotation of sports dance, and promote the development of sports dance can be more comprehensive. In 20s of last century, Chinese Sports Dance Association officially joined the International Sports Dance Association, which also makes our country’s sports dance and international exchange more frequent. However, due to China’s sports dance sports dance learning time is not long, while learning is influenced by Chinese traditional culture, the sports dance movements are too conservative, there is a very large gap and international enthusiasm, bold and unrestrained, the pursuit of individual sports dance in the dance style, music and performance hand. Sports dance originated from abroad, it is produced in the daily life of people in foreign countries. China’s domestic sports dance players in learning dance at the same time, the production and the connotation of dance is not very understanding, therefore, it is difficult to better reflect the emotional expression of sports dance. Although the sports dance is a kind of similar to the competitive projects, but it is also a kind of dance culture, and to constitute a force from the dance art show a detailed study, detailed mining playing officer of sports dance performance further, reducing China’s sports dance and international sports dance gap.

  13. Applying Authentic Data Analysis in Learning Earth Atmosphere

    Science.gov (United States)

    Johan, H.; Suhandi, A.; Samsudin, A.; Wulan, A. R.

    2017-09-01

    The aim of this research was to develop earth science learning material especially earth atmosphere supported by science research with authentic data analysis to enhance reasoning through. Various earth and space science phenomenon require reasoning. This research used experimental research with one group pre test-post test design. 23 pre-service physics teacher participated in this research. Essay test was conducted to get data about reason ability. Essay test was analyzed quantitatively. Observation sheet was used to capture phenomena during learning process. The results showed that student’s reasoning ability improved from unidentified and no reasoning to evidence based reasoning and inductive/deductive rule-based reasoning. Authentic data was considered using Grid Analysis Display System (GrADS). Visualization from GrADS facilitated students to correlate the concepts and bring out real condition of nature in classroom activity. It also helped student to reason the phenomena related to earth and space science concept. It can be concluded that applying authentic data analysis in learning process can help to enhance students reasoning. This study is expected to help lecture to bring out result of geoscience research in learning process and facilitate student understand concepts.

  14. Serial Analysis of Gene Expression: Applications in Human Studies

    Directory of Open Access Journals (Sweden)

    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.

  15. SPI Trend Analysis of New Zealand Applying the ITA Technique

    Directory of Open Access Journals (Sweden)

    Tommaso Caloiero

    2018-03-01

    Full Text Available A natural temporary imbalance of water availability, consisting of persistent lower-than-average or higher-than-average precipitation, can cause extreme dry and wet conditions that adversely impact agricultural yields, water resources, infrastructure, and human systems. In this study, dry and wet periods in New Zealand were expressed using the Standardized Precipitation Index (SPI. First, both the short term (3 and 6 months and the long term (12 and 24 months SPI were estimated, and then, possible trends in the SPI values were detected by means of a new graphical technique, the Innovative Trend Analysis (ITA, which allows the trend identification of the low, medium, and high values of a series. Results show that, in every area currently subject to drought, an increase in this phenomenon can be expected. Specifically, the results of this paper highlight that agricultural regions on the eastern side of the South Island, as well as the north-eastern regions of the North Island, are the most consistently vulnerable areas. In fact, in these regions, the trend analysis mainly showed a general reduction in all the values of the SPI: that is, a tendency toward heavier droughts and weaker wet periods.

  16. Applied research and development of neutron activation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Yong Sam; Moon, Jong Hwa; Kim, Sun Ha; Bak, Sung Ryel; Park, Yong Chul; Kim, Young Ki; Chung, Hwan Sung; Park, Kwang Won; Kang, Sang Hun

    2000-05-01

    This report is written for results of research and development as follows : improvement of neutron irradiation facilities, counting system and development of automation system and capsules for NAA in HANARO ; improvement of analytical procedures and establishment of analytical quality control and assurance system; applied research and development of environment, industry and human health and its standardization. For identification and standardization of analytical method, environmental biological samples and polymer are analyzed and uncertainity of measurement are estimated. Also data intercomparison and proficency test were performed. Using airborne particulate matter chosen as a environmental indicators, trace elemental concentrations of sample collected at urban and rural site are determined and then the calculation of statistics and the factor analysis are carried out for investigation of emission source. International cooperation research project was carried out for utilization of nuclear techniques.

  17. Applied research and development of neutron activation analysis

    International Nuclear Information System (INIS)

    Chung, Yong Sam; Moon, Jong Hwa; Kim, Sun Ha; Bak, Sung Ryel; Park, Yong Chul; Kim, Young Ki; Chung, Hwan Sung; Park, Kwang Won; Kang, Sang Hun

    2000-05-01

    This report is written for results of research and development as follows : improvement of neutron irradiation facilities, counting system and development of automation system and capsules for NAA in HANARO ; improvement of analytical procedures and establishment of analytical quality control and assurance system; applied research and development of environment, industry and human health and its standardization. For identification and standardization of analytical method, environmental biological samples and polymer are analyzed and uncertainity of measurement are estimated. Also data intercomparison and proficency test were performed. Using airborne particulate matter chosen as a environmental indicators, trace elemental concentrations of sample collected at urban and rural site are determined and then the calculation of statistics and the factor analysis are carried out for investigation of emission source. International cooperation research project was carried out for utilization of nuclear techniques

  18. Applying Conjoint Analysis to Study Attitudes of Thai Government Organisations

    Directory of Open Access Journals (Sweden)

    Natee Suriyanon

    2012-11-01

    Full Text Available This article presents the application of choice-based conjointanalysis to analyse the attitude of Thai government organisationstowards the restriction of the contractor’s right to claimcompensation for unfavourable effects from undesirable events.The analysis reveals that the organisations want to restrict only 6out of 14 types of the claiming rights that were studied. The rightthat they want to restrict most is the right to claim for additionaldirect costs due to force majeure. They are willing to pay between0.087% - 0.210% of the total project direct cost for restricting eachtype of contractor right. The total additional cost for restrictingall six types of rights that the organisations are willing to pay is0.882%. The last section of this article applies the knowledgegained from a choice based conjoint analysis experiment to theanalysis of the standard contract of the Thai government. Theanalysis reveals three types of rights where Thai governmentorganisations are willing to forego restrictions, but the presentstandard contract does not grant such rights.

  19. The Evidence-Based Practice of Applied Behavior Analysis.

    Science.gov (United States)

    Slocum, Timothy A; Detrich, Ronnie; Wilczynski, Susan M; Spencer, Trina D; Lewis, Teri; Wolfe, Katie

    2014-05-01

    Evidence-based practice (EBP) is a model of professional decision-making in which practitioners integrate the best available evidence with client values/context and clinical expertise in order to provide services for their clients. This framework provides behavior analysts with a structure for pervasive use of the best available evidence in the complex settings in which they work. This structure recognizes the need for clear and explicit understanding of the strength of evidence supporting intervention options, the important contextual factors including client values that contribute to decision making, and the key role of clinical expertise in the conceptualization, intervention, and evaluation of cases. Opening the discussion of EBP in this journal, Smith (The Behavior Analyst, 36, 7-33, 2013) raised several key issues related to EBP and applied behavior analysis (ABA). The purpose of this paper is to respond to Smith's arguments and extend the discussion of the relevant issues. Although we support many of Smith's (The Behavior Analyst, 36, 7-33, 2013) points, we contend that Smith's definition of EBP is significantly narrower than definitions that are used in professions with long histories of EBP and that this narrowness conflicts with the principles that drive applied behavior analytic practice. We offer a definition and framework for EBP that aligns with the foundations of ABA and is consistent with well-established definitions of EBP in medicine, psychology, and other professions. In addition to supporting the systematic use of research evidence in behavior analytic decision making, this definition can promote clear communication about treatment decisions across disciplines and with important outside institutions such as insurance companies and granting agencies.

  20. To apply or not to apply: a survey analysis of grant writing costs and benefits.

    Science.gov (United States)

    von Hippel, Ted; von Hippel, Courtney

    2015-01-01

    We surveyed 113 astronomers and 82 psychologists active in applying for federally funded research on their grant-writing history between January, 2009 and November, 2012. We collected demographic data, effort levels, success rates, and perceived non-financial benefits from writing grant proposals. We find that the average proposal takes 116 PI hours and 55 CI hours to write; although time spent writing was not related to whether the grant was funded. Effort did translate into success, however, as academics who wrote more grants received more funding. Participants indicated modest non-monetary benefits from grant writing, with psychologists reporting a somewhat greater benefit overall than astronomers. These perceptions of non-financial benefits were unrelated to how many grants investigators applied for, the number of grants they received, or the amount of time they devoted to writing their proposals. We also explored the number of years an investigator can afford to apply unsuccessfully for research grants and our analyses suggest that funding rates below approximately 20%, commensurate with current NIH and NSF funding, are likely to drive at least half of the active researchers away from federally funded research. We conclude with recommendations and suggestions for individual investigators and for department heads.

  1. To apply or not to apply: a survey analysis of grant writing costs and benefits.

    Directory of Open Access Journals (Sweden)

    Ted von Hippel

    Full Text Available We surveyed 113 astronomers and 82 psychologists active in applying for federally funded research on their grant-writing history between January, 2009 and November, 2012. We collected demographic data, effort levels, success rates, and perceived non-financial benefits from writing grant proposals. We find that the average proposal takes 116 PI hours and 55 CI hours to write; although time spent writing was not related to whether the grant was funded. Effort did translate into success, however, as academics who wrote more grants received more funding. Participants indicated modest non-monetary benefits from grant writing, with psychologists reporting a somewhat greater benefit overall than astronomers. These perceptions of non-financial benefits were unrelated to how many grants investigators applied for, the number of grants they received, or the amount of time they devoted to writing their proposals. We also explored the number of years an investigator can afford to apply unsuccessfully for research grants and our analyses suggest that funding rates below approximately 20%, commensurate with current NIH and NSF funding, are likely to drive at least half of the active researchers away from federally funded research. We conclude with recommendations and suggestions for individual investigators and for department heads.

  2. Applied genre analysis: a multi-perspective model

    Directory of Open Access Journals (Sweden)

    Vijay K Bhatia

    2002-04-01

    Full Text Available Genre analysis can be viewed from two different perspectives: it may be seen as a reflection of the complex realities of the world of institutionalised communication, or it may be seen as a pedagogically effective and convenient tool for the design of language teaching programmes, often situated within simulated contexts of classroom activities. This paper makes an attempt to understand and resolve the tension between these two seemingly contentious perspectives to answer the question: "Is generic description a reflection of reality, or a convenient fiction invented by applied linguists?". The paper also discusses issues related to the nature and use of linguistic description in a genre-based educational enterprise, claiming that instead of using generic descriptions as models for linguistic reproduction of conventional forms to respond to recurring social contexts, as is often the case in many communication based curriculum contexts, they can be used as analytical resource to understand and manipulate complex inter-generic and multicultural realisations of professional discourse, which will enable learners to use generic knowledge to respond to novel social contexts and also to create new forms of discourse to achieve pragmatic success as well as other powerful human agendas.

  3. SUCCESS CONCEPT ANALYSIS APPLIED TO THE INFORMATION TECHNOLOGY PROJECT MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Cassio C. Montenegro Duarte

    2012-05-01

    Full Text Available This study evaluates the concept of success in project management that is applicable to the IT universe, from the classical theory associated with the techniques of project management. Therefore, it applies the theoretical analysis associated to the context of information technology in enterprises as well as the classic literature of traditional project management, focusing on its application in business information technology. From the literature developed in the first part of the study, four propositions were prepared for study which formed the basis for the development of the field research with three large companies that develop projects of Information Technology. The methodology used in the study predicted the development of the multiple case study. Empirical evidence suggests that the concept of success found in the classical literature in project management adjusts to the environment management of IT projects. Showed that it is possible to create the model of standard IT projects in order to replicate it in future derivatives projects, which depends on the learning acquired at the end of a long and continuous process and sponsorship of senior management, which ultimately results in its merger into the company culture.

  4. Applying importance-performance analysis to patient safety culture.

    Science.gov (United States)

    Lee, Yii-Ching; Wu, Hsin-Hung; Hsieh, Wan-Lin; Weng, Shao-Jen; Hsieh, Liang-Po; Huang, Chih-Hsuan

    2015-01-01

    The Sexton et al.'s (2006) safety attitudes questionnaire (SAQ) has been widely used to assess staff's attitudes towards patient safety in healthcare organizations. However, to date there have been few studies that discuss the perceptions of patient safety both from hospital staff and upper management. The purpose of this paper is to improve and to develop better strategies regarding patient safety in healthcare organizations. The Chinese version of SAQ based on the Taiwan Joint Commission on Hospital Accreditation is used to evaluate the perceptions of hospital staff. The current study then lies in applying importance-performance analysis technique to identify the major strengths and weaknesses of the safety culture. The results show that teamwork climate, safety climate, job satisfaction, stress recognition and working conditions are major strengths and should be maintained in order to provide a better patient safety culture. On the contrary, perceptions of management and hospital handoffs and transitions are important weaknesses and should be improved immediately. Research limitations/implications - The research is restricted in generalizability. The assessment of hospital staff in patient safety culture is physicians and registered nurses. It would be interesting to further evaluate other staff's (e.g. technicians, pharmacists and others) opinions regarding patient safety culture in the hospital. Few studies have clearly evaluated the perceptions of healthcare organization management regarding patient safety culture. Healthcare managers enable to take more effective actions to improve the level of patient safety by investigating key characteristics (either strengths or weaknesses) that healthcare organizations should focus on.

  5. Applying multicriteria analysis for choosing the best marination for pork

    Directory of Open Access Journals (Sweden)

    Nieto VMOS

    2015-01-01

    Full Text Available Objective. This research aimed to choose a best marination solution using the Analytic Hierarchy Process (AHP. Materials and methods. Pork meat samples were collected in a commercial slaughterhouse, and they were randomly distributed in four treatments with three different salt contents blend. Color, pH, retention of the solution, exudate and cooking loss, shear force and sensory attributes were assessed and evaluated. Multicriteria analysis using AHP was applied to the results in order to choose the best overall marination solution. Criteria used for selection were the physical and sensory characteristics of meat, and based on these criteria were classified solutions marination. Results. Results showed that the combination of the salts was the best alternative (Na2CO3+NaCl+Na5P3O10, followed by the solutions of (Na2CO3 + NaCl, and (Na5P3O10 + NaCl. Conclusions. All tested solutions with the salts used alone or in combination led to better physical and sensory attributes than the meat not marinated.

  6. Simplified inelastic analysis methods applied to fast breeder reactor core design

    International Nuclear Information System (INIS)

    Abo-El-Ata, M.M.

    1978-01-01

    The paper starts with a review of some currently available simplified inelastic analysis methods used in elevated temperature design for evaluating plastic and thermal creep strains. The primary purpose of the paper is to investigate how these simplified methods may be applied to fast breeder reactor core design where neutron irradiation effects are significant. One of the problems discussed is irradiation-induced creep and its effect on shakedown, ratcheting, and plastic cycling. Another problem is the development of swelling-induced stress which is an additional loading mechanism and must be taken into account. In this respect an expression for swelling-induced stress in the presence of irradiation creep is derived and a model for simplifying the stress analysis under these conditions is proposed. As an example, the effects of irradiation creep and swelling induced stress on the analysis of a thin walled tube under constant internal pressure and intermittent heat fluxes, simulating a fuel pin, is presented

  7. Proteomic Analysis of Bacterial Expression Profiles Following ...

    African Journals Online (AJOL)

    mass spectrometry (GC-MS) were performed to determine the phytochemicals in the active fraction. Results: Five differentially expressed bacterial proteins (four from Escherichia coli and one from Staphylococcus aureus), were identified via ...

  8. [Weighted gene co-expression network analysis in biomedicine research].

    Science.gov (United States)

    Liu, Wei; Li, Li; Ye, Hua; Tu, Wei

    2017-11-25

    High-throughput biological technologies are now widely applied in biology and medicine, allowing scientists to monitor thousands of parameters simultaneously in a specific sample. However, it is still an enormous challenge to mine useful information from high-throughput data. The emergence of network biology provides deeper insights into complex bio-system and reveals the modularity in tissue/cellular networks. Correlation networks are increasingly used in bioinformatics applications. Weighted gene co-expression network analysis (WGCNA) tool can detect clusters of highly correlated genes. Therefore, we systematically reviewed the application of WGCNA in the study of disease diagnosis, pathogenesis and other related fields. First, we introduced principle, workflow, advantages and disadvantages of WGCNA. Second, we presented the application of WGCNA in disease, physiology, drug, evolution and genome annotation. Then, we indicated the application of WGCNA in newly developed high-throughput methods. We hope this review will help to promote the application of WGCNA in biomedicine research.

  9. New trends in applied harmonic analysis sparse representations, compressed sensing, and multifractal analysis

    CERN Document Server

    Cabrelli, Carlos; Jaffard, Stephane; Molter, Ursula

    2016-01-01

    This volume is a selection of written notes corresponding to courses taught at the CIMPA School: "New Trends in Applied Harmonic Analysis: Sparse Representations, Compressed Sensing and Multifractal Analysis". New interactions between harmonic analysis and signal and image processing have seen striking development in the last 10 years, and several technological deadlocks have been solved through the resolution of deep theoretical problems in harmonic analysis. New Trends in Applied Harmonic Analysis focuses on two particularly active areas that are representative of such advances: multifractal analysis, and sparse representation and compressed sensing. The contributions are written by leaders in these areas, and covers both theoretical aspects and applications. This work should prove useful not only to PhD students and postdocs in mathematics and signal and image processing, but also to researchers working in related topics.

  10. Biclustering methods: biological relevance and application in gene expression analysis.

    Directory of Open Access Journals (Sweden)

    Ali Oghabian

    Full Text Available DNA microarray technologies are used extensively to profile the expression levels of thousands of genes under various conditions, yielding extremely large data-matrices. Thus, analyzing this information and extracting biologically relevant knowledge becomes a considerable challenge. A classical approach for tackling this challenge is to use clustering (also known as one-way clustering methods where genes (or respectively samples are grouped together based on the similarity of their expression profiles across the set of all samples (or respectively genes. An alternative approach is to develop biclustering methods to identify local patterns in the data. These methods extract subgroups of genes that are co-expressed across only a subset of samples and may feature important biological or medical implications. In this study we evaluate 13 biclustering and 2 clustering (k-means and hierarchical methods. We use several approaches to compare their performance on two real gene expression data sets. For this purpose we apply four evaluation measures in our analysis: (1 we examine how well the considered (biclustering methods differentiate various sample types; (2 we evaluate how well the groups of genes discovered by the (biclustering methods are annotated with similar Gene Ontology categories; (3 we evaluate the capability of the methods to differentiate genes that are known to be specific to the particular sample types we study and (4 we compare the running time of the algorithms. In the end, we conclude that as long as the samples are well defined and annotated, the contamination of the samples is limited, and the samples are well replicated, biclustering methods such as Plaid and SAMBA are useful for discovering relevant subsets of genes and samples.

  11. A comparative analysis of biclustering algorithms for gene expression data

    Science.gov (United States)

    Eren, Kemal; Deveci, Mehmet; Küçüktunç, Onur; Çatalyürek, Ümit V.

    2013-01-01

    The need to analyze high-dimension biological data is driving the development of new data mining methods. Biclustering algorithms have been successfully applied to gene expression data to discover local patterns, in which a subset of genes exhibit similar expression levels over a subset of conditions. However, it is not clear which algorithms are best suited for this task. Many algorithms have been published in the past decade, most of which have been compared only to a small number of algorithms. Surveys and comparisons exist in the literature, but because of the large number and variety of biclustering algorithms, they are quickly outdated. In this article we partially address this problem of evaluating the strengths and weaknesses of existing biclustering methods. We used the BiBench package to compare 12 algorithms, many of which were recently published or have not been extensively studied. The algorithms were tested on a suite of synthetic data sets to measure their performance on data with varying conditions, such as different bicluster models, varying noise, varying numbers of biclusters and overlapping biclusters. The algorithms were also tested on eight large gene expression data sets obtained from the Gene Expression Omnibus. Gene Ontology enrichment analysis was performed on the resulting biclusters, and the best enrichment terms are reported. Our analyses show that the biclustering method and its parameters should be selected based on the desired model, whether that model allows overlapping biclusters, and its robustness to noise. In addition, we observe that the biclustering algorithms capable of finding more than one model are more successful at capturing biologically relevant clusters. PMID:22772837

  12. Current status of neutron activation analysis and applied nuclear chemistry

    International Nuclear Information System (INIS)

    Lyon, W.S.

    1990-01-01

    A review of recent scientometric studies of citations and publication data shows the present state of NAA and applied nuclear chemistry as compared to other analytical techniques. (author) 9 refs.; 7 tabs

  13. 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.

  14. RISK ANALYSIS APPLIED IN OIL EXPLORATION AND PRODUCTION

    African Journals Online (AJOL)

    ES Obe

    aDepartment of Civil Engineering, University of Nigeria, Nsukka, Enugu State, Nigeria. ... The analysis in this work is ... risk analysis, oil field, risk management, projects, investment opportunity. 1. .... own merit but since the company has limited.

  15. Empirical modeling and data analysis for engineers and applied scientists

    CERN Document Server

    Pardo, Scott A

    2016-01-01

    This textbook teaches advanced undergraduate and first-year graduate students in Engineering and Applied Sciences to gather and analyze empirical observations (data) in order to aid in making design decisions. While science is about discovery, the primary paradigm of engineering and "applied science" is design. Scientists are in the discovery business and want, in general, to understand the natural world rather than to alter it. In contrast, engineers and applied scientists design products, processes, and solutions to problems. That said, statistics, as a discipline, is mostly oriented toward the discovery paradigm. Young engineers come out of their degree programs having taken courses such as "Statistics for Engineers and Scientists" without any clear idea as to how they can use statistical methods to help them design products or processes. Many seem to think that statistics is only useful for demonstrating that a device or process actually does what it was designed to do. Statistics courses emphasize creati...

  16. Expressivity in Children's Drawings: A Longitudinal Analysis.

    Science.gov (United States)

    Ives, William

    This paper reports a follow-up study of 5-, 7-, and 9-year-old subjects who had participated in an investigation of the nature of children's and adults' ability to graphically represent expressive qualities (i.e., happy, sad, angry, loud, quiet, hard). In the original study, the use of literal representation (such as a smiling face on a tree) and…

  17. Shrinkage Approach for Gene Expression Data Analysis

    Czech Academy of Sciences Publication Activity Database

    Haman, Jiří; Valenta, Zdeněk; Kalina, Jan

    2013-01-01

    Roč. 1, č. 1 (2013), s. 65-65 ISSN 1805-8698. [EFMI 2013 Special Topic Conference. 17.04.2013-19.04.2013, Prague] Institutional support: RVO:67985807 Keywords : shrinkage estimation * covariance matrix * high dimensional data * gene expression Subject RIV: IN - Informatics, Computer Science

  18. Applying thematic analysis theory to practice: a researcher's experience.

    Science.gov (United States)

    Tuckett, Anthony G

    2005-01-01

    This article describes an experience of thematic analysis. In order to answer the question 'What does analysis look like in practice?' it describes in brief how the methodology of grounded theory, the epistemology of social constructionism, and the theoretical stance of symbolic interactionism inform analysis. Additionally, analysis is examined by evidencing the systematic processes--here termed organising, coding, writing, theorising, and reading--that led the researcher to develop a final thematic schema.

  19. DATE analysis: A general theory of biological change applied to microarray data.

    Science.gov (United States)

    Rasnick, David

    2009-01-01

    In contrast to conventional data mining, which searches for specific subsets of genes (extensive variables) to correlate with specific phenotypes, DATE analysis correlates intensive state variables calculated from the same datasets. At the heart of DATE analysis are two biological equations of state not dependent on genetic pathways. This result distinguishes DATE analysis from other bioinformatics approaches. The dimensionless state variable F quantifies the relative overall cellular activity of test cells compared to well-chosen reference cells. The variable pi(i) is the fold-change in the expression of the ith gene of test cells relative to reference. It is the fraction phi of the genome undergoing differential expression-not the magnitude pi-that controls biological change. The state variable phi is equivalent to the control strength of metabolic control analysis. For tractability, DATE analysis assumes a linear system of enzyme-connected networks and exploits the small average contribution of each cellular component. This approach was validated by reproducible values of the state variables F, RNA index, and phi calculated from random subsets of transcript microarray data. Using published microarray data, F, RNA index, and phi were correlated with: (1) the blood-feeding cycle of the malaria parasite, (2) embryonic development of the fruit fly, (3) temperature adaptation of Killifish, (4) exponential growth of cultured S. pneumoniae, and (5) human cancers. DATE analysis was applied to aCGH data from the great apes. A good example of the power of DATE analysis is its application to genomically unstable cancers, which have been refractory to data mining strategies. 2009 American Institute of Chemical Engineers Biotechnol.

  20. Measurement uncertainty analysis techniques applied to PV performance measurements

    International Nuclear Information System (INIS)

    Wells, C.

    1992-10-01

    The purpose of this presentation is to provide a brief introduction to measurement uncertainty analysis, outline how it is done, and illustrate uncertainty analysis with examples drawn from the PV field, with particular emphasis toward its use in PV performance measurements. The uncertainty information we know and state concerning a PV performance measurement or a module test result determines, to a significant extent, the value and quality of that result. What is measurement uncertainty analysis? It is an outgrowth of what has commonly been called error analysis. But uncertainty analysis, a more recent development, gives greater insight into measurement processes and tests, experiments, or calibration results. Uncertainty analysis gives us an estimate of the I interval about a measured value or an experiment's final result within which we believe the true value of that quantity will lie. Why should we take the time to perform an uncertainty analysis? A rigorous measurement uncertainty analysis: Increases the credibility and value of research results; allows comparisons of results from different labs; helps improve experiment design and identifies where changes are needed to achieve stated objectives (through use of the pre-test analysis); plays a significant role in validating measurements and experimental results, and in demonstrating (through the post-test analysis) that valid data have been acquired; reduces the risk of making erroneous decisions; demonstrates quality assurance and quality control measures have been accomplished; define Valid Data as data having known and documented paths of: Origin, including theory; measurements; traceability to measurement standards; computations; uncertainty analysis of results

  1. An applied general equilibrium model for Dutch agribusiness policy analysis

    NARCIS (Netherlands)

    Peerlings, J.

    1993-01-01

    The purpose of this thesis was to develop a basic static applied general equilibrium (AGE) model to analyse the effects of agricultural policy changes on Dutch agribusiness. In particular the effects on inter-industry transactions, factor demand, income, and trade are of

  2. Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

    Science.gov (United States)

    Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

    2013-01-01

    The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

  3. How Has Applied Behavior Analysis and Behavior Therapy Changed?: An Historical Analysis of Journals

    Science.gov (United States)

    O'Donohue, William; Fryling, Mitch

    2007-01-01

    Applied behavior analysis and behavior therapy are now nearly a half century old. It is interesting to ask if and how these disciplines have changed over time, particularly regarding some of their key internal controversies (e.g., role of cognitions). We examined the first five years and the 2000-2004 five year period of the "Journal of Applied…

  4. Measurement uncertainty analysis techniques applied to PV performance measurements

    Energy Technology Data Exchange (ETDEWEB)

    Wells, C.

    1992-10-01

    The purpose of this presentation is to provide a brief introduction to measurement uncertainty analysis, outline how it is done, and illustrate uncertainty analysis with examples drawn from the PV field, with particular emphasis toward its use in PV performance measurements. The uncertainty information we know and state concerning a PV performance measurement or a module test result determines, to a significant extent, the value and quality of that result. What is measurement uncertainty analysis It is an outgrowth of what has commonly been called error analysis. But uncertainty analysis, a more recent development, gives greater insight into measurement processes and tests, experiments, or calibration results. Uncertainty analysis gives us an estimate of the I interval about a measured value or an experiment's final result within which we believe the true value of that quantity will lie. Why should we take the time to perform an uncertainty analysis A rigorous measurement uncertainty analysis: Increases the credibility and value of research results; allows comparisons of results from different labs; helps improve experiment design and identifies where changes are needed to achieve stated objectives (through use of the pre-test analysis); plays a significant role in validating measurements and experimental results, and in demonstrating (through the post-test analysis) that valid data have been acquired; reduces the risk of making erroneous decisions; demonstrates quality assurance and quality control measures have been accomplished; define Valid Data as data having known and documented paths of: Origin, including theory; measurements; traceability to measurement standards; computations; uncertainty analysis of results.

  5. Measurement uncertainty analysis techniques applied to PV performance measurements

    Energy Technology Data Exchange (ETDEWEB)

    Wells, C

    1992-10-01

    The purpose of this presentation is to provide a brief introduction to measurement uncertainty analysis, outline how it is done, and illustrate uncertainty analysis with examples drawn from the PV field, with particular emphasis toward its use in PV performance measurements. The uncertainty information we know and state concerning a PV performance measurement or a module test result determines, to a significant extent, the value and quality of that result. What is measurement uncertainty analysis? It is an outgrowth of what has commonly been called error analysis. But uncertainty analysis, a more recent development, gives greater insight into measurement processes and tests, experiments, or calibration results. Uncertainty analysis gives us an estimate of the I interval about a measured value or an experiment`s final result within which we believe the true value of that quantity will lie. Why should we take the time to perform an uncertainty analysis? A rigorous measurement uncertainty analysis: Increases the credibility and value of research results; allows comparisons of results from different labs; helps improve experiment design and identifies where changes are needed to achieve stated objectives (through use of the pre-test analysis); plays a significant role in validating measurements and experimental results, and in demonstrating (through the post-test analysis) that valid data have been acquired; reduces the risk of making erroneous decisions; demonstrates quality assurance and quality control measures have been accomplished; define Valid Data as data having known and documented paths of: Origin, including theory; measurements; traceability to measurement standards; computations; uncertainty analysis of results.

  6. Heisenberg principle applied to the analysis of speckle interferometry fringes

    Science.gov (United States)

    Sciammarella, C. A.; Sciammarella, F. M.

    2003-11-01

    Optical techniques that are used to measure displacements utilize a carrier. When a load is applied the displacement field modulates the carrier. The accuracy of the information that can be recovered from the modulated carrier is limited by a number of factors. In this paper, these factors are analyzed and conclusions concerning the limitations in information recovery are illustrated with examples taken from experimental data.

  7. Concluding Essay: On Applied Linguistics and Discourse Analysis.

    Science.gov (United States)

    Kaplan, Robert B.

    1990-01-01

    Discusses trends and problems in regarding discourse analysis as a viable paradigm that can govern research, focusing on such issues as the wide diversity and variety of research that can be considered discourse analysis, the predominant focus on English language, research approaches, and undefined variables affecting research outcomes. (seven…

  8. 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.

  9. Protein expression based multimarker analysis of breast cancer samples

    International Nuclear Information System (INIS)

    Presson, Angela P; Horvath, Steve; Yoon, Nam K; Bagryanova, Lora; Mah, Vei; Alavi, Mohammad; Maresh, Erin L; Rajasekaran, Ayyappan K; Goodglick, Lee; Chia, David

    2011-01-01

    Tissue microarray (TMA) data are commonly used to validate the prognostic accuracy of tumor markers. For example, breast cancer TMA data have led to the identification of several promising prognostic markers of survival time. Several studies have shown that TMA data can also be used to cluster patients into clinically distinct groups. Here we use breast cancer TMA data to cluster patients into distinct prognostic groups. We apply weighted correlation network analysis (WGCNA) to TMA data consisting of 26 putative tumor biomarkers measured on 82 breast cancer patients. Based on this analysis we identify three groups of patients with low (5.4%), moderate (22%) and high (50%) mortality rates, respectively. We then develop a simple threshold rule using a subset of three markers (p53, Na-KATPase-β1, and TGF β receptor II) that can approximately define these mortality groups. We compare the results of this correlation network analysis with results from a standard Cox regression analysis. We find that the rule-based grouping variable (referred to as WGCNA*) is an independent predictor of survival time. While WGCNA* is based on protein measurements (TMA data), it validated in two independent Affymetrix microarray gene expression data (which measure mRNA abundance). We find that the WGCNA patient groups differed by 35% from mortality groups defined by a more conventional stepwise Cox regression analysis approach. We show that correlation network methods, which are primarily used to analyze the relationships between gene products, are also useful for analyzing the relationships between patients and for defining distinct patient groups based on TMA data. We identify a rule based on three tumor markers for predicting breast cancer survival outcomes

  10. Mars Express Lithium Ion Batteries Performance Analysis

    Directory of Open Access Journals (Sweden)

    Dudley G.

    2017-01-01

    Full Text Available Now more than 12 years in orbit, Mars Express battery telemetry during some of the deepest discharge cycles has been analysed with the help of the ESTEC lithium ion cell model. The best-fitting model parameter sets were then used to predict the energy that is expected to be available before the battery voltage drops below the minimum value that can support the power bus. This allows mission planners to determine what future power profiles could be supported without risk of entering safe mode. It also gives some more insights into the ageing properties of these batteries.

  11. Applying causal mediation analysis to personality disorder research.

    Science.gov (United States)

    Walters, Glenn D

    2018-01-01

    This article is designed to address fundamental issues in the application of causal mediation analysis to research on personality disorders. Causal mediation analysis is used to identify mechanisms of effect by testing variables as putative links between the independent and dependent variables. As such, it would appear to have relevance to personality disorder research. It is argued that proper implementation of causal mediation analysis requires that investigators take several factors into account. These factors are discussed under 5 headings: variable selection, model specification, significance evaluation, effect size estimation, and sensitivity testing. First, care must be taken when selecting the independent, dependent, mediator, and control variables for a mediation analysis. Some variables make better mediators than others and all variables should be based on reasonably reliable indicators. Second, the mediation model needs to be properly specified. This requires that the data for the analysis be prospectively or historically ordered and possess proper causal direction. Third, it is imperative that the significance of the identified pathways be established, preferably with a nonparametric bootstrap resampling approach. Fourth, effect size estimates should be computed or competing pathways compared. Finally, investigators employing the mediation method are advised to perform a sensitivity analysis. Additional topics covered in this article include parallel and serial multiple mediation designs, moderation, and the relationship between mediation and moderation. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  12. Signed directed social network analysis applied to group conflict

    DEFF Research Database (Denmark)

    Zheng, Quan; Skillicorn, David; Walther, Olivier

    2015-01-01

    Real-world social networks contain relationships of multiple different types, but this richness is often ignored in graph-theoretic modelling. We show how two recently developed spectral embedding techniques, for directed graphs (relationships are asymmetric) and for signed graphs (relationships...... are both positive and negative), can be combined. This combination is particularly appropriate for intelligence, terrorism, and law enforcement applications. We illustrate by applying the novel embedding technique to datasets describing conflict in North-West Africa, and show how unusual interactions can...

  13. Applied risk analysis to the future Brazilian electricity generation matrix

    Energy Technology Data Exchange (ETDEWEB)

    Maues, Jair; Fernandez, Eloi; Correa, Antonio

    2010-09-15

    This study compares energy conversion systems for the generation of electrical power, with an emphasis on the Brazilian energy matrix. The financial model applied in this comparison is based on the Portfolio Theory, developed by Harry Markowitz. The risk-return ratio related to the electrical generation mix predicted in the National Energy Plan - 2030, published in 2006 by the Brazilian Energy Research Office, is evaluated. The increase of non-traditional renewable energy in this expected electrical generating mix, specifically, residues of sugar cane plantations and wind energy, reduce not only the risk but also the average cost of the kilowatt-hour generated.

  14. Applied network security monitoring collection, detection, and analysis

    CERN Document Server

    Sanders, Chris

    2013-01-01

    Applied Network Security Monitoring is the essential guide to becoming an NSM analyst from the ground up. This book takes a fundamental approach to NSM, complete with dozens of real-world examples that teach you the key concepts of NSM. Network security monitoring is based on the principle that prevention eventually fails. In the current threat landscape, no matter how much you try, motivated attackers will eventually find their way into your network. At that point, it is your ability to detect and respond to that intrusion that can be the difference between a small incident and a major di

  15. Thermoeconomic analysis applied to an alternative wastewater treatment

    Energy Technology Data Exchange (ETDEWEB)

    Lamas, Wendell de Queiroz [University of Taubate, Post-graduate Programme in Mechanical Engineering, Department of Mechanical Engineering, Sp (Brazil); Sao Paulo State University, Faculty of Engineering, Campus of Guaratingueta, Postgraduate Programme in Mechanical Engineering, Sp (Brazil); Silveira, Jose Luz; Mattos dos Reis, Luiz Octavio [Sao Paulo State University, Faculty of Engineering, Campus of Guaratingueta, Postgraduate Programme in Mechanical Engineering, Sp (Brazil); Oscare Giacaglia, Giorgio Eugenio [University of Taubate, Post-graduate Programme in Mechanical Engineering, Department of Mechanical Engineering, Sp (Brazil)

    2010-10-15

    This work develops a methodology for the determination of costs associated to products generated in a small wastewater treatment station. The methodology begins with plant units identification, relating their fluid and thermodynamics features to each point indicated in its process diagram. Following, a functional diagram and a formulation are developed in exergetic basis, describing all equations for these points, which are the constraints for optimisation and are used to determine costs associated to products generated in a Small Wastewater Treatment Station - SWTS. The methodology is applied to a hypothetical system based on SWTS plants and presents consistent results when compared to values based on previous experiments and evaluations. (author)

  16. Comparison of small n statistical tests of differential expression applied to microarrays

    Directory of Open Access Journals (Sweden)

    Lee Anna Y

    2009-02-01

    Full Text Available Abstract Background DNA microarrays provide data for genome wide patterns of expression between observation classes. Microarray studies often have small samples sizes, however, due to cost constraints or specimen availability. This can lead to poor random error estimates and inaccurate statistical tests of differential expression. We compare the performance of the standard t-test, fold change, and four small n statistical test methods designed to circumvent these problems. We report results of various normalization methods for empirical microarray data and of various random error models for simulated data. Results Three Empirical Bayes methods (CyberT, BRB, and limma t-statistics were the most effective statistical tests across simulated and both 2-colour cDNA and Affymetrix experimental data. The CyberT regularized t-statistic in particular was able to maintain expected false positive rates with simulated data showing high variances at low gene intensities, although at the cost of low true positive rates. The Local Pooled Error (LPE test introduced a bias that lowered false positive rates below theoretically expected values and had lower power relative to the top performers. The standard two-sample t-test and fold change were also found to be sub-optimal for detecting differentially expressed genes. The generalized log transformation was shown to be beneficial in improving results with certain data sets, in particular high variance cDNA data. Conclusion Pre-processing of data influences performance and the proper combination of pre-processing and statistical testing is necessary for obtaining the best results. All three Empirical Bayes methods assessed in our study are good choices for statistical tests for small n microarray studies for both Affymetrix and cDNA data. Choice of method for a particular study will depend on software and normalization preferences.

  17. First wall thermal stress analysis for suddenly applied heat fluxes

    International Nuclear Information System (INIS)

    Dalessandro, J.A.

    The failure criterion for a solid first wall of an inertial confinement reactor is investigated. Analytical expressions for induced thermal stresses in a plate are given. Two materials have been chosen for this investigation: grade H-451 graphite and chemically vapor deposited (CVD) β-silicon carbide. Structural failure can be related to either the maximum compressive stress produced on the surface or the maximum tensile stress developed in the interior of the plate; however, it is shown that compressive failure would predominate. A basis for the choice of the thermal shock figure of merit, k(1 - ν) sigma/E α kappa/sup 1/2/, is identified. The result is that graphite and silicon carbide rank comparably

  18. Applying real options analysis to assess cleaner energy development strategies

    International Nuclear Information System (INIS)

    Cheng, Ching-Tsung; Lo, Shang-Lien; Lin, Tyrone T.

    2011-01-01

    The energy industry, accounts for the largest portion of CO 2 emissions, is facing the issue of compliance with the national clean energy policy. The methodology for evaluating the energy mix policy is crucial because of the characteristics of lead time embedded with the power generation facilities investment and the uncertainty of future electricity demand. In this paper, a modified binomial model based on sequential compound options, which may account for the lead time and uncertainty as a whole is established, and a numerical example on evaluating the optional strategies and the strategic value of the cleaner energy policy is also presented. It is found that the optimal decision at some nodes in the binomial tree is path dependent, which is different from the standard sequential compound option model with lead time or time lag concept. The proposed modified binomial sequential compound real options model can be generalized and extensively applied to solve the general decision problems that deal with the long lead time of many government policies as well as capital intensive investments. - Highlights: → Introducing a flexible strategic management approach for government policy making. → Developing a modified binomial real options model based on sequential compound options. → Proposing an innovative model for managing the long term policy with lead time. → Applying to evaluate the options of various scenarios of cleaner energy strategies.

  19. Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.

    Science.gov (United States)

    Guthke, Reinhard; Möller, Ulrich; Hoffmann, Martin; Thies, Frank; Töpfer, Susanne

    2005-04-15

    The immune response to bacterial infection represents a complex network of dynamic gene and protein interactions. We present an optimized reverse engineering strategy aimed at a reconstruction of this kind of interaction networks. The proposed approach is based on both microarray data and available biological knowledge. The main kinetics of the immune response were identified by fuzzy clustering of gene expression profiles (time series). The number of clusters was optimized using various evaluation criteria. For each cluster a representative gene with a high fuzzy-membership was chosen in accordance with available physiological knowledge. Then hypothetical network structures were identified by seeking systems of ordinary differential equations, whose simulated kinetics could fit the gene expression profiles of the cluster-representative genes. For the construction of hypothetical network structures singular value decomposition (SVD) based methods and a newly introduced heuristic Network Generation Method here were compared. It turned out that the proposed novel method could find sparser networks and gave better fits to the experimental data. Reinhard.Guthke@hki-jena.de.

  20. Applying the breaks on gene expression - mRNA deadenylation by Pop2p

    DEFF Research Database (Denmark)

    Andersen, Kasper Røjkjær; Jonstrup, Anette Thyssen; Van, Lan Bich

    When driving a car, control of the brakes is just as important as control of the accelerator pedal. Likewise, in gene expression, regulation of mRNA degradation is as important as regulation of its synthesis (Mühlemann, 2005). The rate-determining step of mRNA decay in eukaryotes seems to be the ......When driving a car, control of the brakes is just as important as control of the accelerator pedal. Likewise, in gene expression, regulation of mRNA degradation is as important as regulation of its synthesis (Mühlemann, 2005). The rate-determining step of mRNA decay in eukaryotes seems...... to be the shortening of the poly(A) tail (deadenylation), as this step is slower than the subsequent decapping and degradation of the mRNA body. The Mega-Dalton Ccr4-Not complex contains two exonucleases, Ccr4p and Pop2p, responsible for this process. It is not known at present why two conserved nucleases are needed...

  1. 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, ...

  2. 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.

  3. Concept of spatial channel theory applied to reactor shielding analysis

    International Nuclear Information System (INIS)

    Williams, M.L.; Engle, W.W. Jr.

    1977-01-01

    The concept of channel theory is used to locate spatial regions that are important in contributing to a shielding response. The method is analogous to the channel-theory method developed for ascertaining important energy channels in cross-section analysis. The mathematical basis for the theory is shown to be the generalized reciprocity relation, and sample problems are given to exhibit and verify properties predicted by the mathematical equations. A practical example is cited from the shielding analysis of the Fast Flux Test Facility performed at Oak Ridge National Laboratory, in which a perspective plot of channel-theory results was found useful in locating streaming paths around the reactor cavity shield

  4. Computational modeling applied to stress gradient analysis for metallic alloys

    International Nuclear Information System (INIS)

    Iglesias, Susana M.; Assis, Joaquim T. de; Monine, Vladimir I.

    2009-01-01

    Nowadays composite materials including materials reinforced by particles are the center of the researcher's attention. There are problems with the stress measurements in these materials, connected with the superficial stress gradient caused by the difference of the stress state of particles on the surface and in the matrix of the composite material. Computer simulation of diffraction profile formed by superficial layers of material allows simulate the diffraction experiment and gives the possibility to resolve the problem of stress measurements when the stress state is characterized by strong gradient. The aim of this paper is the application of computer simulation technique, initially developed for homogeneous materials, for diffraction line simulation of composite materials and alloys. Specifically we applied this technique for siluminum fabricated by powder metallurgy. (author)

  5. Performance analysis of numeric solutions applied to biokinetics of radionuclides

    International Nuclear Information System (INIS)

    Mingatos, Danielle dos Santos; Bevilacqua, Joyce da Silva

    2013-01-01

    Biokinetics models for radionuclides applied to dosimetry problems are constantly reviewed by ICRP. The radionuclide trajectory could be represented by compartmental models, assuming constant transfer rates between compartments. A better understanding of physiological or biochemical phenomena, improve the comprehension of radionuclide behavior in the human body and, in general, more complex compartmental models are proposed, increasing the difficulty of obtaining the analytical solution for the system of first order differential equations. Even with constant transfer rates numerical solutions must be carefully implemented because of almost singular characteristic of the matrix of coefficients. In this work we compare numerical methods with different strategies for ICRP-78 models for Thorium-228 and Uranium-234. The impact of uncertainty in the parameters of the equations is also estimated for local and global truncation errors. (author)

  6. Condition Monitoring of a Process Filter Applying Wireless Vibration Analysis

    Directory of Open Access Journals (Sweden)

    Pekka KOSKELA

    2011-05-01

    Full Text Available This paper presents a novel wireless vibration-based method for monitoring the degree of feed filter clogging. In process industry, these filters are applied to prevent impurities entering the process. During operation, the filters gradually become clogged, decreasing the feed flow and, in the worst case, preventing it. The cleaning of the filter should therefore be carried out predictively in order to avoid equipment damage and unnecessary process downtime. The degree of clogging is estimated by first calculating the time domain indices from low frequency accelerometer samples and then taking the median of the processed values. Nine different statistical quantities are compared based on the estimation accuracy and criteria for operating in resource-constrained environments with particular focus on energy efficiency. The initial results show that the method is able to detect the degree of clogging, and the approach may be applicable to filter clogging monitoring.

  7. Sensitivity Analysis Applied in Design of Low Energy Office Building

    DEFF Research Database (Denmark)

    Heiselberg, Per; Brohus, Henrik

    2008-01-01

    satisfies the design requirements and objectives. In the design of sustainable Buildings it is beneficial to identify the most important design parameters in order to develop more efficiently alternative design solutions or reach optimized design solutions. A sensitivity analysis makes it possible...

  8. Applying Skinner's Analysis of Verbal Behavior to Persons with Dementia

    Science.gov (United States)

    Dixon, Mark; Baker, Jonathan C.; Sadowski, Katherine Ann

    2011-01-01

    Skinner's 1957 analysis of verbal behavior has demonstrated a fair amount of utility to teach language to children with autism and other various disorders. However, the learning of language can be forgotten, as is the case for many elderly suffering from dementia or other degenerative diseases. It appears possible that Skinner's operants may…

  9. Applying an Activity System to Online Collaborative Group Work Analysis

    Science.gov (United States)

    Choi, Hyungshin; Kang, Myunghee

    2010-01-01

    This study determines whether an activity system provides a systematic framework to analyse collaborative group work. Using an activity system as a unit of analysis, the research examined learner behaviours, conflicting factors and facilitating factors while students engaged in collaborative work via asynchronous computer-mediated communication.…

  10. Visual Analytics Applied to Image Analysis : From Segmentation to Classification

    NARCIS (Netherlands)

    Rauber, Paulo

    2017-01-01

    Image analysis is the field of study concerned with extracting information from images. This field is immensely important for commercial and scientific applications, from identifying people in photographs to recognizing diseases in medical images. The goal behind the work presented in this thesis is

  11. Applying AI tools to operational space environmental analysis

    Science.gov (United States)

    Krajnak, Mike; Jesse, Lisa; Mucks, John

    1995-01-01

    The U.S. Air Force and National Oceanic Atmospheric Agency (NOAA) space environmental operations centers are facing increasingly complex challenges meeting the needs of their growing user community. These centers provide current space environmental information and short term forecasts of geomagnetic activity. Recent advances in modeling and data access have provided sophisticated tools for making accurate and timely forecasts, but have introduced new problems associated with handling and analyzing large quantities of complex data. AI (Artificial Intelligence) techniques have been considered as potential solutions to some of these problems. Fielding AI systems has proven more difficult than expected, in part because of operational constraints. Using systems which have been demonstrated successfully in the operational environment will provide a basis for a useful data fusion and analysis capability. Our approach uses a general purpose AI system already in operational use within the military intelligence community, called the Temporal Analysis System (TAS). TAS is an operational suite of tools supporting data processing, data visualization, historical analysis, situation assessment and predictive analysis. TAS includes expert system tools to analyze incoming events for indications of particular situations and predicts future activity. The expert system operates on a knowledge base of temporal patterns encoded using a knowledge representation called Temporal Transition Models (TTM's) and an event database maintained by the other TAS tools. The system also includes a robust knowledge acquisition and maintenance tool for creating TTM's using a graphical specification language. The ability to manipulate TTM's in a graphical format gives non-computer specialists an intuitive way of accessing and editing the knowledge base. To support space environmental analyses, we used TAS's ability to define domain specific event analysis abstractions. The prototype system defines

  12. CARVEDILOL POPULATION PHARMACOKINETIC ANALYSISAPPLIED VALIDATION PROCEDURE

    Directory of Open Access Journals (Sweden)

    Aleksandra Catić-Đorđević

    2013-09-01

    Full Text Available Carvedilol is a nonselective beta blocker/alpha-1 blocker, which is used for treatment of essential hypertension, chronic stable angina, unstable angina and ischemic left ventricular dysfunction. The aim of this study was to describe carvedilol population pharmacokinetic (PK analysis as well as the validation of analytical procedure, which is an important step regarding this approach. In contemporary clinical practice, population PK analysis is often more important than standard PK approach in setting a mathematical model that describes the PK parameters. Also, it includes the variables that have particular importance in the drugs pharmacokinetics such as sex, body mass, dosage, pharmaceutical form, pathophysiological state, disease associated with the organism or the presence of a specific polymorphism in the isoenzyme important for biotransformation of the drug. One of the most frequently used approach in population PK analysis is the Nonlinear Modeling of Mixed Effects - NONMEM modeling. Analytical methods used in the data collection period is of great importance for the implementation of a population PK analysis of carvedilol in order to obtain reliable data that can be useful in clinical practice. High performance liquid chromatography (HPLC analysis of carvedilol is used to confirm the identity of a drug and provide quantitative results and also to monitor the efficacy of the therapy. Analytical procedures used in other studies could not be fully implemented in our research as it was necessary to perform certain modification and validation of the method with the aim of using the obtained results for the purpose of a population pharmacokinetic analysis. Validation process is a logical terminal phase of analytical procedure development that provides applicability of the procedure itself. The goal of validation is to ensure consistency of the method and accuracy of results or to confirm the selection of analytical method for a given sample

  13. 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 ...

  14. Diffusing wave spectroscopy applied to material analysis and process control

    International Nuclear Information System (INIS)

    Lloyd, Christopher James

    1997-01-01

    Diffusing Wave Spectroscopy (DWS) was studied as a method of laboratory analysis of sub-micron particles, and developed as a prospective in-line, industrial, process control sensor, capable of near real-time feedback. No sample pre-treatment was required and measurement was via a non-invasive, flexible, dip in probe. DWS relies on the concept of the diffusive migration of light, as opposed to the ballistic scatter model used in conventional dynamic light scattering. The specific requirements of the optoelectronic hardware, data analysis methods and light scattering model were studied experimentally and, where practical, theoretically resulting in a novel technique of analysis of particle suspensions and emulsions of volume fractions between 0.01 and 0.4. Operation at high concentrations made the technique oblivious to dust and contamination. A pure homodyne (autodyne) experimental arrangement described was resilient to environmental disturbances, unlike many other systems which utilise optical fibres or heterodyne operation. Pilot and subsequent prototype development led to a highly accurate method of size ranking, suitable for analysis of a wide range of suspensions and emulsions. The technique was shown to operate on real industrial samples with statistical variance as low as 0.3% with minimal software processing. Whilst the application studied was the analysis of TiO 2 suspensions, a diverse range of materials including polystyrene beads, cell pastes and industrial cutting fluid emulsions were tested. Results suggest that, whilst all sizing should be comparative to suitable standards, concentration effects may be minimised and even completely modelled-out in many applications. Adhesion to the optical probe was initially a significant problem but was minimised after the evaluation and use of suitable non stick coating materials. Unexpected behaviour in the correlation in the region of short decay times led to consideration of the effects of rotational diffusion

  15. Thermodynamic analysis applied to a food-processing plant

    Energy Technology Data Exchange (ETDEWEB)

    Ho, J C; Chandratilleke, T T

    1987-01-01

    Two production lines of a multi-product, food-processing plant are selected for energy auditing and analysis. Thermodynamic analysis showed that the first-law and second-law efficiencies are 81.5% and 26.1% for the instant-noodles line and 23.6% and 7.9% for the malt-beverage line. These efficiency values are dictated primarily by the major energy-consuming sub-processes of each production line. Improvements in both first-law and second-law efficiencies are possible for the plants if the use of steam for heating is replaced by gaseous or liquid fuels, the steam ejectors for creating vacuum are replaced by a mechanical pump, and employing the cooler surroundings to assist in the cooling process.

  16. Current Human Reliability Analysis Methods Applied to Computerized Procedures

    Energy Technology Data Exchange (ETDEWEB)

    Ronald L. Boring

    2012-06-01

    Computerized procedures (CPs) are an emerging technology within nuclear power plant control rooms. While CPs have been implemented internationally in advanced control rooms, to date no US nuclear power plant has implemented CPs in its main control room (Fink et al., 2009). Yet, CPs are a reality of new plant builds and are an area of considerable interest to existing plants, which see advantages in terms of enhanced ease of use and easier records management by omitting the need for updating hardcopy procedures. The overall intent of this paper is to provide a characterization of human reliability analysis (HRA) issues for computerized procedures. It is beyond the scope of this document to propose a new HRA approach or to recommend specific methods or refinements to those methods. Rather, this paper serves as a review of current HRA as it may be used for the analysis and review of computerized procedures.

  17. Environmental analysis applied to schools. Methodologies for data acquisition

    International Nuclear Information System (INIS)

    Andriola, L.; Ceccacci, R.

    2001-01-01

    The environment analysis is the basis of environmental management for organizations and it is considered as the first step in EMAS. It allows to identify, deal with the issues and have a clear knowledge on environmental performances of organizations. Schools can be included in the organizations. Nevertheless, the complexity of environmental issues and applicable regulations makes very difficult for a school, that wants to implement an environmental management system (EMAS, ISO 14001, etc.), to face this first step. So, it has been defined an instrument, that is easy but complete and coherent with reference standard, to let schools choose their process for elaborating the initial environmental revue. This instrument consists, essentially, in cards that, if completed, facilitate the drafting of the environmental analysis report [it

  18. Ion beam analysis techniques applied to large scale pollution studies

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, D D; Bailey, G; Martin, J; Garton, D; Noorman, H; Stelcer, E; Johnson, P [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)

    1994-12-31

    Ion Beam Analysis (IBA) techniques are ideally suited to analyse the thousands of filter papers a year that may originate from a large scale aerosol sampling network. They are fast multi-elemental and, for the most part, non-destructive so other analytical methods such as neutron activation and ion chromatography can be performed afterwards. ANSTO in collaboration with the NSW EPA, Pacific Power and the Universities of NSW and Macquarie has established a large area fine aerosol sampling network covering nearly 80,000 square kilometres of NSW with 25 fine particle samplers. This network known as ASP was funded by the Energy Research and Development Corporation (ERDC) and commenced sampling on 1 July 1991. The cyclone sampler at each site has a 2.5 {mu}m particle diameter cut off and runs for 24 hours every Sunday and Wednesday using one Gillman 25mm diameter stretched Teflon filter for each day. These filters are ideal targets for ion beam analysis work. Currently ANSTO receives 300 filters per month from this network for analysis using its accelerator based ion beam techniques on the 3 MV Van de Graaff accelerator. One week a month of accelerator time is dedicated to this analysis. Four simultaneous accelerator based IBA techniques are used at ANSTO, to analyse for the following 24 elements: H, C, N, O, F, Na, Al, Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Cu, Ni, Co, Zn, Br and Pb. The IBA techniques were proved invaluable in identifying sources of fine particles and their spatial and seasonal variations accross the large area sampled by the ASP network. 3 figs.

  19. Ion beam analysis techniques applied to large scale pollution studies

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, D.D.; Bailey, G.; Martin, J.; Garton, D.; Noorman, H.; Stelcer, E.; Johnson, P. [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)

    1993-12-31

    Ion Beam Analysis (IBA) techniques are ideally suited to analyse the thousands of filter papers a year that may originate from a large scale aerosol sampling network. They are fast multi-elemental and, for the most part, non-destructive so other analytical methods such as neutron activation and ion chromatography can be performed afterwards. ANSTO in collaboration with the NSW EPA, Pacific Power and the Universities of NSW and Macquarie has established a large area fine aerosol sampling network covering nearly 80,000 square kilometres of NSW with 25 fine particle samplers. This network known as ASP was funded by the Energy Research and Development Corporation (ERDC) and commenced sampling on 1 July 1991. The cyclone sampler at each site has a 2.5 {mu}m particle diameter cut off and runs for 24 hours every Sunday and Wednesday using one Gillman 25mm diameter stretched Teflon filter for each day. These filters are ideal targets for ion beam analysis work. Currently ANSTO receives 300 filters per month from this network for analysis using its accelerator based ion beam techniques on the 3 MV Van de Graaff accelerator. One week a month of accelerator time is dedicated to this analysis. Four simultaneous accelerator based IBA techniques are used at ANSTO, to analyse for the following 24 elements: H, C, N, O, F, Na, Al, Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Cu, Ni, Co, Zn, Br and Pb. The IBA techniques were proved invaluable in identifying sources of fine particles and their spatial and seasonal variations accross the large area sampled by the ASP network. 3 figs.

  20. Pair distribution function analysis applied to decahedral gold nanoparticles

    International Nuclear Information System (INIS)

    Nakotte, H; Silkwood, C; Kiefer, B; Karpov, D; Fohtung, E; Page, K; Wang, H-W; Olds, D; Manna, S; Fullerton, E E

    2017-01-01

    The five-fold symmetry of face-centered cubic (fcc) derived nanoparticles is inconsistent with the translational symmetry of a Bravais lattice and generally explained by multiple twinning of a tetrahedral subunit about a (joint) symmetry axis, with or without structural modification to the fcc motif. Unlike in bulk materials, five-fold twinning in cubic nanoparticles is common and strongly affects their structural, chemical, and electronic properties. To test and verify theoretical approaches, it is therefore pertinent that the local structural features of such materials can be fully characterized. The small size of nanoparticles severely limits the application of traditional analysis techniques, such as Bragg diffraction. A complete description of the atomic arrangement in nanoparticles therefore requires a departure from the concept of translational symmetry, and prevents fully evaluating all the structural features experimentally. We describe how recent advances in instrumentation, together with the increasing power of computing, are shaping the development of alternative analysis methods of scattering data for nanostructures. We present the application of Debye scattering and pair distribution function (PDF) analysis towards modeling of the total scattering data for the example of decahedral gold nanoparticles. PDF measurements provide a statistical description of the pair correlations of atoms within a material, allowing one to evaluate the probability of finding two atoms within a given distance. We explored the sensitivity of existing synchrotron x-ray PDF instruments for distinguishing four different simple models for our gold nanoparticles: a multiply twinned fcc decahedron with either a single gap or multiple distributed gaps, a relaxed body-centered orthorhombic (bco) decahedron, and a hybrid decahedron. The data simulations of the models were then compared with experimental data from synchrotron x-ray total scattering. We present our experimentally

  1. The colour analysis method applied to homogeneous rocks

    Directory of Open Access Journals (Sweden)

    Halász Amadé

    2015-12-01

    Full Text Available Computer-aided colour analysis can facilitate cyclostratigraphic studies. Here we report on a case study involving the development of a digital colour analysis method for examination of the Boda Claystone Formation which is the most suitable in Hungary for the disposal of high-level radioactive waste. Rock type colours are reddish brown or brownish red, or any shade between brown and red. The method presented here could be used to differentiate similar colours and to identify gradual transitions between these; the latter are of great importance in a cyclostratigraphic analysis of the succession. Geophysical well-logging has demonstrated the existence of characteristic cyclic units, as detected by colour and natural gamma. Based on our research, colour, natural gamma and lithology correlate well. For core Ib-4, these features reveal the presence of orderly cycles with thicknesses of roughly 0.64 to 13 metres. Once the core has been scanned, this is a time- and cost-effective method.

  2. 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.

  3. Applying reliability centered maintenance analysis principles to inservice testing

    International Nuclear Information System (INIS)

    Flude, J.W.

    1994-01-01

    Federal regulations require nuclear power plants to use inservice test (IST) programs to ensure the operability of safety-related equipment. IST programs are based on American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code requirements. Many of these plants also use Reliability Centered Maintenance (RCM) to optimize system maintenance. ASME Code requirements are hard to change. The process for requesting authority to use an alternate strategy is long and expensive. The difficulties of obtaining this authority make the use of RCM method on safety-related systems not cost effective. An ASME research task force on Risk Based Inservice Testing is investigating changing the Code. The change will allow plants to apply RCM methods to the problem of maintenance strategy selection for safety-related systems. The research task force is working closely with the Codes and Standards sections to develop a process related to the RCM process. Some day plants will be able to use this process to develop more efficient and safer maintenance strategies

  4. A Multifactorial Analysis of Reconstruction Methods Applied After Total Gastrectomy

    Directory of Open Access Journals (Sweden)

    Oktay Büyükaşık

    2010-12-01

    Full Text Available Aim: The aim of this study was to evaluate the reconstruction methods applied after total gastrectomy in terms of postoperative symptomology and nutrition. Methods: This retrospective study was conducted on 31 patients who underwent total gastrectomy due to gastric cancer in 2. Clinic of General Surgery, SSK Ankara Training Hospital. 6 different reconstruction methods were used and analyzed in terms of age, sex and postoperative complications. One from esophagus and two biopsy specimens from jejunum were taken through upper gastrointestinal endoscopy from all cases, and late period morphological and microbiological changes were examined. Postoperative weight change, dumping symptoms, reflux esophagitis, solid/liquid dysphagia, early satiety, postprandial pain, diarrhea and anorexia were assessed. Results: Of 31 patients,18 were males and 13 females; the youngest one was 33 years old, while the oldest- 69 years old. It was found that reconstruction without pouch was performed in 22 cases and with pouch in 9 cases. Early satiety, postprandial pain, dumping symptoms, diarrhea and anemia were found most commonly in cases with reconstruction without pouch. The rate of bacterial colonization of the jejunal mucosa was identical in both groups. Reflux esophagitis was most commonly seen in omega esophagojejunostomy (EJ, while the least-in Roux-en-Y, Tooley and Tanner 19 EJ. Conclusion: Reconstruction with pouch performed after total gastrectomy is still a preferable method. (The Medical Bulletin of Haseki 2010; 48:126-31

  5. Structural analysis of fuel rod applied to pressurized water reactors

    Energy Technology Data Exchange (ETDEWEB)

    Faria, Danilo P.; Pinheiro, Andre Ricardo M.; Lotto, André A., E-mail: danilo.pinheiro@marinha.mil.br [Centro Tecnológico da Marinha em São Paulo (CTMSP), São Paulo, SP (Brazil)

    2017-07-01

    The design of fuel assemblies applied to Pressurized Water Reactors (PWR) has several requirements and acceptance criteria that must be attended for licensing. In the case of PWR fuel rods, an important mechanical structural requirement is to keep the radial stability when submitted to the coolant external pressure. In the framework of the Accident Tolerant Fuel (ATF) program new materials have been studied to replace zirconium based alloys as cladding, including iron-based alloys. In this sense, efforts have been made to evaluate the behavior of these materials under PWR conditions. The present work aims to evaluate the collapse cold pressure of a stainless steel thin-walled tube similar to that used as cladding material of fuel rods by means of the comparison of numeric data, and experimental results. As a result of the simulations, it was observed that the collapse pressure has a value intermediate value between those found by regulatory requirements and analytical calculations. The experiment was carried out for the validation of the computational model using test specimens of thin-walled tubes considering empty tube. The test specimens were sealed at both ends by means of welding. They were subjected to a high pressure device until the collapse of the tubes. Preliminary results obtained from experiments with the empty test specimens indicate that the computational model can be validated for stainless steel cladding, considering the difference between collapse pressure indicated in the regulatory document and the actual limit pressure concerning to radial instability of tubes with the studied characteristics. (author)

  6. Framework for applying probabilistic safety analysis in nuclear regulation

    International Nuclear Information System (INIS)

    Dimitrijevic, V.B.

    1997-01-01

    The traditional regulatory framework has served well to assure the protection of public health and safety. It has been recognized, however, that in a few circumstances, this deterministic framework has lead to an extensive expenditure on matters hat have little to do with the safe and reliable operation of the plant. Developments of plant-specific PSA have offered a new and powerful analytical tool in the evaluation of the safety of the plant. Using PSA insights as an aid to decision making in the regulatory process is now known as 'risk-based' or 'risk-informed' regulation. Numerous activities in the U.S. nuclear industry are focusing on applying this new approach to modify regulatory requirements. In addition, other approaches to regulations are in the developmental phase and are being evaluated. One is based on the performance monitoring and results and it is known as performance-based regulation. The other, called the blended approach, combines traditional deterministic principles with PSA insights and performance results. (author)

  7. 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

  8. Statistical analysis applied to safety culture self-assessment

    International Nuclear Information System (INIS)

    Macedo Soares, P.P.

    2002-01-01

    Interviews and opinion surveys are instruments used to assess the safety culture in an organization as part of the Safety Culture Enhancement Programme. Specific statistical tools are used to analyse the survey results. This paper presents an example of an opinion survey with the corresponding application of the statistical analysis and the conclusions obtained. Survey validation, Frequency statistics, Kolmogorov-Smirnov non-parametric test, Student (T-test) and ANOVA means comparison tests and LSD post-hoc multiple comparison test, are discussed. (author)

  9. Prompt gamma cold neutron activation analysis applied to biological materials

    International Nuclear Information System (INIS)

    Rossbach, M.; Hiep, N.T.

    1992-01-01

    Cold neutrons at the external neutron guide laboratory (ELLA) of the KFA Juelich are used to demonstrate their profitable application for multielement characterization of biological materials. The set-up and experimental conditions of the Prompt Gamma Cold Neutron Activation Analysis (PGCNAA) device is described in detail. Results for C, H, N, S, K, B, and Cd using synthetic standards and the 'ratio' technique for calculation are reported for several reference materials and prove the method to be reliable and complementary with respect to the elements being determined by INAA. (orig.)

  10. Methods of economic analysis applied to fusion research. Final report

    International Nuclear Information System (INIS)

    1983-01-01

    In this and previous efforts ECON has provided economic assessment of a fusion research program. This phase of study focused on two tasks, the first concerned with the economics of fusion in an economy that relies heavily upon synthetic fuels, and the second concerned with the overall economic effects of pursuing soft energy technologies instead of hard technologies. This report is organized in two parts, the first entitled An Economic Analysis of Coproduction of Fusion-Electric Energy and Other Products, and the second entitled Arguments Associated with the Choice of Potential Energy Futures

  11. Artificial Neural Network methods applied to sentiment analysis

    OpenAIRE

    Ebert, Sebastian

    2017-01-01

    Sentiment Analysis (SA) is the study of opinions and emotions that are conveyed by text. This field of study has commercial applications for example in market research (e.g., “What do customers like and dislike about a product?”) and consumer behavior (e.g., “Which book will a customer buy next when he wrote a positive review about book X?”). A private person can benefit from SA by automatic movie or restaurant recommendations, or from applications on the computer or smart phone that adapt to...

  12. Dynamical Systems Analysis Applied to Working Memory Data

    Directory of Open Access Journals (Sweden)

    Fidan eGasimova

    2014-07-01

    Full Text Available In the present paper we investigate weekly fluctuations in the working memory capacity (WMC assessed over a period of two years. We use dynamical system analysis, specifically a second order linear differential equation, to model weekly variability in WMC in a sample of 112 9th graders. In our longitudinal data we use a B-spline imputation method to deal with missing data. The results show a significant negative frequency parameter in the data, indicating a cyclical pattern in weekly memory updating performance across time. We use a multilevel modeling approach to capture individual differences in model parameters and find that a higher initial performance level and a slower improvement at the MU task is associated with a slower frequency of oscillation. Additionally, we conduct a simulation study examining the analysis procedure’s performance using different numbers of B-spline knots and values of time delay embedding dimensions. Results show that the number of knots in the B-spline imputation influence accuracy more than the number of embedding dimensions.

  13. Confirmatory factor analysis applied to the Force Concept Inventory

    Science.gov (United States)

    Eaton, Philip; Willoughby, Shannon D.

    2018-06-01

    In 1995, Huffman and Heller used exploratory factor analysis to draw into question the factors of the Force Concept Inventory (FCI). Since then several papers have been published examining the factors of the FCI on larger sets of student responses and understandable factors were extracted as a result. However, none of these proposed factor models have been verified to not be unique to their original sample through the use of independent sets of data. This paper seeks to confirm the factor models proposed by Scott et al. in 2012, and Hestenes et al. in 1992, as well as another expert model proposed within this study through the use of confirmatory factor analysis (CFA) and a sample of 20 822 postinstruction student responses to the FCI. Upon application of CFA using the full sample, all three models were found to fit the data with acceptable global fit statistics. However, when CFA was performed using these models on smaller sample sizes the models proposed by Scott et al. and Eaton and Willoughby were found to be far more stable than the model proposed by Hestenes et al. The goodness of fit of these models to the data suggests that the FCI can be scored on factors that are not unique to a single class. These scores could then be used to comment on how instruction methods effect the performance of students along a single factor and more in-depth analyses of curriculum changes may be possible as a result.

  14. Multivariate calibration applied to the quantitative analysis of infrared spectra

    Energy Technology Data Exchange (ETDEWEB)

    Haaland, D.M.

    1991-01-01

    Multivariate calibration methods are very useful for improving the precision, accuracy, and reliability of quantitative spectral analyses. Spectroscopists can more effectively use these sophisticated statistical tools if they have a qualitative understanding of the techniques involved. A qualitative picture of the factor analysis multivariate calibration methods of partial least squares (PLS) and principal component regression (PCR) is presented using infrared calibrations based upon spectra of phosphosilicate glass thin films on silicon wafers. Comparisons of the relative prediction abilities of four different multivariate calibration methods are given based on Monte Carlo simulations of spectral calibration and prediction data. The success of multivariate spectral calibrations is demonstrated for several quantitative infrared studies. The infrared absorption and emission spectra of thin-film dielectrics used in the manufacture of microelectronic devices demonstrate rapid, nondestructive at-line and in-situ analyses using PLS calibrations. Finally, the application of multivariate spectral calibrations to reagentless analysis of blood is presented. We have found that the determination of glucose in whole blood taken from diabetics can be precisely monitored from the PLS calibration of either mind- or near-infrared spectra of the blood. Progress toward the non-invasive determination of glucose levels in diabetics is an ultimate goal of this research. 13 refs., 4 figs.

  15. Principles of Micellar Electrokinetic Capillary Chromatography Applied in Pharmaceutical Analysis

    Directory of Open Access Journals (Sweden)

    Árpád Gyéresi

    2013-02-01

    Full Text Available Since its introduction capillary electrophoresis has shown great potential in areas where electrophoretic techniques have rarely been used before, including here the analysis of pharmaceutical substances. The large majority of pharmaceutical substances are neutral from electrophoretic point of view, consequently separations by the classic capillary zone electrophoresis; where separation is based on the differences between the own electrophoretic mobilities of the analytes; are hard to achieve. Micellar electrokinetic capillary chromatography, a hybrid method that combines chromatographic and electrophoretic separation principles, extends the applicability of capillary electrophoretic methods to neutral analytes. In micellar electrokinetic capillary chromatography, surfactants are added to the buffer solution in concentration above their critical micellar concentrations, consequently micelles are formed; micelles that undergo electrophoretic migration like any other charged particle. The separation is based on the differential partitioning of an analyte between the two-phase system: the mobile aqueous phase and micellar pseudostationary phase. The present paper aims to summarize the basic aspects regarding separation principles and practical applications of micellar electrokinetic capillary chromatography, with particular attention to those relevant in pharmaceutical analysis.

  16. Two-dimensional DFA scaling analysis applied to encrypted images

    Science.gov (United States)

    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.

  17. Applying Multi-Criteria Analysis Methods for Fire Risk Assessment

    Directory of Open Access Journals (Sweden)

    Pushkina Julia

    2015-11-01

    Full Text Available The aim of this paper is to prove the application of multi-criteria analysis methods for optimisation of fire risk identification and assessment process. The object of this research is fire risk and risk assessment. The subject of the research is studying the application of analytic hierarchy process for modelling and influence assessment of various fire risk factors. Results of research conducted by the authors can be used by insurance companies to perform the detailed assessment of fire risks on the object and to calculate a risk extra charge to an insurance premium; by the state supervisory institutions to determine the compliance of a condition of object with requirements of regulations; by real state owners and investors to carry out actions for decrease in degree of fire risks and minimisation of possible losses.

  18. Neutron activation analysis applied to nutritional and foodstuff studies

    International Nuclear Information System (INIS)

    Maihara, Vera A.; Santos, Paola S.; Moura, Patricia L.C.; Castro, Lilian P. de; Avegliano, Roseane P.

    2009-01-01

    Neutron Activation Analysis, NAA, has been successfully used on a regularly basis in several areas of nutrition and foodstuffs. NAA has become an important and useful research tool due to the methodology's advantages. These include high accuracy, small quantities of samples and no chemical treatment. This technique allows the determination of important elements directly related to human health. NAA also provides data concerning essential and toxic concentrations in foodstuffs and specific diets. In this paper some studies in the area of nutrition which have been carried out at the Neutron Activation Laboratory of IPEN/CNEN-SP will be presented: a Brazilian total diet study: nutritional element dietary intakes of Sao Paulo state population; a study of trace element in maternal milk and the determination of essential trace elements in some edible mushrooms. (author)

  19. Downside Risk analysis applied to the Hedge Funds universe

    Science.gov (United States)

    Perelló, Josep

    2007-09-01

    Hedge Funds are considered as one of the portfolio management sectors which shows a fastest growing for the past decade. An optimal Hedge Fund management requires an appropriate risk metrics. The classic CAPM theory and its Ratio Sharpe fail to capture some crucial aspects due to the strong non-Gaussian character of Hedge Funds statistics. A possible way out to this problem while keeping the CAPM simplicity is the so-called Downside Risk analysis. One important benefit lies in distinguishing between good and bad returns, that is: returns greater or lower than investor's goal. We revisit most popular Downside Risk indicators and provide new analytical results on them. We compute these measures by taking the Credit Suisse/Tremont Investable Hedge Fund Index Data and with the Gaussian case as a benchmark. In this way, an unusual transversal lecture of the existing Downside Risk measures is provided.

  20. Applying importance-performance analysis to evaluate banking service quality

    Directory of Open Access Journals (Sweden)

    André Luís Policani Freitas

    2012-11-01

    Full Text Available In an increasingly competitive market, the identification of the most important aspects and the measurement of service quality as perceived by the customers are important actions taken by organizations which seek the competitive advantage. In particular, this scenario is typical of Brazilian banking sector. In this context, this article presents an exploratory case study in which the Importance-Performance Analysis (IPA was used to identify the strong and the weak points related to services provided by a bank. In order to check the reliability of the questionnaire, Cronbach's alpha and correlation analyses were used. The results are presented and some actions have been defined in order to improve the quality of services.

  1. Painleve singularity analysis applied to charged particle dynamics during reconnection

    International Nuclear Information System (INIS)

    Larson, J.W.

    1992-01-01

    For a plasma in the collisionless regime, test-particle modelling can lend some insight into the macroscopic behavior of the plasma, e.g. conductivity and heating. A common example for which this technique is used is a system with electric and magnetic fields given by B = δyx + zy + yz and E = εz, where δ, γ, and ε are constant parameters. This model can be used to model plasma behavior near neutral lines, (γ = 0), as well as current sheets (γ = 0, δ = 0). The integrability properties of the particle motion in such fields might affect the plasma's macroscopic behavior, and the author has asked the question open-quotes For what values of δ, γ, and ε is the system integrable?close quotes To answer this question, the author has employed Painleve singularity analysis, which is an examination of the singularity properties of a test particle's equations of motion in the complex time plane. This analysis has identified two field geometries for which the system's particle dynamics are integrable in terms of the second Painleve transcendent: the circular O-line case and the case of the neutral sheet configuration. These geometries yield particle dynamics that are integrable in the Liouville sense (i.e., there exist the proper number of integrals in involution) in an extended phase space which includes the time as a canonical coordinate, and this property is also true for nonzero γ. The singularity property tests also identified a large, dense set of X-line and O-line field geometries that yield dynamics that may possess the weak Painleve property. In the case of the X-line geometries, this result shows little relevance to the physical nature of the system, but the existence of a dense set of elliptical O-line geometries with this property may be related to the fact that for ε positive, one can construct asymptotic solutions in the limit t → ∞

  2. Economic analysis of medical management applied for left colostomy.

    Science.gov (United States)

    Savlovschi, C; Serban, D; Andreescu, Cv; Dascalu, Am; Pantu, H

    2013-01-01

    This paper presents an analysis of surgical treatment costs for left colostomy, aiming to calculate a medium cost per procedure and to identify the means to maximize the economic management of this type of surgicale procedure. A retrospective study was conducted on a group of 8 patients hospitalized in the 4th Surgery Department,Emergency University Hospital Bucharest, during the year 2012 for left colic neoplasms with obstruction signs that were operated on with a left colostomy. The followed parameters in the studied group of patients were represented by medical expenses, divided in: preoperative, intra-operative and immediate postoperative (postop. hospitalization). Two major types of colostomy were performed: left loop colostomy with intact tumour for 6 patients and left end colostomy and tumour resection (Hartmann's procedure) for 2 patients. The medium cost of this type of surgical intervention was 4396.807 RON, representing 1068.742 euro. Statistic data analysis didn't reveal average costs to vary with the type of procedure. The age of the study subjects was between 49 and 88, with an average of 61 years, without it being possible to establish a correlation between patient age and the level of medical spendings. Reducing the costs involved by left colostomy can be efficiently done by decreasing the number of days of hospitalisation in the following ways: preoperative preparation and assessment of the subject in an outpatient regimen; the accuracy of the surgical procedure with the decrease of early postoperative complications and antibiotherapy- the second major cause of increased postoperative costs. Celsius.

  3. An Inverse Kinematic Approach Using Groebner Basis Theory Applied to Gait Cycle Analysis

    Science.gov (United States)

    2013-03-01

    AN INVERSE KINEMATIC APPROACH USING GROEBNER BASIS THEORY APPLIED TO GAIT CYCLE ANALYSIS THESIS Anum Barki AFIT-ENP-13-M-02 DEPARTMENT OF THE AIR...copyright protection in the United States. AFIT-ENP-13-M-02 AN INVERSE KINEMATIC APPROACH USING GROEBNER BASIS THEORY APPLIED TO GAIT CYCLE ANALYSIS THESIS...APPROACH USING GROEBNER BASIS THEORY APPLIED TO GAIT CYCLE ANALYSIS Anum Barki, BS Approved: Dr. Ronald F. Tuttle (Chairman) Date Dr. Kimberly Kendricks

  4. Transcriptomic analysis in the developing zebrafish embryo after compound exposure: Individual gene expression and pathway regulation

    Energy Technology Data Exchange (ETDEWEB)

    Hermsen, Sanne A.B., E-mail: Sanne.Hermsen@rivm.nl [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht (Netherlands); Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.178, 3508 TD, Utrecht (Netherlands); Pronk, Tessa E. [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht (Netherlands); Brandhof, Evert-Jan van den [Centre for Environmental Quality, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Ven, Leo T.M. van der [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Piersma, Aldert H. [Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven (Netherlands); Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80.178, 3508 TD, Utrecht (Netherlands)

    2013-10-01

    The zebrafish embryotoxicity test is a promising alternative assay for developmental toxicity. Classically, morphological assessment of the embryos is applied to evaluate the effects of compound exposure. However, by applying differential gene expression analysis the sensitivity and predictability of the test may be increased. For defining gene expression signatures of developmental toxicity, we explored the possibility of using gene expression signatures of compound exposures based on commonly expressed individual genes as well as based on regulated gene pathways. Four developmental toxic compounds were tested in concentration-response design, caffeine, carbamazepine, retinoic acid and valproic acid, and two non-embryotoxic compounds, D-mannitol and saccharin, were included. With transcriptomic analyses we were able to identify commonly expressed genes, which were mostly development related, after exposure to the embryotoxicants. We also identified gene pathways regulated by the embryotoxicants, suggestive of their modes of action. Furthermore, whereas pathways may be regulated by all compounds, individual gene expression within these pathways can differ for each compound. Overall, the present study suggests that the use of individual gene expression signatures as well as pathway regulation may be useful starting points for defining gene biomarkers for predicting embryotoxicity. - Highlights: • The zebrafish embryotoxicity test in combination with transcriptomics was used. • We explored two approaches of defining gene biomarkers for developmental toxicity. • Four compounds in concentration-response design were tested. • We identified commonly expressed individual genes as well as regulated gene pathways. • Both approaches seem suitable starting points for defining gene biomarkers.

  5. Differential expression analysis for RNAseq using Poisson mixed models.

    Science.gov (United States)

    Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny; Zhou, Xiang

    2017-06-20

    Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Perturbation Method of Analysis Applied to Substitution Measurements of Buckling

    Energy Technology Data Exchange (ETDEWEB)

    Persson, Rolf

    1966-11-15

    Calculations with two-group perturbation theory on substitution experiments with homogenized regions show that a condensation of the results into a one-group formula is possible, provided that a transition region is introduced in a proper way. In heterogeneous cores the transition region comes in as a consequence of a new cell concept. By making use of progressive substitutions the properties of the transition region can be regarded as fitting parameters in the evaluation procedure. The thickness of the region is approximately equal to the sum of 1/(1/{tau} + 1/L{sup 2}){sup 1/2} for the test and reference regions. Consequently a region where L{sup 2} >> {tau}, e.g. D{sub 2}O, contributes with {radical}{tau} to the thickness. In cores where {tau} >> L{sup 2} , e.g. H{sub 2}O assemblies, the thickness of the transition region is determined by L. Experiments on rod lattices in D{sub 2}O and on test regions of D{sub 2}O alone (where B{sup 2} = - 1/L{sup 2} ) are analysed. The lattice measurements, where the pitches differed by a factor of {radical}2, gave excellent results, whereas the determination of the diffusion length in D{sub 2}O by this method was not quite successful. Even regions containing only one test element can be used in a meaningful way in the analysis.

  7. Soft tissue cephalometric analysis applied to Himachali ethnic population

    Directory of Open Access Journals (Sweden)

    Isha Aggarwal

    2016-01-01

    Full Text Available Introduction: The modern society considers facial attractiveness as an important physical attribute. The great variance in soft tissue drape of the human face complicates accurate assessment of the soft tissue profile, and it is a known fact that facial features of different ethnic groups differ significantly. This study was undertaken to establish norms for Himachali ethnic population. Materials and Methods: The sample comprised lateral cephalograms taken in natural head position of 100 normal individuals (50 males, 50 females. The cephalograms were analyzed by Arnett soft tissue cephalometric analysis for orthodontic diagnosis and treatment planning. Student's t-test was used to compare the means of the two groups. Results: Statistically significant differences were found between Himachali males and females in certain key parameters. Males have thicker soft tissue structures and a more acute nasolabial angle than females. Males have longer faces and females have greater interlabial gap and maxillary incisor exposure. Males have more deep-set facial structures than females. Conclusions: Statistically significant differences were found between Himachali males and females in certain key parameters. Differences were also noted between other ethnic groups and Himachali faces.

  8. MULTI-CRITERIA ANALYSIS APPLIED TO LANDSLIDE SUSCEPTIBILITY MAPPING

    Directory of Open Access Journals (Sweden)

    Mariana Madruga de Brito

    2017-10-01

    Full Text Available This paper presents the application of a multi-criteria analysis (MCA tool for landslide susceptibility assessment in Porto Alegre municipality, southern Brazil. A knowledge driven approach was used, aiming to ensure an optimal use of the available information. The landslide conditioning factors considered were slope, lithology, flow accumulation and distance from lineaments. Standardization of these factors was done through fuzzy membership functions, and evaluation of their relative importance for landslide predisposition was supported by the analytic hierarchy process (AHP, based on local expert knowledge. Finally, factors were integrated in a GIS environment using the weighted linear combination (WLC method. For validation, an inventory, including 107 landslide points recorded between 2007 and 2013 was used. Results indicated that 8.2% (39.40 km² of the study area are highly and very highly susceptible to landslides. An overall accuracy of 95% was found, with an area under the receiver operating characteristic (ROC curve of 0.960. Therefore, the resulting map can be regarded as useful for monitoring landslide-prone areas. Based on the findings, it is concluded that the proposed method is effective for susceptibility assessment since it yielded meaningful results and does not require extensive input data.

  9. Applying Hierarchical Task Analysis Method to Discovery Layer Evaluation

    Directory of Open Access Journals (Sweden)

    Marlen Promann

    2015-03-01

    Full Text Available Libraries are implementing discovery layers to offer better user experiences. While usability tests have been helpful in evaluating the success or failure of implementing discovery layers in the library context, the focus has remained on its relative interface benefits over the traditional federated search. The informal site- and context specific usability tests have offered little to test the rigor of the discovery layers against the user goals, motivations and workflow they have been designed to support. This study proposes hierarchical task analysis (HTA as an important complementary evaluation method to usability testing of discovery layers. Relevant literature is reviewed for the discovery layers and the HTA method. As no previous application of HTA to the evaluation of discovery layers was found, this paper presents the application of HTA as an expert based and workflow centered (e.g. retrieving a relevant book or a journal article method to evaluating discovery layers. Purdue University’s Primo by Ex Libris was used to map eleven use cases as HTA charts. Nielsen’s Goal Composition theory was used as an analytical framework to evaluate the goal carts from two perspectives: a users’ physical interactions (i.e. clicks, and b user’s cognitive steps (i.e. decision points for what to do next. A brief comparison of HTA and usability test findings is offered as a way of conclusion.

  10. Applied and computational harmonic analysis on graphs and networks

    Science.gov (United States)

    Irion, Jeff; Saito, Naoki

    2015-09-01

    In recent years, the advent of new sensor technologies and social network infrastructure has provided huge opportunities and challenges for analyzing data recorded on such networks. In the case of data on regular lattices, computational harmonic analysis tools such as the Fourier and wavelet transforms have well-developed theories and proven track records of success. It is therefore quite important to extend such tools from the classical setting of regular lattices to the more general setting of graphs and networks. In this article, we first review basics of graph Laplacian matrices, whose eigenpairs are often interpreted as the frequencies and the Fourier basis vectors on a given graph. We point out, however, that such an interpretation is misleading unless the underlying graph is either an unweighted path or cycle. We then discuss our recent effort of constructing multiscale basis dictionaries on a graph, including the Hierarchical Graph Laplacian Eigenbasis Dictionary and the Generalized Haar-Walsh Wavelet Packet Dictionary, which are viewed as generalizations of the classical hierarchical block DCTs and the Haar-Walsh wavelet packets, respectively, to the graph setting. Finally, we demonstrate the usefulness of our dictionaries by using them to simultaneously segment and denoise 1-D noisy signals sampled on regular lattices, a problem where classical tools have difficulty.

  11. Applying revised gap analysis model in measuring hotel service quality.

    Science.gov (United States)

    Lee, Yu-Cheng; Wang, Yu-Che; Chien, Chih-Hung; Wu, Chia-Huei; Lu, Shu-Chiung; Tsai, Sang-Bing; Dong, Weiwei

    2016-01-01

    With the number of tourists coming to Taiwan growing by 10-20 % since 2010, the number has increased due to an increasing number of foreign tourists, particularly after deregulation allowed admitting tourist groups, followed later on by foreign individual tourists, from mainland China. The purpose of this study is to propose a revised gap model to evaluate and improve service quality in Taiwanese hotel industry. Thus, service quality could be clearly measured through gap analysis, which was more effective for offering direction in developing and improving service quality. The HOLSERV instrument was used to identify and analyze service gaps from the perceptions of internal and external customers. The sample for this study included three main categories of respondents: tourists, employees, and managers. The results show that five gaps influenced tourists' evaluations of service quality. In particular, the study revealed that Gap 1 (management perceptions vs. customer expectations) and Gap 9 (service provider perceptions of management perceptions vs. service delivery) were more critical than the others in affecting perceived service quality, making service delivery the main area of improvement. This study contributes toward an evaluation of the service quality of the Taiwanese hotel industry from the perspectives of customers, service providers, and managers, which is considerably valuable for hotel managers. It was the aim of this study to explore all of these together in order to better understand the possible gaps in the hotel industry in Taiwan.

  12. 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

  13. Comparative analysis of clustering methods for gene expression time course data

    Directory of Open Access Journals (Sweden)

    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.

  14. PCR Expression Analysis Of the Estrogeninducible Gene Bcei in Gastrointestinal and Other Human Tumors

    Directory of Open Access Journals (Sweden)

    Iris Wundrack

    1994-01-01

    Full Text Available A polymerase chain reaction (PCR assay was developed to test for tumor cell specific expression of the BCEI gene. This new marker gene, reported at first for human breast cancer, was found specifically active in various gastrointestinal carcinomas by previously applying immunohistochemistry and RNA (Northern blot analysis. Presently, by using reverse transcription -PCR analysis, a series of primary tumor tissues and established tumor cell lines were testcd for BCEI transcription. This approach was compared to immunostaining achieved by an antibody directed against the BCEI gene’s product. The result demonstrate the superior sensitivity of PCR by indicating the gene’ s expression in cases where immunohistochemical testing remained negative.

  15. Statistical analysis and Kalman filtering applied to nuclear materials accountancy

    International Nuclear Information System (INIS)

    Annibal, P.S.

    1990-08-01

    Much theoretical research has been carried out on the development of statistical methods for nuclear material accountancy. In practice, physical, financial and time constraints mean that the techniques must be adapted to give an optimal performance in plant conditions. This thesis aims to bridge the gap between theory and practice, to show the benefits to be gained from a knowledge of the facility operation. Four different aspects are considered; firstly, the use of redundant measurements to reduce the error on the estimate of the mass of heavy metal in an 'accountancy tank' is investigated. Secondly, an analysis of the calibration data for the same tank is presented, establishing bounds for the error and suggesting a means of reducing them. Thirdly, a plant-specific method of producing an optimal statistic from the input, output and inventory data, to help decide between 'material loss' and 'no loss' hypotheses, is developed and compared with existing general techniques. Finally, an application of the Kalman Filter to materials accountancy is developed, to demonstrate the advantages of state-estimation techniques. The results of the analyses and comparisons illustrate the importance of taking into account a complete and accurate knowledge of the plant operation, measurement system, and calibration methods, to derive meaningful results from statistical tests on materials accountancy data, and to give a better understanding of critical random and systematic error sources. The analyses were carried out on the head-end of the Fast Reactor Reprocessing Plant, where fuel from the prototype fast reactor is cut up and dissolved. However, the techniques described are general in their application. (author)

  16. Improving the flash flood frequency analysis applying dendrogeomorphological evidences

    Science.gov (United States)

    Ruiz-Villanueva, V.; Ballesteros, J. A.; Bodoque, J. M.; Stoffel, M.; Bollschweiler, M.; Díez-Herrero, A.

    2009-09-01

    Flash floods are one of the natural hazards that cause major damages worldwide. Especially in Mediterranean areas they provoke high economic losses every year. In mountain areas with high stream gradients, floods events are characterized by extremely high flow and debris transport rates. Flash flood analysis in mountain areas presents specific scientific challenges. On one hand, there is a lack of information on precipitation and discharge due to a lack of spatially well distributed gauge stations with long records. On the other hand, gauge stations may not record correctly during extreme events when they are damaged or the discharge exceeds the recordable level. In this case, no systematic data allows improvement of the understanding of the spatial and temporal occurrence of the process. Since historic documentation is normally scarce or even completely missing in mountain areas, tree-ring analysis can provide an alternative approach. Flash floods may influence trees in different ways: (1) tilting of the stem through the unilateral pressure of the flowing mass or individual boulders; (2) root exposure through erosion of the banks; (3) injuries and scars caused by boulders and wood transported in the flow; (4) decapitation of the stem and resulting candelabra growth through the severe impact of boulders; (5) stem burial through deposition of material. The trees react to these disturbances with specific growth changes such as abrupt change of the yearly increment and anatomical changes like reaction wood or callus tissue. In this study, we sampled 90 cross sections and 265 increment cores of trees heavily affected by past flash floods in order to date past events and to reconstruct recurrence intervals in two torrent channels located in the Spanish Central System. The first study site is located along the Pelayo River, a torrent in natural conditions. Based on the external disturbances of trees and their geomorphological position, 114 Pinus pinaster (Ait

  17. Applied machine learning in greenhouse simulation; new application and analysis

    Directory of Open Access Journals (Sweden)

    Morteza Taki

    2018-06-01

    Full Text Available Prediction the inside environment variables in greenhouses is very important because they play a vital role in greenhouse cultivation and energy lost especially in cold and hot regions. The greenhouse environment is an uncertain nonlinear system which classical modeling methods have some problems to solve it. So the main goal of this study is to select the best method between Artificial Neural Network (ANN and Support Vector Machine (SVM to estimate three different variables include inside air, soil and plant temperatures (Ta, Ts, Tp and also energy exchange in a polyethylene greenhouse in Shahreza city, Isfahan province, Iran. The environmental factors which influencing all the inside temperatures such as outside air temperature, wind speed and outside solar radiation were collected as data samples. In this research, 13 different training algorithms were used for ANN models (MLP-RBF. Based on K-fold cross validation and Randomized Complete Block (RCB methodology, the best model was selected. The results showed that the type of training algorithm and kernel function are very important factors in ANN (RBF and MLP and SVM models performance, respectively. Comparing RBF, MLP and SVM models showed that the performance of RBF to predict Ta, Tp and Ts variables is better according to small values of RMSE and MAPE and large value of R2 indices. The range of RMSE and MAPE factors for RBF model to predict Ta, Tp and Ts were between 0.07 and 0.12 °C and 0.28–0.50%, respectively. Generalizability and stability of the RBF model with 5-fold cross validation analysis showed that this method can use with small size of data groups. The performance of best model (RBF to estimate the energy lost and exchange in the greenhouse with heat transfer models showed that this method can estimate the real data in greenhouse and then predict the energy lost and exchange with high accuracy. Keywords: Black box method, Energy lost, Environmental situation, Energy

  18. 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.

  19. Global gene expression analysis for evaluation and design of biomaterials

    Directory of Open Access Journals (Sweden)

    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.

  20. 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)

  1. Exploratory Factor Analysis as a Construct Validation Tool: (Mis)applications in Applied Linguistics Research

    Science.gov (United States)

    Karami, Hossein

    2015-01-01

    Factor analysis has been frequently exploited in applied research to provide evidence about the underlying factors in various measurement instruments. A close inspection of a large number of studies published in leading applied linguistic journals shows that there is a misconception among applied linguists as to the relative merits of exploratory…

  2. Applied Drama and the Higher Education Learning Spaces: A Reflective Analysis

    Science.gov (United States)

    Moyo, Cletus

    2015-01-01

    This paper explores Applied Drama as a teaching approach in Higher Education learning spaces. The exploration takes a reflective analysis approach by first examining the impact that Applied Drama has had on my career as a Lecturer/Educator/Teacher working in Higher Education environments. My engagement with Applied Drama practice and theory is…

  3. A novel bi-level meta-analysis approach: applied to biological pathway analysis.

    Science.gov (United States)

    Nguyen, Tin; Tagett, Rebecca; Donato, Michele; Mitrea, Cristina; Draghici, Sorin

    2016-02-01

    The accumulation of high-throughput data in public repositories creates a pressing need for integrative analysis of multiple datasets from independent experiments. However, study heterogeneity, study bias, outliers and the lack of power of available methods present real challenge in integrating genomic data. One practical drawback of many P-value-based meta-analysis methods, including Fisher's, Stouffer's, minP and maxP, is that they are sensitive to outliers. Another drawback is that, because they perform just one statistical test for each individual experiment, they may not fully exploit the potentially large number of samples within each study. We propose a novel bi-level meta-analysis approach that employs the additive method and the Central Limit Theorem within each individual experiment and also across multiple experiments. We prove that the bi-level framework is robust against bias, less sensitive to outliers than other methods, and more sensitive to small changes in signal. For comparative analysis, we demonstrate that the intra-experiment analysis has more power than the equivalent statistical test performed on a single large experiment. For pathway analysis, we compare the proposed framework versus classical meta-analysis approaches (Fisher's, Stouffer's and the additive method) as well as against a dedicated pathway meta-analysis package (MetaPath), using 1252 samples from 21 datasets related to three human diseases, acute myeloid leukemia (9 datasets), type II diabetes (5 datasets) and Alzheimer's disease (7 datasets). Our framework outperforms its competitors to correctly identify pathways relevant to the phenotypes. The framework is sufficiently general to be applied to any type of statistical meta-analysis. The R scripts are available on demand from the authors. sorin@wayne.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e

  4. 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...

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

    Science.gov (United States)

    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

  6. 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

  7. 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.

  8. Beyond Time out and Table Time: Today's Applied Behavior Analysis for Students with Autism

    Science.gov (United States)

    Boutot, E. Amanda; Hume, Kara

    2012-01-01

    Recent mandates related to the implementation of evidence-based practices for individuals with autism spectrum disorder (ASD) require that autism professionals both understand and are able to implement practices based on the science of applied behavior analysis (ABA). The use of the term "applied behavior analysis" and its related concepts…

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.

    Science.gov (United States)

    Jiang, Jinjin; Wang, Yue; Zhu, Bao; Fang, Tingting; Fang, Yujie; Wang, Youping

    2015-01-27

    Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale. We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species. Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.

  12. Meta Analysis of Gene Expression Data within and Across Species.

    Science.gov (United States)

    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.

  13. Integrating Biological Perspectives:. a Quantum Leap for Microarray Expression Analysis

    Science.gov (United States)

    Wanke, Dierk; Kilian, Joachim; Bloss, Ulrich; Mangelsen, Elke; Supper, Jochen; Harter, Klaus; Berendzen, Kenneth W.

    2009-02-01

    Biologists and bioinformatic scientists cope with the analysis of transcript abundance and the extraction of meaningful information from microarray expression data. By exploiting biological information accessible in public databases, we try to extend our current knowledge over the plant model organism Arabidopsis thaliana. Here, we give two examples of increasing the quality of information gained from large scale expression experiments by the integration of microarray-unrelated biological information: First, we utilize Arabidopsis microarray data to demonstrate that expression profiles are usually conserved between orthologous genes of different organisms. In an initial step of the analysis, orthology has to be inferred unambiguously, which then allows comparison of expression profiles between orthologs. We make use of the publicly available microarray expression data of Arabidopsis and barley, Hordeum vulgare. We found a generally positive correlation in expression trajectories between true orthologs although both organisms are only distantly related in evolutionary time scale. Second, extracting clusters of co-regulated genes implies similarities in transcriptional regulation via similar cis-regulatory elements (CREs). Vice versa approaches, where co-regulated gene clusters are found by investigating on CREs were not successful in general. Nonetheless, in some cases the presence of CREs in a defined position, orientation or CRE-combinations is positively correlated with co-regulated gene clusters. Here, we make use of genes involved in the phenylpropanoid biosynthetic pathway, to give one positive example for this approach.

  14. 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

  15. Introduction to applied statistical signal analysis guide to biomedical and electrical engineering applications

    CERN Document Server

    Shiavi, Richard

    2007-01-01

    Introduction to Applied Statistical Signal Analysis is designed for the experienced individual with a basic background in mathematics, science, and computer. With this predisposed knowledge, the reader will coast through the practical introduction and move on to signal analysis techniques, commonly used in a broad range of engineering areas such as biomedical engineering, communications, geophysics, and speech.Introduction to Applied Statistical Signal Analysis intertwines theory and implementation with practical examples and exercises. Topics presented in detail include: mathematical

  16. Inclusive Elementary Classroom Teacher Knowledge of and Attitudes toward Applied Behavior Analysis and Autism Spectrum Disorder and Their Use of Applied Behavior Analysis

    Science.gov (United States)

    McCormick, Jennifer A.

    2011-01-01

    The purpose of this study was to examine inclusive elementary teacher knowledge and attitude toward Autism Spectrum Disorder (ASD) and applied behavior analysis (ABA) and their use of ABA. Furthermore, this study examined if knowledge and attitude predicted use of ABA. A survey was developed and administered through a web-based program. Of the…

  17. Nuclear physical express analysis of solid fuel sulphur content

    International Nuclear Information System (INIS)

    Pak, Yu.; Ponomaryova, M

    2005-01-01

    Full text: Sulphur content is an important qualitative coal parameter. The problem of coal sulphur content determining remains one of the most important both in Kazakhstan and in other coal-mining countries. The traditional method of sampling, the final stage of which is chemical analysis of coal for sulphur, is characterized by high labour intensity and low productivity. That's why it is ineffective for mass express analytical quality control and technological schemes of coal processing control. In this connection it is very urgent to develop a method of coal sulphur content on the base of a series nuclear-geophysical equipment with an isotope source of primary radiation, allowing to increase analysis representativity and maximally take into account coal real composition inconstancy. To solve the problem set it is necessary to study the main laws of X-ray-radiometric method applied to the coal quality analysis for working out instrumental methods of speed determining of coal sulphur content with satisfactory accuracy for technological tasks, to determine laws of changing the flows of characteristic X-ray and scattered radiation from coal sulphur content of various real composition and to optimize methodical and hardware parameters, providing minimal error of sulphur content control. On the base of studying laws of real composition coal components and their interconnections with sulphur content there has been substantiated the expediency of using hardware functions of calcium and iron to control coal sulphur contents; there has been suggested a model to estimate the methodical error of coal sulphur content determining on the base of the data about sensitivity to sulphur and effecting factors using ultimate methods of coal components substitution methods allowing to optimize sulphur control parameters; there has been worked out an algorithm of X-ray-radiometric control of sulphur content based on the sequential radiating the analyzed coal with gamma-radiation of

  18. 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.

  19. 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 (+) ...

  20. 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 ...

  1. 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

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. 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.

  5. Neisseria meningitidis rifampicin resistant strains: analysis of protein differentially expressed

    Directory of Open Access Journals (Sweden)

    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

  6. Cloning, characterization and expression analysis of porcine microRNAs

    Directory of Open Access Journals (Sweden)

    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.

  7. 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

  8. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    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.

  9. 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...

  10. 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.

  11. Research in progress in applied mathematics, numerical analysis, and computer science

    Science.gov (United States)

    1990-01-01

    Research conducted at the Institute in Science and Engineering in applied mathematics, numerical analysis, and computer science is summarized. The Institute conducts unclassified basic research in applied mathematics in order to extend and improve problem solving capabilities in science and engineering, particularly in aeronautics and space.

  12. Model Proposition for the Fiscal Policies Analysis Applied in Economic Field

    Directory of Open Access Journals (Sweden)

    Larisa Preda

    2007-05-01

    Full Text Available This paper presents a study about fiscal policy applied in economic development. Correlations between macroeconomics and fiscal indicators signify the first steep in our analysis. Next step is a new model proposal for the fiscal and budgetary choices. This model is applied on the date of the Romanian case.

  13. Advantages and Drawbacks of Applying Periodic Time-Variant Modal Analysis to Spur Gear Dynamics

    DEFF Research Database (Denmark)

    Pedersen, Rune; Santos, Ilmar; Hede, Ivan Arthur

    2010-01-01

    to ensure sufficient accuracy of the results. The method of time-variant modal analysis is applied, and the changes in the fundamental and the parametric resonance frequencies as a function of the rotational speed of the gears, are found. By obtaining the stationary and parametric parts of the time...... of applying the methodology to wind turbine gearboxes are addressed and elucidated....

  14. Applied behavior analysis: understanding and changing behavior in the community-a representative review.

    Science.gov (United States)

    Luyben, Paul D

    2009-01-01

    Applied behavior analysis, a psychological discipline, has been characterized as the science of behavior change (Chance, 2006). Research in applied behavior analysis has been published for approximately 40 years since the initial publication of the Journal of Applied Behavior Analysis in 1968. The field now encompasses a wide range of human behavior. Although much of the published research centers on problem behaviors that occur in schools and among people with disabilities, a substantial body of knowledge has emerged in community settings. This article provides a review of the behavioral community research published in the Journal of Applied Behavior Analysis as representative of this work, including research in the areas of home and family, health, safety, community involvement and the environment, recreation and sports, crime and delinquency, and organizations. In the interest of space, research in schools and with people with disabilities has been excluded from this review.

  15. Microarray gene expression profiling and analysis in renal cell carcinoma

    Directory of Open Access Journals (Sweden)

    Sadhukhan Provash

    2004-06-01

    Full Text Available Abstract Background Renal cell carcinoma (RCC is the most common cancer in adult kidney. The accuracy of current diagnosis and prognosis of the disease and the effectiveness of the treatment for the disease are limited by the poor understanding of the disease at the molecular level. To better understand the genetics and biology of RCC, we profiled the expression of 7,129 genes in both clear cell RCC tissue and cell lines using oligonucleotide arrays. Methods Total RNAs isolated from renal cell tumors, adjacent normal tissue and metastatic RCC cell lines were hybridized to affymatrix HuFL oligonucleotide arrays. Genes were categorized into different functional groups based on the description of the Gene Ontology Consortium and analyzed based on the gene expression levels. Gene expression profiles of the tissue and cell line samples were visualized and classified by singular value decomposition. Reverse transcription polymerase chain reaction was performed to confirm the expression alterations of selected genes in RCC. Results Selected genes were annotated based on biological processes and clustered into functional groups. The expression levels of genes in each group were also analyzed. Seventy-four commonly differentially expressed genes with more than five-fold changes in RCC tissues were identified. The expression alterations of selected genes from these seventy-four genes were further verified using reverse transcription polymerase chain reaction (RT-PCR. Detailed comparison of gene expression patterns in RCC tissue and RCC cell lines shows significant differences between the two types of samples, but many important expression patterns were preserved. Conclusions This is one of the initial studies that examine the functional ontology of a large number of genes in RCC. Extensive annotation, clustering and analysis of a large number of genes based on the gene functional ontology revealed many interesting gene expression patterns in RCC. Most

  16. GECKO: a complete large-scale gene expression analysis platform

    Directory of Open Access Journals (Sweden)

    Heuer Michael

    2004-12-01

    Full Text Available Abstract Background Gecko (Gene Expression: Computation and Knowledge Organization is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. Results Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing ~ 50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph, in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (~ 100 users and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data. Conclusions The Gecko system is being made publicly available as free software http://sourceforge.net/projects/geckoe. In totality or in parts, the Gecko framework should prove useful to users and system developers with a broad range of analysis needs.

  17. Evaluation of schistosome promoter expression for transgenesis and genetic analysis.

    Directory of Open Access Journals (Sweden)

    Shuang Liang

    Full Text Available Schistosome worms of the genus Schistosoma are the causative agents of schistosomiasis, a devastating parasitic disease affecting more than 240 million people worldwide. Schistosomes have complex life cycles, and have been challenging to manipulate genetically due to the dearth of molecular tools. Although the use of gene overexpression, gene knockouts or knockdowns are straight-forward genetic tools applied in many model systems, gene misexpression and genetic manipulation of schistosome genes in vivo has been exceptionally challenging, and plasmid based transfection inducing gene expression is limited. We recently reported the use of polyethyleneimine (PEI as a simple and effective method for schistosome transfection and gene expression. Here, we use PEI-mediated schistosome plasmid transgenesis to define and compare gene expression profiles from endogenous and nonendogenous promoters in the schistosomula stage of schistosomes that are potentially useful to misexpress (underexpress or overexpress gene product levels. In addition, we overexpress schistosome genes in vivo using a strong promoter and show plasmid-based misregulation of genes in schistosomes, producing a clear and distinct phenotype--death. These data focus on the schistosomula stage, but they foreshadow strong potential for genetic characterization of schistosome molecular pathways, and potential for use in overexpression screens and drug resistance studies in schistosomes using plasmid-based gene expression.

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

    Science.gov (United States)

    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.

  19. Cost-effectiveness analysis in melanoma detection: A transition model applied to dermoscopy.

    Science.gov (United States)

    Tromme, Isabelle; Legrand, Catherine; Devleesschauwer, Brecht; Leiter, Ulrike; Suciu, Stefan; Eggermont, Alexander; Sacré, Laurine; Baurain, Jean-François; Thomas, Luc; Beutels, Philippe; Speybroeck, Niko

    2016-11-01

    The main aim of this study is to demonstrate how our melanoma disease model (MDM) can be used for cost-effectiveness analyses (CEAs) in the melanoma detection field. In particular, we used the data of two cohorts of Belgian melanoma patients to investigate the cost-effectiveness of dermoscopy. A MDM, previously constructed to calculate the melanoma burden, was slightly modified to be suitable for CEAs. Two cohorts of patients entered into the model to calculate morbidity, mortality and costs. These cohorts were constituted by melanoma patients diagnosed by dermatologists adequately, or not adequately, trained in dermoscopy. Effectiveness and costs were calculated for each cohort and compared. Effectiveness was expressed in quality-adjusted life years (QALYs), a composite measure depending on melanoma-related morbidity and mortality. Costs included costs of treatment and follow-up as well as costs of detection in non-melanoma patients and costs of excision and pathology of benign lesions excised to rule out melanoma. The result of our analysis concluded that melanoma diagnosis by dermatologists adequately trained in dermoscopy resulted in both a gain of QALYs (less morbidity and/or mortality) and a reduction in costs. This study demonstrates how our MDM can be used in CEAs in the melanoma detection field. The model and the methodology suggested in this paper were applied to two cohorts of Belgian melanoma patients. Their analysis concluded that adequate dermoscopy training is cost-effective. The results should be confirmed by a large-scale randomised study. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  2. The application of DNA microarrays in gene expression analysis.

    Science.gov (United States)

    van Hal, N L; Vorst, O; van Houwelingen, A M; Kok, E J; Peijnenburg, A; Aharoni, A; van Tunen, A J; Keijer, J

    2000-03-31

    DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed. These comprise array manufacturing and design, array hybridisation, scanning, and data handling. Furthermore, it is discussed how DNA microarrays can be applied in the working fields of: safety, functionality and health of food and gene discovery and pathway engineering in plants.

  3. Problems of Understanding English Ironic Expressions by M.A. Students of Applied Linguistics at Mu'tah University in Jordan

    Science.gov (United States)

    Al Khawaldeh, Suhaib

    2015-01-01

    The present study attempts to investigate the problems of understanding English ironic expressions M.A. of Applied Linguistics students at Mu'tah University in Jordan. This quantitative and qualitative study includes 15 of M.A. students of Applied Linguistics at Mu'tah University. The participants were selected randomly. Two research instruments…

  4. 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.

  5. 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.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Critical Analysis of a Website: A Critique based on Critical Applied Linguistics and Critical Discourse Analysis

    Directory of Open Access Journals (Sweden)

    Rina Agustina

    2013-05-01

    Full Text Available E-learning was easily found through browsing internet, which was mostly free of charge and provided various learning materials. Spellingcity.com was one of e-learning websites for teaching and learning English to learn spelling, vocabulary and writing, which offered various games and activities for young learners, 6 until 8 year old learners in particular. Having considered those constraints, this paper aimed to analyse the website from two different views: (1 critical applied linguistics  (CAL aspects and (2 critical  discourse analysis (CDA. After analysing the website using CAL and CDA, it was found that the website was adequate for beginner, in which it provided fun learning through games as well as challenged learners’ to test their vocabulary. Despite of these strengths, there were several issues required further thinking in terms of learners’ broad knowledge, such as, some of learning materials focused on states in America. It was quite difficult for EFL learners if they did not have adequate general knowledge. Thus, the findings implied that the website could be used as a supporting learning material, which accompanied textbooks and vocabulary exercise books.

  9. Gene expression analysis of embryonic stem cells expressing VE-cadherin (CD144 during endothelial differentiation

    Directory of Open Access Journals (Sweden)

    Libermann Towia

    2008-05-01

    Full Text Available Abstract Background Endothelial differentiation occurs during normal vascular development in the developing embryo. This process is recapitulated in the adult when endothelial progenitor cells are generated in the bone marrow and can contribute to vascular repair or angiogenesis at sites of vascular injury or ischemia. The molecular mechanisms of endothelial differentiation remain incompletely understood. Novel approaches are needed to identify the factors that regulate endothelial differentiation. Methods Mouse embryonic stem (ES cells were used to further define the molecular mechanisms of endothelial differentiation. By flow cytometry a population of VEGF-R2 positive cells was identified as early as 2.5 days after differentiation of ES cells, and a subset of VEGF-R2+ cells, that were CD41 positive at 3.5 days. A separate population of VEGF-R2+ stem cells expressing the endothelial-specific marker CD144 (VE-cadherin was also identified at this same time point. Channels lined by VE-cadherin positive cells developed within the embryoid bodies (EBs formed by differentiating ES cells. VE-cadherin and CD41 expressing cells differentiate in close proximity to each other within the EBs, supporting the concept of a common origin for cells of hematopoietic and endothelial lineages. Results Microarray analysis of >45,000 transcripts was performed on RNA obtained from cells expressing VEGF-R2+, CD41+, and CD144+ and VEGF-R2-, CD41-, and CD144-. All microarray experiments were performed in duplicate using RNA obtained from independent experiments, for each subset of cells. Expression profiling confirmed the role of several genes involved in hematopoiesis, and identified several putative genes involved in endothelial differentiation. Conclusion The isolation of CD144+ cells during ES cell differentiation from embryoid bodies provides an excellent model system and method for identifying genes that are expressed during endothelial differentiation and that

  10. Applied Behavior Analysis: Its Impact on the Treatment of Mentally Retarded Emotionally Disturbed People.

    Science.gov (United States)

    Matson, Johnny L.; Coe, David A.

    1992-01-01

    This article reviews applications of the applied behavior analysis ideas of B. F. Skinner and others to persons with both mental retardation and emotional disturbance. The review examines implications of behavior analysis for operant conditioning and radical behaviorism, schedules of reinforcement, and emotion and mental illness. (DB)

  11. An Objective Comparison of Applied Behavior Analysis and Organizational Behavior Management Research

    Science.gov (United States)

    Culig, Kathryn M.; Dickinson, Alyce M.; McGee, Heather M.; Austin, John

    2005-01-01

    This paper presents an objective review, analysis, and comparison of empirical studies targeting the behavior of adults published in Journal of Applied Behavior Analysis (JABA) and Journal of Organizational Behavior Management (JOBM) between 1997 and 2001. The purpose of the comparisons was to identify similarities and differences with respect to…

  12. Sociosexuality Education for Persons with Autism Spectrum Disorders Using Principles of Applied Behavior Analysis

    Science.gov (United States)

    Wolfe, Pamela S.; Condo, Bethany; Hardaway, Emily

    2009-01-01

    Applied behavior analysis (ABA) has emerged as one of the most effective empirically based strategies for instructing individuals with autism spectrum disorders (ASD). Four ABA-based strategies that have been found effective are video modeling, visual strategies, social script fading, and task analysis. Individuals with ASD often struggle with…

  13. Applying Fuzzy and Probabilistic Uncertainty Concepts to the Material Flow Analysis of Palladium in Austria

    DEFF Research Database (Denmark)

    Laner, David; Rechberger, Helmut; Astrup, Thomas Fruergaard

    2015-01-01

    Material flow analysis (MFA) is a widely applied tool to investigate resource and recycling systems of metals and minerals. Owing to data limitations and restricted system understanding, MFA results are inherently uncertain. To demonstrate the systematic implementation of uncertainty analysis in ...

  14. A practical guide to propensity score analysis for applied clinical research.

    Science.gov (United States)

    Lee, Jaehoon; Little, Todd D

    2017-11-01

    Observational studies are often the only viable options in many clinical settings, especially when it is unethical or infeasible to randomly assign participants to different treatment régimes. In such case propensity score (PS) analysis can be applied to accounting for possible selection bias and thereby addressing questions of causal inference. Many PS methods exist, yet few guidelines are available to aid applied researchers in their conduct and evaluation of a PS analysis. In this article we give an overview of available techniques for PS estimation and application, balance diagnostic, treatment effect estimation, and sensitivity assessment, as well as recent advances. We also offer a tutorial that can be used to emulate the steps of PS analysis. Our goal is to provide information that will bring PS analysis within the reach of applied clinical researchers and practitioners. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. 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®.

  16. Paired Expression Analysis of Tumor Cell Surface Antigens

    Directory of Open Access Journals (Sweden)

    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

  17. Multivariate analysis of microarray data: differential expression and differential connection.

    Science.gov (United States)

    Kiiveri, Harri T

    2011-02-01

    Typical analysis of microarray data ignores the correlation between gene expression values. In this paper we present a model for microarray data which specifically allows for correlation between genes. As a result we combine gene network ideas with linear models and differential expression. We use sparse inverse covariance matrices and their associated graphical representation to capture the notion of gene networks. An important issue in using these models is the identification of the pattern of zeroes in the inverse covariance matrix. The limitations of existing methods for doing this are discussed and we provide a workable solution for determining the zero pattern. We then consider a method for estimating the parameters in the inverse covariance matrix which is suitable for very high dimensional matrices. We also show how to construct multivariate tests of hypotheses. These overall multivariate tests can be broken down into two components, the first one being similar to tests for differential expression and the second involving the connections between genes. The methods in this paper enable the extraction of a wealth of information concerning the relationships between genes which can be conveniently represented in graphical form. Differentially expressed genes can be placed in the context of the gene network and places in the gene network where unusual or interesting patterns have emerged can be identified, leading to the formulation of hypotheses for future experimentation.

  18. Multivariate analysis of microarray data: differential expression and differential connection

    Directory of Open Access Journals (Sweden)

    Kiiveri Harri T

    2011-02-01

    Full Text Available Abstract Background Typical analysis of microarray data ignores the correlation between gene expression values. In this paper we present a model for microarray data which specifically allows for correlation between genes. As a result we combine gene network ideas with linear models and differential expression. Results We use sparse inverse covariance matrices and their associated graphical representation to capture the notion of gene networks. An important issue in using these models is the identification of the pattern of zeroes in the inverse covariance matrix. The limitations of existing methods for doing this are discussed and we provide a workable solution for determining the zero pattern. We then consider a method for estimating the parameters in the inverse covariance matrix which is suitable for very high dimensional matrices. We also show how to construct multivariate tests of hypotheses. These overall multivariate tests can be broken down into two components, the first one being similar to tests for differential expression and the second involving the connections between genes. Conclusion The methods in this paper enable the extraction of a wealth of information concerning the relationships between genes which can be conveniently represented in graphical form. Differentially expressed genes can be placed in the context of the gene network and places in the gene network where unusual or interesting patterns have emerged can be identified, leading to the formulation of hypotheses for future experimentation.

  19. 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.

  20. Gene Expression Signature in Endemic Osteoarthritis by Microarray Analysis

    Directory of Open Access Journals (Sweden)

    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.

  1. An Analysis of Methods Section of Research Reports in Applied Linguistics

    OpenAIRE

    Patrícia Marcuzzo

    2011-01-01

    This work aims at identifying analytical categories and research procedures adopted in the analysis of research article in Applied Linguistics/EAP in order to propose a systematization of the research procedures in Genre Analysis. For that purpose, 12 research reports and interviews with four authors were analyzed. The analysis showed that the studies are concentrated on the investigation of the macrostructure or on the microstructure of research articles in different fields. Studies about th...

  2. Gene expression analysis of FABP4 in gastric cancer

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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.

  4. Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

    Directory of Open Access Journals (Sweden)

    Kleinjans Jos

    2008-09-01

    Full Text Available Abstract Background In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, game theory has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions. Results In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called Comparative Analysis of Shapley value (shortly, CASh, is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability. Conclusion CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a

  5. Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution.

    Science.gov (United States)

    Moretti, Stefano; van Leeuwen, Danitsja; Gmuender, Hans; Bonassi, Stefano; van Delft, Joost; Kleinjans, Jos; Patrone, Fioravante; Merlo, Domenico Franco

    2008-09-02

    In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, game theory has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions. In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called Comparative Analysis of Shapley value (shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability. CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that

  6. Pattern Recognition of Gene Expression with Singular Spectrum Analysis

    Directory of Open Access Journals (Sweden)

    Hossein Hassani

    2014-07-01

    Full Text Available Drosophila segmentation as a model organism is one of the most highly studied. Among many maternal segmentation coordinate genes, bicoid protein pattern plays a significant role during Drosophila embryogenesis, since this gradient determines most aspects of head and thorax development. Despite the fact that several models have been proposed to describe the bicoid gradient, due to its association with considerable error, each can only partially explain bicoid characteristics. In this paper, a modified version of singular spectrum analysis is examined for filtering and extracting the bicoid gene expression signal. The results with strong evidence indicate that the proposed technique is able to remove noise more effectively and can be considered as a promising method for filtering gene expression measurements for other applications.

  7. Analysis of the promoters involved in enterocin AS-48 expression.

    Science.gov (United States)

    Cebrián, Rubén; Rodríguez-Ruano, Sonia; Martínez-Bueno, Manuel; Valdivia, Eva; Maqueda, Mercedes; Montalbán-López, Manuel

    2014-01-01

    The enterocin AS-48 is the best characterized antibacterial circular protein in prokaryotes. It is a hydrophobic and cationic bacteriocin, which is ribosomally synthesized by enterococcal cells and post-translationally cyclized by a head-to-tail peptide bond. The production of and immunity towards AS-48 depend upon the coordinated expression of ten genes organized in two operons, as-48ABC (where genes encoding enzymes with processing, secretion, and immunity functions are adjacent to the structural as-48A gene) and as-48C1DD1EFGH. The current study describes the identification of the promoters involved in AS-48 expression. Seven putative promoters have been here amplified, and separately inserted into the promoter-probe vector pTLR1, to create transcriptional fusions with the mCherry gene used as a reporter. The activity of these promoter regions was assessed measuring the expression of the fluorescent mCherry protein using the constitutive pneumococcal promoter PX as a reference. Our results revealed that only three promoters PA, P2(2) and PD1 were recognized in Enterococcus faecalis, Lactococcus lactis and Escherichia coli, in the conditions tested. The maximal fluorescence was obtained with PX in all the strains, followed by the P2(2) promoter, which level of fluorescence was 2-fold compared to PA and 4-fold compared to PD1. Analysis of putative factors influencing the promoter activity in single and double transformants in E. faecalis JH2-2 demonstrated that, in general, a better expression was achieved in presence of pAM401-81. In addition, the P2(2) promoter could be regulated in a negative fashion by genes existing in the native pMB-2 plasmid other than those of the as-48 cluster, while the pH seems to affect differently the as-48 promoter expression.

  8. Analysis of the promoters involved in enterocin AS-48 expression.

    Directory of Open Access Journals (Sweden)

    Rubén Cebrián

    Full Text Available The enterocin AS-48 is the best characterized antibacterial circular protein in prokaryotes. It is a hydrophobic and cationic bacteriocin, which is ribosomally synthesized by enterococcal cells and post-translationally cyclized by a head-to-tail peptide bond. The production of and immunity towards AS-48 depend upon the coordinated expression of ten genes organized in two operons, as-48ABC (where genes encoding enzymes with processing, secretion, and immunity functions are adjacent to the structural as-48A gene and as-48C1DD1EFGH. The current study describes the identification of the promoters involved in AS-48 expression. Seven putative promoters have been here amplified, and separately inserted into the promoter-probe vector pTLR1, to create transcriptional fusions with the mCherry gene used as a reporter. The activity of these promoter regions was assessed measuring the expression of the fluorescent mCherry protein using the constitutive pneumococcal promoter PX as a reference. Our results revealed that only three promoters PA, P2(2 and PD1 were recognized in Enterococcus faecalis, Lactococcus lactis and Escherichia coli, in the conditions tested. The maximal fluorescence was obtained with PX in all the strains, followed by the P2(2 promoter, which level of fluorescence was 2-fold compared to PA and 4-fold compared to PD1. Analysis of putative factors influencing the promoter activity in single and double transformants in E. faecalis JH2-2 demonstrated that, in general, a better expression was achieved in presence of pAM401-81. In addition, the P2(2 promoter could be regulated in a negative fashion by genes existing in the native pMB-2 plasmid other than those of the as-48 cluster, while the pH seems to affect differently the as-48 promoter expression.

  9. Towards factor analysis exploration applied to positron emission tomography functional imaging for breast cancer characterization

    International Nuclear Information System (INIS)

    Rekik, W.; Ketata, I.; Sellami, L.; Ben slima, M.; Ben Hamida, A.; Chtourou, K.; Ruan, S.

    2011-01-01

    This paper aims to explore the factor analysis when applied to a dynamic sequence of medical images obtained using nuclear imaging modality, Positron Emission Tomography (PET). This latter modality allows obtaining information on physiological phenomena, through the examination of radiotracer evolution during time. Factor analysis of dynamic medical images sequence (FADMIS) estimates the underlying fundamental spatial distributions by factor images and the associated so-called fundamental functions (describing the signal variations) by factors. This method is based on an orthogonal analysis followed by an oblique analysis. The results of the FADMIS are physiological curves showing the evolution during time of radiotracer within homogeneous tissues distributions. This functional analysis of dynamic nuclear medical images is considered to be very efficient for cancer diagnostics. In fact, it could be applied for cancer characterization, vascularization as well as possible evaluation of response to therapy.

  10. Microarray analysis of gene expression profiles in ripening pineapple fruits.

    Science.gov (United States)

    Koia, Jonni H; Moyle, Richard L; Botella, Jose R

    2012-12-18

    Pineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening. Microarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested. This is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit

  11. Uncertainty propagation analysis applied to volcanic ash dispersal at Mt. Etna by using a Lagrangian model

    Science.gov (United States)

    de'Michieli Vitturi, Mattia; Pardini, Federica; Spanu, Antonio; Neri, Augusto; Vittoria Salvetti, Maria

    2015-04-01

    Volcanic ash clouds represent a major hazard for populations living nearby volcanic centers producing a risk for humans and a potential threat to crops, ground infrastructures, and aviation traffic. Lagrangian particle dispersal models are commonly used for tracking ash particles emitted from volcanic plumes and transported under the action of atmospheric wind fields. In this work, we present the results of an uncertainty propagation analysis applied to volcanic ash dispersal from weak plumes with specific focus on the uncertainties related to the grain-size distribution of the mixture. To this aim, the Eulerian fully compressible mesoscale non-hydrostatic model WRF was used to generate the driving wind, representative of the atmospheric conditions occurring during the event of November 24, 2006 at Mt. Etna. Then, the Lagrangian particle model LPAC (de' Michieli Vitturi et al., JGR 2010) was used to simulate the transport of mass particles under the action of atmospheric conditions. The particle motion equations were derived by expressing the Lagrangian particle acceleration as the sum of the forces acting along its trajectory, with drag forces calculated as a function of particle diameter, density, shape and Reynolds number. The simulations were representative of weak plume events of Mt. Etna and aimed to quantify the effect on the dispersal process of the uncertainty in the particle sphericity and in the mean and variance of a log-normal distribution function describing the grain-size of ash particles released from the eruptive column. In order to analyze the sensitivity of particle dispersal to these uncertain parameters with a reasonable number of simulations, and therefore with affordable computational costs, response surfaces in the parameter space were built by using the generalized polynomial chaos technique. The uncertainty analysis allowed to quantify the most probable values, as well as their pdf, of the number of particles as well as of the mean and

  12. Protein expression analysis of inflammation-related colon carcinogenesis

    Directory of Open Access Journals (Sweden)

    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.

  13. Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age.

    Science.gov (United States)

    Anand Brown, Andrew; Ding, Zhihao; Viñuela, Ana; Glass, Dan; Parts, Leopold; Spector, Tim; Winn, John; Durbin, Richard

    2015-03-09

    Statistical factor analysis methods have previously been used to remove noise components from high-dimensional data prior to genetic association mapping and, in a guided fashion, to summarize biologically relevant sources of variation. Here, we show how the derived factors summarizing pathway expression can be used to analyze the relationships between expression, heritability, and aging. We used skin gene expression data from 647 twins from the MuTHER Consortium and applied factor analysis to concisely summarize patterns of gene expression to remove broad confounding influences and to produce concise pathway-level phenotypes. We derived 930 "pathway phenotypes" that summarized patterns of variation across 186 KEGG pathways (five phenotypes per pathway). We identified 69 significant associations of age with phenotype from 57 distinct KEGG pathways at a stringent Bonferroni threshold ([Formula: see text]). These phenotypes are more heritable ([Formula: see text]) than gene expression levels. On average, expression levels of 16% of genes within these pathways are associated with age. Several significant pathways relate to metabolizing sugars and fatty acids; others relate to insulin signaling. We have demonstrated that factor analysis methods combined with biological knowledge can produce more reliable phenotypes with less stochastic noise than the individual gene expression levels, which increases our power to discover biologically relevant associations. These phenotypes could also be applied to discover associations with other environmental factors. Copyright © 2015 Brown et al.

  14. Identification and validation of Asteraceae miRNAs by the expressed sequence tag analysis.

    Science.gov (United States)

    Monavar Feshani, Aboozar; Mohammadi, Saeed; Frazier, Taylor P; Abbasi, Abbas; Abedini, Raha; Karimi Farsad, Laleh; Ehya, Farveh; Salekdeh, Ghasem Hosseini; Mardi, Mohsen

    2012-02-10

    MicroRNAs (miRNAs) are small non-coding RNA molecules that play a vital role in the regulation of gene expression. Despite their identification in hundreds of plant species, few miRNAs have been identified in the Asteraceae, a large family that comprises approximately one tenth of all flowering plants. In this study, we used the expressed sequence tag (EST) analysis to identify potential conserved miRNAs and their putative target genes in the Asteraceae. We applied quantitative Real-Time PCR (qRT-PCR) to confirm the expression of eight potential miRNAs in Carthamus tinctorius and Helianthus annuus. We also performed qRT-PCR analysis to investigate the differential expression pattern of five newly identified miRNAs during five different cotyledon growth stages in safflower. Using these methods, we successfully identified and characterized 151 potentially conserved miRNAs, belonging to 26 miRNA families, in 11 genus of Asteraceae. EST analysis predicted that the newly identified conserved Asteraceae miRNAs target 130 total protein-coding ESTs in sunflower and safflower, as well as 433 additional target genes in other plant species. We experimentally confirmed the existence of seven predicted miRNAs, (miR156, miR159, miR160, miR162, miR166, miR396, and miR398) in safflower and sunflower seedlings. We also observed that five out of eight miRNAs are differentially expressed during cotyledon development. Our results indicate that miRNAs may be involved in the regulation of gene expression during seed germination and the formation of the cotyledons in the Asteraceae. The findings of this study might ultimately help in the understanding of miRNA-mediated gene regulation in important crop species. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. The First Molecular Identification of an Olive Collection Applying Standard Simple Sequence Repeats and Novel Expressed Sequence Tag Markers.

    Science.gov (United States)

    Mousavi, Soraya; Mariotti, Roberto; Regni, Luca; Nasini, Luigi; Bufacchi, Marina; Pandolfi, Saverio; Baldoni, Luciana; Proietti, Primo

    2017-01-01

    Germplasm collections of tree crop species represent fundamental tools for conservation of diversity and key steps for its characterization and evaluation. For the olive tree, several collections were created all over the world, but only few of them have been fully characterized and molecularly identified. The olive collection of Perugia University (UNIPG), established in the years' 60, represents one of the first attempts to gather and safeguard olive diversity, keeping together cultivars from different countries. In the present study, a set of 370 olive trees previously uncharacterized was screened with 10 standard simple sequence repeats (SSRs) and nine new EST-SSR markers, to correctly and thoroughly identify all genotypes, verify their representativeness of the entire cultivated olive variation, and validate the effectiveness of new markers in comparison to standard genotyping tools. The SSR analysis revealed the presence of 59 genotypes, corresponding to 72 well known cultivars, 13 of them resulting exclusively present in this collection. The new EST-SSRs have shown values of diversity parameters quite similar to those of best standard SSRs. When compared to hundreds of Mediterranean cultivars, the UNIPG olive accessions were splitted into the three main populations (East, Center and West Mediterranean), confirming that the collection has a good representativeness of the entire olive variability. Furthermore, Bayesian analysis, performed on the 59 genotypes of the collection by the use of both sets of markers, have demonstrated their splitting into four clusters, with a well balanced membership obtained by EST respect to standard SSRs. The new OLEST ( Olea expressed sequence tags) SSR markers resulted as effective as the best standard markers. The information obtained from this study represents a high valuable tool for ex situ conservation and management of olive genetic resources, useful to build a common database from worldwide olive cultivar collections

  16. Porcine UCHL1: genomic organization, chromosome localization and expression analysis

    DEFF Research Database (Denmark)

    Larsen, Knud; Madsen, Lone Bruhn; Bendixen, Christian

    2012-01-01

    to and protection from Parkinson’s disease. Here we report cloning, characterization, expression analysis and mapping of porcine UCHL1. The UCHL1 cDNA was amplified by reverse transcriptase polymerase chain reaction (RT-PCR) using oligonucleotide primers derived from in silico sequences. The porcine cDNA codes...... in developing porcine embryos. UCHL1 transcript was detected as early as 40 days of gestation. A significant decrease in UCHL1 transcript was detected in basal ganglia from day 60 to day 115 of gestation...

  17. Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia

    Directory of Open Access Journals (Sweden)

    Borlawsky Tara B

    2010-10-01

    Full Text Available Abstract Background Chronic lymphocytic leukemia (CLL is the most common adult leukemia. It is a highly heterogeneous disease, and can be divided roughly into indolent and progressive stages based on classic clinical markers. Immunoglobin heavy chain variable region (IgVH mutational status was found to be associated with patient survival outcome, and biomarkers linked to the IgVH status has been a focus in the CLL prognosis research field. However, biomarkers highly correlated with IgVH mutational status which can accurately predict the survival outcome are yet to be discovered. Results In this paper, we investigate the use of gene co-expression network analysis to identify potential biomarkers for CLL. Specifically we focused on the co-expression network involving ZAP70, a well characterized biomarker for CLL. We selected 23 microarray datasets corresponding to multiple types of cancer from the Gene Expression Omnibus (GEO and used the frequent network mining algorithm CODENSE to identify highly connected gene co-expression networks spanning the entire genome, then evaluated the genes in the co-expression network in which ZAP70 is involved. We then applied a set of feature selection methods to further select genes which are capable of predicting IgVH mutation status from the ZAP70 co-expression network. Conclusions We have identified a set of genes that are potential CLL prognostic biomarkers IL2RB, CD8A, CD247, LAG3 and KLRK1, which can predict CLL patient IgVH mutational status with high accuracies. Their prognostic capabilities were cross-validated by applying these biomarker candidates to classify patients into different outcome groups using a CLL microarray datasets with clinical information.

  18. Expression and Interaction Analysis among Saffron ALDHs and Crocetin Dialdehyde

    Directory of Open Access Journals (Sweden)

    Lourdes Gómez-Gómez

    2018-05-01

    Full Text Available In saffron, the cleavage of zeaxanthin by means of CCD2 generates crocetin dialdehyde, which is then converted by an unknown aldehyde dehydrogenase to crocetin. A proteome from saffron stigma was released recently and, based on the expression pattern and correlation analyses, five aldehyde dehydrogenases (ALDHs were suggested as possible candidates to generate crocetin from crocetin dialdehydes. We selected four of the suggested ALDHs and analyzed their expression in different tissues, determined their activity over crocetin dialdehyde, and performed structure modeling and docking calculation to find their specificity. All the ALDHs were able to convert crocetin dialdehyde to crocetin, but two of them were stigma tissue-specific. Structure modeling and docking analyses revealed that, in all cases, there was a high coverage of residues in the models. All of them showed a very close conformation, indicated by the low root-mean-square deviation (RMSD values of backbone atoms, which indicate a high similarity among them. However, low affinity between the enzymes and the crocetin dialdehyde were observed. Phylogenetic analysis and binding affinities calculations, including some ALDHs from Gardenia jasmonoides, Crocus sieberi, and Buddleja species that accumulate crocetin and Bixa orellana synthetizing the apocarotenoid bixin selected on their expression pattern matching with the accumulation of either crocins or bixin, pointed out that family 2 C4 members might be involved in the conversion of crocetin dialdehyde to crocetin with high specificity.

  19. 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.

  20. Prognostic value of stromal decorin expression in patients with breast cancer: a meta-analysis.

    Science.gov (United States)

    Li, Shuang-Jiang; Chen, Da-Li; Zhang, Wen-Biao; Shen, Cheng; Che, Guo-Wei

    2015-11-01

    Numbers of studies have investigated the biological functions of decorin (DCN) in oncogenesis, tumor progression, angiogenesis and metastasis. Although many of them aim to highlight the prognostic value of stromal DCN expression in breast cancer, some controversial results still exist and a consensus has not been reached until now. Therefore, our meta-analysis aims to determine the prognostic significance of stromal DCN expression in breast cancer patients. PubMed, EMBASE, the Web of Science and China National Knowledge Infrastructure (CNKI) databases were searched for full-text literatures met out inclusion criteria. We applied the hazard ratio (HR) with 95% confidence interval (CI) as the appropriate summarized statistics. Q-test and I(2) statistic were employed to estimate the level of heterogeneity across the included studies. Sensitivity analysis was conducted to further identify the possible origins of heterogeneity. The publication bias was detected by Begg's test and Egger's test. There were three English literatures (involving 6 studies) included into our meta-analysis. On the one hand, both the summarized outcomes based on univariate analysis (HR: 0.513; 95% CI: 0.406-0.648; Panalysis (HR: 0.544; 95% CI: 0.388-0.763; Panalysis (HR: 0.504; 95% CI: 0.389-0.651; Panalysis (HR: 0.568; 95% CI: 0.400-0.806; P=0.002) also indicated that stromal DCN expression was positively associated with high disease-free survival (DFS) of breast cancer patients. No significant heterogeneity or publication bias was observed within this meta-analysis. The present evidences indicate that high stromal DCN expression can significantly predict the good prognosis in patients with breast cancer. The discoveries from our meta-analysis have better be confirmed in the updated review pooling more relevant investigations in the future.

  1. Digital gene expression analysis of corky split vein caused by boron deficiency in 'Newhall' Navel Orange (Citrus sinensis Osbeck for selecting differentially expressed genes related to vascular hypertrophy.

    Directory of Open Access Journals (Sweden)

    Cheng-Quan Yang

    Full Text Available Corky split vein caused by boron (B deficiency in 'Newhall' Navel Orange was studied in the present research. The boron-deficient citrus exhibited a symptom of corky split vein in mature leaves. Morphologic and anatomical surveys at four representative phases of corky split veins showed that the symptom was the result of vascular hypertrophy. Digital gene expression (DGE analysis was performed based on the Illumina HiSeq™ 2000 platform, which was applied to analyze the gene expression profilings of corky split veins at four morphologic phases. Over 5.3 million clean reads per library were successfully mapped to the reference database and more than 22897 mapped genes per library were simultaneously obtained. Analysis of the differentially expressed genes (DEGs revealed that the expressions of genes associated with cytokinin signal transduction, cell division, vascular development, lignin biosynthesis and photosynthesis in corky split veins were all affected. The expressions of WOL and ARR12 involved in the cytokinin signal transduction pathway were up-regulated at 1(st phase of corky split vein development. Furthermore, the expressions of some cell cycle genes, CYCs and CDKB, and vascular development genes, WOX4 and VND7, were up-regulated at the following 2(nd and 3(rd phases. These findings indicated that the cytokinin signal transduction pathway may play a role in initiating symptom observed in our study.

  2. Comprehensive evaluation of gene expression signatures in response to electroacupuncture stimulation at Zusanli (ST36) acupoint by transcriptomic analysis.

    Science.gov (United States)

    Wu, Jing-Shan; Lo, Hsin-Yi; Li, Chia-Cheng; Chen, Feng-Yuan; Hsiang, Chien-Yun; Ho, Tin-Yun

    2017-08-15

    Electroacupuncture (EA) has been applied to treat and prevent diseases for years. However, molecular events happened in both the acupunctured site and the internal organs after EA stimulation have not been clarified. Here we applied transcriptomic analysis to explore the gene expression signatures after EA stimulation. Mice were applied EA stimulation at ST36 for 15 min and nine tissues were collected three hours later for microarray analysis. We found that EA affected the expression of genes not only in the acupunctured site but also in the internal organs. EA commonly affected biological networks involved in cytoskeleton and cell adhesion, and also regulated unique process networks in specific organs, such as γ-aminobutyric acid-ergic neurotransmission in brain and inflammation process in lung. In addition, EA affected the expression of genes related to various diseases, such as neurodegenerative diseases in brain and obstructive pulmonary diseases in lung. This report applied, for the first time, a global comprehensive genome-wide approach to analyze the gene expression profiling of acupunctured site and internal organs after EA stimulation. The connection between gene expression signatures, biological processes, and diseases might provide a basis for prediction and explanation on the therapeutic potentials of acupuncture in organs.

  3. Exploring Peer Relationships, Friendships and Group Work Dynamics in Higher Education: Applying Social Network Analysis

    Science.gov (United States)

    Mamas, Christoforos

    2018-01-01

    This study primarily applied social network analysis (SNA) to explore the relationship between friendships, peer social interactions and group work dynamics within a higher education undergraduate programme in England. A critical case study design was adopted so as to allow for an in-depth exploration of the students' voice. In doing so, the views…

  4. Conversation after Right Hemisphere Brain Damage: Motivations for Applying Conversation Analysis

    Science.gov (United States)

    Barnes, Scott; Armstrong, Elizabeth

    2010-01-01

    Despite the well documented pragmatic deficits that can arise subsequent to Right Hemisphere Brain Damage (RHBD), few researchers have directly studied everyday conversations involving people with RHBD. In recent years, researchers have begun applying Conversation Analysis (CA) to the everyday talk of people with aphasia. This research programme…

  5. Evolution of Applied Behavior Analysis in the Treatment of Individuals With Autism

    Science.gov (United States)

    Wolery, Mark; Barton, Erin E.; Hine, Jeffrey F.

    2005-01-01

    Two issues of each volume of the Journal of Applied Behavior Analysis were reviewed to identify research reports focusing on individuals with autism. The identified articles were analyzed to describe the ages of individuals with autism, the settings in which the research occurred, the nature of the behaviors targeted for intervention, and the…

  6. Lovaas Model of Applied Behavior Analysis. What Works Clearinghouse Intervention Report

    Science.gov (United States)

    What Works Clearinghouse, 2010

    2010-01-01

    The "Lovaas Model of Applied Behavior Analysis" is a type of behavioral therapy that initially focuses on discrete trials: brief periods of one-on-one instruction, during which a teacher cues a behavior, prompts the appropriate response, and provides reinforcement to the child. Children in the program receive an average of 35 to 40 hours…

  7. Applied Behavior Analysis Programs for Autism: Sibling Psychosocial Adjustment during and Following Intervention Use

    Science.gov (United States)

    Cebula, Katie R.

    2012-01-01

    Psychosocial adjustment in siblings of children with autism whose families were using a home-based, applied behavior analysis (ABA) program was compared to that of siblings in families who were not using any intensive autism intervention. Data gathered from parents, siblings and teachers indicated that siblings in ABA families experienced neither…

  8. Applied Behavior Analysis in Autism Spectrum Disorders: Recent Developments, Strengths, and Pitfalls

    Science.gov (United States)

    Matson, Johnny L.; Turygin, Nicole C.; Beighley, Jennifer; Rieske, Robert; Tureck, Kimberly; Matson, Michael L.

    2012-01-01

    Autism has become one of the most heavily researched topics in the field of mental health and education. While genetics has been the most studied of all topics, applied behavior analysis (ABA) has also received a great deal of attention, and has arguably yielded the most promising results of any research area to date. The current paper provides a…

  9. A Self-Administered Parent Training Program Based upon the Principles of Applied Behavior Analysis

    Science.gov (United States)

    Maguire, Heather M.

    2012-01-01

    Parents often respond to challenging behavior exhibited by their children in such a way that unintentionally strengthens it. Applied behavior analysis (ABA) is a research-based science that has been proven effective in remediating challenging behavior in children. Although many parents could benefit from using strategies from the field of ABA with…

  10. A National UK Census of Applied Behavior Analysis School Provision for Children with Autism

    Science.gov (United States)

    Griffith, G. M.; Fletcher, R.; Hastings, R. P.

    2012-01-01

    Over more than a decade, specialist Applied Behavior Analysis (ABA) schools or classes for children with autism have developed in the UK and Ireland. However, very little is known internationally about how ABA is defined in practice in school settings, the characteristics of children supported in ABA school settings, and the staffing structures…

  11. A Case Study in the Misrepresentation of Applied Behavior Analysis in Autism: The Gernsbacher Lectures

    Science.gov (United States)

    Morris, Edward K

    2009-01-01

    I know that most men, including those at ease with problems of the greatest complexity, can seldom accept the simplest and most obvious truth if it be such as would oblige them to admit the falsity of conclusions which they have proudly taught to others, and which they have woven, thread by thread, into the fabrics of their life. (Tolstoy, 1894) This article presents a case study in the misrepresentation of applied behavior analysis for autism based on Morton Ann Gernsbacher's presentation of a lecture titled “The Science of Autism: Beyond the Myths and Misconceptions.” Her misrepresentations involve the characterization of applied behavior analysis, descriptions of practice guidelines, reviews of the treatment literature, presentations of the clinical trials research, and conclusions about those trials (e.g., children's improvements are due to development, not applied behavior analysis). The article also reviews applied behavior analysis' professional endorsements and research support, and addresses issues in professional conduct. It ends by noting the deleterious effects that misrepresenting any research on autism (e.g., biological, developmental, behavioral) have on our understanding and treating it in a transdisciplinary context. PMID:22478522

  12. Gene expression analysis to identify molecular correlates of pre- and post-conditioning derived neuroprotection.

    Science.gov (United States)

    Prasad, Shiv S; Russell, Marsha; Nowakowska, Margeryta; Williams, Andrew; Yauk, Carole

    2012-06-01

    Mild ischaemic exposures before or after severe injurious ischaemia that elicit neuroprotective responses are referred to as preconditioning and post-conditioning. The corresponding molecular mechanisms of neuroprotection are not completely understood. Identification of the genes and associated pathways of corresponding neuroprotection would provide insight into neuronal survival, potential therapeutic approaches and assessments of therapies for stroke. The objectives of this study were to use global gene expression approach to infer the molecular mechanisms in pre- and post-conditioning-derived neuroprotection in cortical neurons following oxygen and glucose deprivation (OGD) in vitro and then to apply these findings to predict corresponding functional pathways. To this end, microarray analysis was applied to rat cortical neurons with or without the pre- and post-conditioning treatments at 3-h post-reperfusion, and differentially expressed transcripts were subjected to statistical, hierarchical clustering and pathway analyses. The expression patterns of 3,431 genes altered under all conditions of ischaemia (with and without pre- or post-conditioning). We identified 1,595 genes that were commonly regulated within both the pre- and post-conditioning treatments. Cluster analysis revealed that transcription profiles clustered tightly within controls, non-conditioned OGD and neuroprotected groups. Two clusters defining neuroprotective conditions associated with up- and downregulated genes were evident. The five most upregulated genes within the neuroprotective clusters were Tagln, Nes, Ptrf, Vim and Adamts9, and the five most downregulated genes were Slc7a3, Bex1, Brunol4, Nrxn3 and Cpne4. Pathway analysis revealed that the intracellular and second messenger signalling pathways in addition to cell death were predominantly associated with downregulated pre- and post-conditioning associated genes, suggesting that modulation of cell death and signal transduction pathways

  13. Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes

    Science.gov (United States)

    Johnstone, Daniel M.; Riveros, Carlos; Heidari, Moones; Graham, Ross M.; Trinder, Debbie; Berretta, Regina; Olynyk, John K.; Scott, Rodney J.; Moscato, Pablo; Milward, Elizabeth A.

    2013-01-01

    While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation—if not adequately minimized by effective normalization—may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes. PMID:27605185

  14. Comparative expression pathway analysis of human and canine mammary tumors

    Directory of Open Access Journals (Sweden)

    Marconato Laura

    2009-03-01

    Full Text Available Abstract Background Spontaneous tumors in dog have been demonstrated to share many features with their human counterparts, including relevant molecular targets, histological appearance, genetics, biological behavior and response to conventional treatments. Mammary tumors in dog therefore provide an attractive alternative to more classical mouse models, such as transgenics or xenografts, where the tumour is artificially induced. To assess the extent to which dog tumors represent clinically significant human phenotypes, we performed the first genome-wide comparative analysis of transcriptional changes occurring in mammary tumors of the two species, with particular focus on the molecular pathways involved. Results We analyzed human and dog gene expression data derived from both tumor and normal mammary samples. By analyzing the expression levels of about ten thousand dog/human orthologous genes we observed a significant overlap of genes deregulated in the mammary tumor samples, as compared to their normal counterparts. Pathway analysis of gene expression data revealed a great degree of similarity in the perturbation of many cancer-related pathways, including the 'PI3K/AKT', 'KRAS', 'PTEN', 'WNT-beta catenin' and 'MAPK cascade'. Moreover, we show that the transcriptional relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Conclusion Our data confirm and further strengthen the value of the canine mammary cancer model and open up new perspectives for the evaluation of novel cancer therapeutics and the development of prognostic and diagnostic biomarkers to be used in clinical studies.

  15. 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

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

    Directory of Open Access Journals (Sweden)

    Eils Roland

    2005-11-01

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

  17. The practical problems of applying cost-effectiveness analysis to joint finance programmes

    OpenAIRE

    Karen Gerard; Ken Wright

    1990-01-01

    Joint finance is money allocated by the Department of Health to NHS authorities to promote policies of inter-agency collaboration which prevent people being admitted to hospital or facilitate earlier discharge from hospital or save on NHS resources generally. Worries have been expressed that joint finance has not been used as effectively or efficiency as it might have been. This paper is concerned with the practical application of cost-effectiveness analysis to policies or schemes which typic...

  18. Preliminary Hazard Analysis applied to Uranium Hexafluoride - UF6 production plant

    International Nuclear Information System (INIS)

    Tomzhinsky, David; Bichmacher, Ricardo; Braganca Junior, Alvaro; Peixoto, Orpet Jose

    1996-01-01

    The purpose of this paper is to present the results of the Preliminary hazard Analysis applied to the UF 6 Production Process, which is part of the UF 6 Conversion Plant. The Conversion Plant has designed to produce a high purified UF 6 in accordance with the nuclear grade standards. This Preliminary Hazard Analysis is the first step in the Risk Management Studies, which are under current development. The analysis evaluated the impact originated from the production process in the plant operators, members of public, equipment, systems and installations as well as the environment. (author)

  19. Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer

    International Nuclear Information System (INIS)

    Thomassen, Mads; Tan, Qihua; Kruse, Torben A

    2008-01-01

    Metastasis is believed to progress in several steps including different pathways but the determination and understanding of these mechanisms is still fragmentary. Microarray analysis of gene expression patterns in breast tumors has been used to predict outcome in recent studies. Besides classification of outcome, these global expression patterns may reflect biological mechanisms involved in metastasis of breast cancer. Our purpose has been to investigate pathways and transcription factors involved in metastasis by use of gene expression data sets. We have analyzed 8 publicly available gene expression data sets. A global approach, 'gene set enrichment analysis' as well as an approach focusing on a subset of significantly differently regulated genes, GenMAPP, has been applied to rank pathway gene sets according to differential regulation in metastasizing tumors compared to non-metastasizing tumors. Meta-analysis has been used to determine overrepresentation of pathways and transcription factors targets, concordant deregulated in metastasizing breast tumors, in several data sets. The major findings are up-regulation of cell cycle pathways and a metabolic shift towards glucose metabolism reflected in several pathways in metastasizing tumors. Growth factor pathways seem to play dual roles; EGF and PDGF pathways are decreased, while VEGF and sex-hormone pathways are increased in tumors that metastasize. Furthermore, migration, proteasome, immune system, angiogenesis, DNA repair and several signal transduction pathways are associated to metastasis. Finally several transcription factors e.g. E2F, NFY, and YY1 are identified as being involved in metastasis. By pathway meta-analysis many biological mechanisms beyond major characteristics such as proliferation are identified. Transcription factor analysis identifies a number of key factors that support central pathways. Several previously proposed treatment targets are identified and several new pathways that may

  20. Analysis of Gene Expression Variance in Schizophrenia Using Structural Equation Modeling

    Directory of Open Access Journals (Sweden)

    Anna A. Igolkina

    2018-06-01

    Full Text Available Schizophrenia (SCZ is a psychiatric disorder of unknown etiology. There is evidence suggesting that aberrations in neurodevelopment are a significant attribute of schizophrenia pathogenesis and progression. To identify biologically relevant molecular abnormalities affecting neurodevelopment in SCZ we used cultured neural progenitor cells derived from olfactory neuroepithelium (CNON cells. Here, we tested the hypothesis that variance in gene expression differs between individuals from SCZ and control groups. In CNON cells, variance in gene expression was significantly higher in SCZ samples in comparison with control samples. Variance in gene expression was enriched in five molecular pathways: serine biosynthesis, PI3K-Akt, MAPK, neurotrophin and focal adhesion. More than 14% of variance in disease status was explained within the logistic regression model (C-value = 0.70 by predictors accounting for gene expression in 69 genes from these five pathways. Structural equation modeling (SEM was applied to explore how the structure of these five pathways was altered between SCZ patients and controls. Four out of five pathways showed differences in the estimated relationships among genes: between KRAS and NF1, and KRAS and SOS1 in the MAPK pathway; between PSPH and SHMT2 in serine biosynthesis; between AKT3 and TSC2 in the PI3K-Akt signaling pathway; and between CRK and RAPGEF1 in the focal adhesion pathway. Our analysis provides evidence that variance in gene expression is an important characteristic of SCZ, and SEM is a promising method for uncovering altered relationships between specific genes thus suggesting affected gene regulation associated with the disease. We identified altered gene-gene interactions in pathways enriched for genes with increased variance in expression in SCZ. These pathways and loci were previously implicated in SCZ, providing further support for the hypothesis that gene expression variance plays important role in the etiology

  1. Research in progress in applied mathematics, numerical analysis, fluid mechanics, and computer science

    Science.gov (United States)

    1994-01-01

    This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period October 1, 1993 through March 31, 1994. The major categories of the current ICASE research program are: (1) applied and numerical mathematics, including numerical analysis and algorithm development; (2) theoretical and computational research in fluid mechanics in selected areas of interest to LaRC, including acoustics and combustion; (3) experimental research in transition and turbulence and aerodynamics involving LaRC facilities and scientists; and (4) computer science.

  2. Reliability analysis of reactor systems by applying probability method; Analiza pouzdanosti reaktorskih sistema primenom metoda verovatnoce

    Energy Technology Data Exchange (ETDEWEB)

    Milivojevic, S [Institute of Nuclear Sciences Boris Kidric, Vinca, Beograd (Serbia and Montenegro)

    1974-12-15

    Probability method was chosen for analysing the reactor system reliability is considered realistic since it is based on verified experimental data. In fact this is a statistical method. The probability method developed takes into account the probability distribution of permitted levels of relevant parameters and their particular influence on the reliability of the system as a whole. The proposed method is rather general, and was used for problem of thermal safety analysis of reactor system. This analysis enables to analyze basic properties of the system under different operation conditions, expressed in form of probability they show the reliability of the system on the whole as well as reliability of each component.

  3. Molecular cloning and expression analysis of annexin A2 gene in sika deer antler tip

    Directory of Open Access Journals (Sweden)

    Yanling Xia

    2018-04-01

    Full Text Available Objective Molecular cloning and bioinformatics analysis of annexin A2 (ANXA2 gene in sika deer antler tip were conducted. The role of ANXA2 gene in the growth and development of the antler were analyzed initially. Methods The reverse transcriptase polymerase chain reaction (RT-PCR was used to clone the cDNA sequence of the ANXA2 gene from antler tip of sika deer (Cervus Nippon hortulorum and the bioinformatics methods were applied to analyze the amino acid sequence of Anxa2 protein. The mRNA expression levels of the ANXA2 gene in different growth stages were examined by real time reverse transcriptase polymerase chain reaction (real time RT-PCR. Results The nucleotide sequence analysis revealed an open reading frame of 1,020 bp encoding 339 amino acids long protein of calculated molecular weight 38.6 kDa and isoelectric point 6.09. Homologous sequence alignment and phylogenetic analysis indicated that the Anxa2 mature protein of sika deer had the closest genetic distance with Cervus elaphus and Bos mutus. Real time RT-PCR results showed that the gene had differential expression levels in different growth stages, and the expression level of the ANXA2 gene was the highest at metaphase (rapid growing period. Conclusion ANXA2 gene may promote the cell proliferation, and the finding suggested Anxa2 as an important candidate for regulating the growth and development of deer antler.

  4. National youth sedentary behavior and physical activity daily patterns using latent class analysis applied to accelerometry.

    Science.gov (United States)

    Evenson, Kelly R; Wen, Fang; Hales, Derek; Herring, Amy H

    2016-05-03

    Applying latent class analysis (LCA) to accelerometry can help elucidated underlying patterns. This study described the patterns of accelerometer-determined sedentary behavior and physical activity among youth by applying LCA to a nationally representative United States (US) sample. Using 2003-2006 National Health and Nutrition Examination Survey data, 3998 youths 6-17 years wore an ActiGraph 7164 accelerometer for one week, providing > =3 days of wear for > =8 h/day from 6:00 am-midnight. Cutpoints defined sedentary behavior ( = 2296 counts/minute), and vigorous activity (> = 4012 counts/minute). To account for wear time differences, outcomes were expressed as percent of day in a given intensity. LCA was used to classify daily (Monday through Sunday) patterns of average counts/minute, sedentary behavior, light activity, MVPA, and vigorous activity separately. The latent classes were explored overall and by age (6-11, 12-14, 15-17 years), gender, and whether or not youth attended school during measurement. Estimates were weighted to account for the sampling frame. For average counts/minute/day, four classes emerged from least to most active: 40.9% of population (mean 323.5 counts/minute/day), 40.3% (559.6 counts/minute/day), 16.5% (810.0 counts/minute/day), and 2.3% (1132.9 counts/minute/day). For percent of sedentary behavior, four classes emerged: 13.5% of population (mean 544.6 min/day), 30.1% (455.1 min/day), 38.5% (357.7 min/day), and 18.0% (259.2 min/day). For percent of light activity, four classes emerged: 12.3% of population (mean 222.6 min/day), 29.3% (301.7 min/day), 41.8% (384.0 min/day), and 16.6% (455.5 min/day). For percent of MVPA, four classes emerged: 59.9% of population (mean 25.0 min/day), 33.3% (60.9 min/day), 3.1% (89.0 min/day), and 3.6% (109.3 min/day). For percent of vigorous activity, three classes emerged: 76.8% of population (mean 7.1 min/day), 18.5% (23.9 min/day), and 4.7% (47.4 min/day). Classes were developed by age

  5. A Study in the Founding of Applied Behavior Analysis Through Its Publications

    Science.gov (United States)

    Morris, Edward K.; Altus, Deborah E.; Smith, Nathaniel G.

    2013-01-01

    This article reports a study of the founding of applied behavior analysis through its publications. Our methods included hand searches of sources (e.g., journals, reference lists), search terms (i.e., early, applied, behavioral, research, literature), inclusion criteria (e.g., the field's applied dimension), and (d) challenges to their face and content validity. Our results were 36 articles published between 1959 and 1967 that we organized into 4 groups: 12 in 3 programs of research and 24 others. Our discussion addresses (a) limitations in our method (e.g., the completeness of our search), (b) challenges to the validity of our methods and results (e.g., convergent validity), and (c) priority claims about the field's founding. We conclude that the claims are irresolvable because identification of the founding publications depends significantly on methods and because the field's founding was an evolutionary process. We close with suggestions for future research. PMID:25729133

  6. [Statistical analysis of articles in "Chinese journal of applied physiology" from 1999 to 2008].

    Science.gov (United States)

    Du, Fei; Fang, Tao; Ge, Xue-ming; Jin, Peng; Zhang, Xiao-hong; Sun, Jin-li

    2010-05-01

    To evaluate the academic level and influence of "Chinese Journal of Applied Physiology" through statistical analysis for the fund sponsored articles published in the recent ten years. The articles of "Chinese Journal of Applied Physiology" from 1999 to 2008 were investigated. The number and the percentage of the fund sponsored articles, the fund organization and the author region were quantitatively analyzed by using the literature metrology method. The number of the fund sponsored articles increased unceasingly. The ratio of the fund from local government significantly enhanced in the latter five years. Most of the articles were from institutes located at Beijing, Zhejiang and Tianjin. "Chinese Journal of Applied Physiology" has a fine academic level and social influence.

  7. A study in the founding of applied behavior analysis through its publications.

    Science.gov (United States)

    Morris, Edward K; Altus, Deborah E; Smith, Nathaniel G

    2013-01-01

    This article reports a study of the founding of applied behavior analysis through its publications. Our methods included hand searches of sources (e.g., journals, reference lists), search terms (i.e., early, applied, behavioral, research, literature), inclusion criteria (e.g., the field's applied dimension), and (d) challenges to their face and content validity. Our results were 36 articles published between 1959 and 1967 that we organized into 4 groups: 12 in 3 programs of research and 24 others. Our discussion addresses (a) limitations in our method (e.g., the completeness of our search), (b) challenges to the validity of our methods and results (e.g., convergent validity), and (c) priority claims about the field's founding. We conclude that the claims are irresolvable because identification of the founding publications depends significantly on methods and because the field's founding was an evolutionary process. We close with suggestions for future research.

  8. Mathematical adventures in performance analysis from storage systems, through airplane boarding, to express line queues

    CERN Document Server

    Bachmat, Eitan

    2014-01-01

    This monograph describes problems in the field of performance analysis, primarily the study of storage systems and the diverse mathematical techniques that are required for solving such problems. Topics covered include best practices for scheduling I/O requests to a disk drive, how this problem is related to airplane boarding, and how both problems can be modeled using space-time geometry. The author also explains how Riemann's proof of the analytic continuation and functional equation of the Riemann zeta function can be used to analyze express-line queues in a minimarket. Overall, the book reveals the surprising applicability of abstract mathematical ideas that are not usually associated with applied topics. Advanced undergraduate students or graduate students with an interest in the applications of mathematics will find this book a useful resource. It will also be of interest to professional mathematicians who want exposure to the surprising ways that theoretical mathematics may be applied to engineering pr...

  9. Expression analysis of a ''Cucurbita'' cDNA encoding endonuclease

    International Nuclear Information System (INIS)

    Szopa, J.

    1995-01-01

    The nuclear matrices of plant cell nuclei display intrinsic nuclease activity which consists in nicking supercoiled DNA. A cDNA encoding a 32 kDa endonuclease has been cloned and sequenced. The nucleotide and deduced amino-acid sequences show high homology to known 14-3-3-protein sequences from other sources. The amino-acid sequence shows agreement with consensus sequences for potential phosphorylation by protein kinase A and C and for calcium, lipid and membrane-binding sites. The nucleotide-binding site is also present within the conserved part of the sequence. By Northern blot analysis, the differential expression of the corresponding mRNA was detected; it was the strongest in sink tissues. The endonuclease activity found on DNA-polyacrylamide gel electrophoresis coincided with mRNA content and was the highest in tuber. (author). 22 refs, 6 figs

  10. Computational analysis and functional expression of ancestral copepod luciferase.

    Science.gov (United States)

    Takenaka, Yasuhiro; Noda-Ogura, Akiko; Imanishi, Tadashi; Yamaguchi, Atsushi; Gojobori, Takashi; Shigeri, Yasushi

    2013-10-10

    We recently reported the cDNA sequences of 11 copepod luciferases from the superfamily Augaptiloidea in the order Calanoida. They were classified into two groups, Metridinidae and Heterorhabdidae/Lucicutiidae families, by phylogenetic analyses. To elucidate the evolutionary processes, we have now further isolated 12 copepod luciferases from Augaptiloidea species (Metridia asymmetrica, Metridia curticauda, Pleuromamma scutullata, Pleuromamma xiphias, Lucicutia ovaliformis and Heterorhabdus tanneri). Codon-based synonymous/nonsynonymous tests of positive selection for 25 identified copepod luciferases suggested that positive Darwinian selection operated in the evolution of Heterorhabdidae luciferases, whereas two types of Metridinidae luciferases had diversified via neutral mechanism. By in silico analysis of the decoded amino acid sequences of 25 copepod luciferases, we inferred two protein sequences as ancestral copepod luciferases. They were expressed in HEK293 cells where they exhibited notable luciferase activity both in intracellular lysates and cultured media, indicating that the luciferase activity was established before evolutionary diversification of these copepod species. © 2013.

  11. Reliability analysis of protection systems in NPP applying fault-tree analysis method

    International Nuclear Information System (INIS)

    Bokor, J.; Gaspar, P.; Hetthessy, J.; Szabo, G.

    1998-01-01

    This paper demonstrates the applicability and limits of dependability analysis in nuclear power plants (NPPS) based on the reactor protection refurbishment project (RRP) in NPP Paks. This paper illustrates case studies from the reliability analysis for NPP Paks. It also investigates the solutions for the connection between the data acquisition and subsystem control units (TSs) and the voter units (VTs), it analyzes the influence of the voting in the VT computer level, it studies the effects of the testing procedures to the dependability parameters. (author)

  12. Applying behavior analysis to school violence and discipline problems: Schoolwide positive behavior support

    Science.gov (United States)

    Anderson, Cynthia M.; Kincaid, Donald

    2005-01-01

    School discipline is a growing concern in the United States. Educators frequently are faced with discipline problems ranging from infrequent but extreme problems (e.g., shootings) to less severe problems that occur at high frequency (e.g., bullying, insubordination, tardiness, and fighting). Unfortunately, teachers report feeling ill prepared to deal effectively with discipline problems in schools. Further, research suggests that many commonly used strategies, such as suspension, expulsion, and other reactive strategies, are not effective for ameliorating discipline problems and may, in fact, make the situation worse. The principles and technology of behavior analysis have been demonstrated to be extremely effective for decreasing problem behavior and increasing social skills exhibited by school children. Recently, these principles and techniques have been applied at the level of the entire school, in a movement termed schoolwide positive behavior support. In this paper we review the tenets of schoolwide positive behavior support, demonstrating the relation between this technology and applied behavior analysis. PMID:22478439

  13. Common cause evaluations in applied risk analysis of nuclear power plants

    International Nuclear Information System (INIS)

    Taniguchi, T.; Ligon, D.; Stamatelatos, M.

    1983-04-01

    Qualitative and quantitative approaches were developed for the evaluation of common cause failures (CCFs) in nuclear power plants and were applied to the analysis of the auxiliary feedwater systems of several pressurized water reactors (PWRs). Key CCF variables were identified through a survey of experts in the field and a review of failure experience in operating PWRs. These variables were classified into categories of high, medium, and low defense against a CCF. Based on the results, a checklist was developed for analyzing CCFs of systems. Several known techniques for quantifying CCFs were also reviewed. The information provided valuable insights in the development of a new model for estimating CCF probabilities, which is an extension of and improvement over the Beta Factor method. As applied to the analysis of the PWR auxiliary feedwater systems, the method yielded much more realistic values than the original Beta Factor method for a one-out-of-three system

  14. Residual analysis applied to S-N data of a surface rolled cast iron

    Directory of Open Access Journals (Sweden)

    Omar Maluf

    2005-09-01

    Full Text Available Surface rolling is a process extensively employed in the manufacture of ductile cast iron crankshafts, specifically in regions containing stress concentrators with the main aim to enhance fatigue strength. Such process hardens and introduces compressive residual stresses to the surface as a result of controlled strains, reducing cyclic tensile stresses near the surface of the part. The main purpose of this work was to apply the residual analysis to check the suitability of the S-N approach to describe the fatigue properties of a surface rolled cast iron. The analysis procedure proved to be very efficient and easy to implement and it can be applied in the verification of any other statistical model used to describe fatigue behavior. Results show that the conventional S-N methodology is able to model the high cycle fatigue behavior of surface rolled notch testpieces of a pearlitic ductile cast iron submitted to rotating bending fatigue tests.

  15. 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.

  16. Genome-wide expression analysis of salt-stressed diploid and autotetraploid Paulownia tomentosa.

    Directory of Open Access Journals (Sweden)

    Zhenli Zhao

    Full Text Available Paulownia tomentosa is a fast-growing tree species with multiple uses. It is grown worldwide, but is native to China, where it is widely cultivated in saline regions. We previously confirmed that autotetraploid P. tomentosa plants are more stress-tolerant than the diploid plants. However, the molecular mechanism underlying P. tomentosa salinity tolerance has not been fully characterized. Using the complete Paulownia fortunei genome as a reference, we applied next-generation RNA-sequencing technology to analyze the effects of salt stress on diploid and autotetraploid P. tomentosa plants. We generated 175 million clean reads and identified 15,873 differentially expressed genes (DEGs from four P. tomentosa libraries (two diploid and two autotetraploid. Functional annotations of the differentially expressed genes using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases revealed that plant hormone signal transduction and photosynthetic activities are vital for plant responses to high-salt conditions. We also identified several transcription factors, including members of the AP2/EREBP, bHLH, MYB, and NAC families. Quantitative real-time PCR analysis validated the expression patterns of eight differentially expressed genes. Our findings and the generated transcriptome data may help to accelerate the genetic improvement of cultivated P. tomentosa and other plant species for enhanced growth in saline soils.

  17. Applying circular economy innovation theory in business process modeling and analysis

    Science.gov (United States)

    Popa, V.; Popa, L.

    2017-08-01

    The overall aim of this paper is to develop a new conceptual framework for business process modeling and analysis using circular economy innovative theory as a source for business knowledge management. The last part of the paper presents an author’s proposed basic structure for a new business models applying circular economy innovation theories. For people working on new innovative business models in the field of the circular economy this paper provides new ideas for clustering their concepts.

  18. Applied behavior analysis as intervention for autism: definition, features and philosophical concepts

    Directory of Open Access Journals (Sweden)

    Síglia Pimentel Höher Camargo

    2013-11-01

    Full Text Available Autism spectrum disorder (ASD is a lifelong pervasive developmental disorder with no known causes and cure. However, educational and behavioral interventions with a foundation in applied behavior analysis (ABA have been shown to improve a variety of skill areas such as communication, social, academic, and adaptive behaviors of individuals with ASD. The goal of this work is to present the definition, features and philosophical concepts that underlie ABA and make this science an effective intervention method for people with autism.

  19. Assimilation of tourism satellite accounts and applied general equilibrium models to inform tourism policy analysis

    OpenAIRE

    Rossouw, Riaan; Saayman, Melville

    2011-01-01

    Historically, tourism policy analysis in South Africa has posed challenges to accurate measurement. The primary reason for this is that tourism is not designated as an 'industry' in standard economic accounts. This paper therefore demonstrates the relevance and need for applied general equilibrium (AGE) models to be completed and extended through an integration with tourism satellite accounts (TSAs) as a tool for policy makers (especially tourism policy makers) in South Africa. The paper sets...

  20. Classical linear-control analysis applied to business-cycle dynamics and stability

    Science.gov (United States)

    Wingrove, R. C.

    1983-01-01

    Linear control analysis is applied as an aid in understanding the fluctuations of business cycles in the past, and to examine monetary policies that might improve stabilization. The analysis shows how different policies change the frequency and damping of the economic system dynamics, and how they modify the amplitude of the fluctuations that are caused by random disturbances. Examples are used to show how policy feedbacks and policy lags can be incorporated, and how different monetary strategies for stabilization can be analytically compared. Representative numerical results are used to illustrate the main points.

  1. The Applied Behavior Analysis Research Paradigm and Single-Subject Designs in Adapted Physical Activity Research.

    Science.gov (United States)

    Haegele, Justin A; Hodge, Samuel Russell

    2015-10-01

    There are basic philosophical and paradigmatic assumptions that guide scholarly research endeavors, including the methods used and the types of questions asked. Through this article, kinesiology faculty and students with interests in adapted physical activity are encouraged to understand the basic assumptions of applied behavior analysis (ABA) methodology for conducting, analyzing, and presenting research of high quality in this paradigm. The purposes of this viewpoint paper are to present information fundamental to understanding the assumptions undergirding research methodology in ABA, describe key aspects of single-subject research designs, and discuss common research designs and data-analysis strategies used in single-subject studies.

  2. Improving skill development: an exploratory study comparing a philosophical and an applied ethical analysis technique

    Science.gov (United States)

    Al-Saggaf, Yeslam; Burmeister, Oliver K.

    2012-09-01

    This exploratory study compares and contrasts two types of critical thinking techniques; one is a philosophical and the other an applied ethical analysis technique. The two techniques analyse an ethically challenging situation involving ICT that a recent media article raised to demonstrate their ability to develop the ethical analysis skills of ICT students and professionals. In particular the skill development focused on includes: being able to recognise ethical challenges and formulate coherent responses; distancing oneself from subjective judgements; developing ethical literacy; identifying stakeholders; and communicating ethical decisions made, to name a few.

  3. On the use of the term 'frequency' in applied behavior analysis.

    Science.gov (United States)

    Carr, James E; Nosik, Melissa R; Luke, Molli M

    2018-04-01

    There exists a terminological problem in applied behavior analysis: the term frequency has been used as a synonym for both rate (the number of responses per time) and count (the number of responses). To guide decisions about the use and meaning of frequency, we surveyed the usage of frequency in contemporary behavior-analytic journals and textbooks and found that the predominant usage of frequency was as count, not rate. Thus, we encourage behavior analysts to use frequency as a synonym for count. © 2018 Society for the Experimental Analysis of Behavior.

  4. The x-rays fluorescence applied to the analysis of alloys

    International Nuclear Information System (INIS)

    Gutierrez, D.A.

    1997-01-01

    This work is based on the utilization of the Fluorescence of X Rays. This technique of non destructive trial, has the purpose to establish a routine method, for the control of the conformation of industrial samples used. It makes an analysis with a combination of the algorithms of Rasberry-Heinrich and Claisse-Thinh. Besides, the numerical implementation of non usual techniques in this type of analysis. Such as the Linear Programming applied to the solution of super determined systems, of equations and the utilization of methods of relaxation to facilitate the convergence to the solutions. (author) [es

  5. Fatigue Analysis of Tubesheet/Shell Juncture Applying the Mitigation Factor for Over-conservatism

    International Nuclear Information System (INIS)

    Kang, Deog Ji; Kim, Kyu Hyoung; Lee, Jae Gon

    2009-01-01

    If the environmental fatigue requirements are applied to the primary components of a nuclear power plant, to which the present ASME Code fatigue curves are applied, some locations with high level CUF (Cumulative Usage Factor) are anticipated not to meet the code criteria. The application of environmental fatigue damage is still particularly controversial for plants with 60-year design lives. Therefore, it is need to develop a detailed fatigue analysis procedure to identify the conservatisms in the procedure and to lower the cumulative usage factor. Several factors are being considered to mitigate the conservatism such as three-dimensional finite element modeling. In the present analysis, actual pressure transient data instead of conservative maximum and minimum pressure data was applied as one of mitigation factors. Unlike in the general method, individual transient events were considered instead of the grouped transient events. The tubesheet/shell juncture in the steam generator assembly is the one of the weak locations and was, therefore, selected as a target to evaluate the mitigation factor in the present analysis

  6. System Sensitivity Analysis Applied to the Conceptual Design of a Dual-Fuel Rocket SSTO

    Science.gov (United States)

    Olds, John R.

    1994-01-01

    This paper reports the results of initial efforts to apply the System Sensitivity Analysis (SSA) optimization method to the conceptual design of a single-stage-to-orbit (SSTO) launch vehicle. SSA is an efficient, calculus-based MDO technique for generating sensitivity derivatives in a highly multidisciplinary design environment. The method has been successfully applied to conceptual aircraft design and has been proven to have advantages over traditional direct optimization methods. The method is applied to the optimization of an advanced, piloted SSTO design similar to vehicles currently being analyzed by NASA as possible replacements for the Space Shuttle. Powered by a derivative of the Russian RD-701 rocket engine, the vehicle employs a combination of hydrocarbon, hydrogen, and oxygen propellants. Three primary disciplines are included in the design - propulsion, performance, and weights & sizing. A complete, converged vehicle analysis depends on the use of three standalone conceptual analysis computer codes. Efforts to minimize vehicle dry (empty) weight are reported in this paper. The problem consists of six system-level design variables and one system-level constraint. Using SSA in a 'manual' fashion to generate gradient information, six system-level iterations were performed from each of two different starting points. The results showed a good pattern of convergence for both starting points. A discussion of the advantages and disadvantages of the method, possible areas of improvement, and future work is included.

  7. Ongoing Analysis of Rocket Based Combined Cycle Engines by the Applied Fluid Dynamics Analysis Group at Marshall Space Flight Center

    Science.gov (United States)

    Ruf, Joseph; Holt, James B.; Canabal, Francisco

    1999-01-01

    This paper presents the status of analyses on three Rocket Based Combined Cycle configurations underway in the Applied Fluid Dynamics Analysis Group (TD64). TD64 is performing computational fluid dynamics analysis on a Penn State RBCC test rig, the proposed Draco axisymmetric RBCC engine and the Trailblazer engine. The intent of the analysis on the Penn State test rig is to benchmark the Finite Difference Navier Stokes code for ejector mode fluid dynamics. The Draco engine analysis is a trade study to determine the ejector mode performance as a function of three engine design variables. The Trailblazer analysis is to evaluate the nozzle performance in scramjet mode. Results to date of each analysis are presented.

  8. PRO-ELICERE: A Hazard Analysis Automation Process Applied to Space Systems

    Directory of Open Access Journals (Sweden)

    Tharcius Augusto Pivetta

    2016-07-01

    Full Text Available In the last decades, critical systems have increasingly been developed using computers and software even in space area, where the project approach is usually very conservative. In the projects of rockets, satellites and its facilities, like ground support systems, simulators, among other critical operations for the space mission, it must be applied a hazard analysis. The ELICERE process was created to perform a hazard analysis mainly over computer critical systems, in order to define or evaluate its safety and dependability requirements, strongly based on Hazards and Operability Study and Failure Mode and Effect Analysis techniques. It aims to improve the project design or understand the potential hazards of existing systems improving their functions related to functional or non-functional requirements. Then, the main goal of the ELICERE process is to ensure the safety and dependability goals of a space mission. The process, at the beginning, was created to operate manually in a gradual way. Nowadays, a software tool called PRO-ELICERE was developed, in such a way to facilitate the analysis process and store the results for reuse in another system analysis. To understand how ELICERE works and its tool, a small example of space study case was applied, based on a hypothetical rocket of the Cruzeiro do Sul family, developed by the Instituto de Aeronáutica e Espaço in Brazil.

  9. Sensitivity and uncertainty analysis applied to a repository in rock salt

    International Nuclear Information System (INIS)

    Polle, A.N.

    1996-12-01

    This document describes the sensitivity and uncertainty analysis with UNCSAM, as applied to a repository in rock salt for the EVEREST project. UNCSAM is a dedicated software package for sensitivity and uncertainty analysis, which was already used within the preceding PROSA project. The use of UNCSAM provides a flexible interface to EMOS ECN by substituting the sampled values in the various input files to be used by EMOS ECN ; the model calculations for this repository were performed with the EMOS ECN code. Preceding the sensitivity and uncertainty analysis, a number of preparations has been carried out to facilitate EMOS ECN with the probabilistic input data. For post-processing the EMOS ECN results, the characteristic output signals were processed. For the sensitivity and uncertainty analysis with UNCSAM the stochastic input, i.e. sampled values, and the output for the various EMOS ECN runs have been analyzed. (orig.)

  10. The evolution of applied harmonic analysis models of the real world

    CERN Document Server

    Prestini, Elena

    2016-01-01

    A sweeping exploration of the development and far-reaching applications of harmonic analysis such as signal processing, digital music, optics, radio astronomy, crystallography, medical imaging, spectroscopy, and more. Featuring a wealth of illustrations, examples, and material not found in other harmonic analysis books, this unique monograph skillfully blends together historical narrative with scientific exposition to create a comprehensive yet accessible work. While only an understanding of calculus is required to appreciate it, there are more technical sections that will charm even specialists in harmonic analysis. From undergraduates to professional scientists, engineers, and mathematicians, there is something for everyone here. The second edition of The Evolution of Applied Harmonic Analysis contains a new chapter on atmospheric physics and climate change, making it more relevant for today’s audience. Praise for the first edition: "…can be thoroughly recommended to any reader who is curious about the ...

  11. [Cloning and expressing of cyclophilin B gene from Schistosoma japonnicum and the analysis of immunoprotective effect].

    Science.gov (United States)

    Peng, Jinbiao; Han, Hongxiao; Hong, Yang; Wang, Yan; Guo, Fanji; Shi, Yaojun; Fu, Zhiqiang; Liu, Jinming; Cheng, Guofeng; Lin, Jiaojiao

    2010-03-01

    The present study was intend to clone and express the cDNA encoding Cyclophilin B (CyPB) of Schistosoma japonicum, its preliminary biological function and further immunoprotective effect against schistosome infection in mice. RT-PCR technique was applied to amplify a full-length cDNA encoding protein Cyclophilin B (Sj CyPB) from schistosomula cDNA. The expression profiles of Sj CyPB were determined by Real-time PCR using the template cDNAs isolated from 7, 13, 18, 23, 32 and 42 days parasites. The cDNA containing the Open Reading Frame of CyPB was then subcloned into a pGEX-6P-1 vector and transformed into competent Escherichia coli BL21 for expressing. The recombinant protein was renaturated, purified and its antigenicity were detected by Western blotting, and the immunoprotective effect induced by recombinant Sj CyPB was evaluated in Balb/C mice. The cDNA containing the ORF of Sj CyPB was cloned with the length of 672 base pairs, encoding 223 amino acids. Real-time PCR analysis revealed that the gene had the highest expression in 18-day schistosomula, suggesting that Sj CyPB was schistosomula differentially expressed gene. The recombinant protein showed a good antigenicity detected by Western blotting. Animal experiment indicated that the vaccination of recombinant CyPB protein in mice led to 31.5% worm and 41.01% liver egg burden reduction, respectively, compared with those of the control. A full-length cDNA differentially expressed in schistosomula was obtained. The recombinant Sj CyPB protein could induce partial protection against schistosome infection.

  12. Expression

    Directory of Open Access Journals (Sweden)

    Wang-Xia Wang

    2014-02-01

    Full Text Available The miR-15/107 family comprises a group of 10 paralogous microRNAs (miRNAs, sharing a 5′ AGCAGC sequence. These miRNAs have overlapping targets. In order to characterize the expression of miR-15/107 family miRNAs, we employed customized TaqMan Low-Density micro-fluid PCR-array to investigate the expression of miR-15/107 family members, and other selected miRNAs, in 11 human tissues obtained at autopsy including the cerebral cortex, frontal cortex, primary visual cortex, thalamus, heart, lung, liver, kidney, spleen, stomach and skeletal muscle. miR-103, miR-195 and miR-497 were expressed at similar levels across various tissues, whereas miR-107 is enriched in brain samples. We also examined the expression patterns of evolutionarily conserved miR-15/107 miRNAs in three distinct primary rat brain cell preparations (enriched for cortical neurons, astrocytes and microglia, respectively. In primary cultures of rat brain cells, several members of the miR-15/107 family are enriched in neurons compared to other cell types in the central nervous system (CNS. In addition to mature miRNAs, we also examined the expression of precursors (pri-miRNAs. Our data suggested a generally poor correlation between the expression of mature miRNAs and their precursors. In summary, we provide a detailed study of the tissue and cell type-specific expression profile of this highly expressed and phylogenetically conserved family of miRNA genes.

  13. A comparative study of techniques for differential expression analysis on RNA-Seq data.

    Directory of Open Access Journals (Sweden)

    Zong Hong Zhang

    Full Text Available Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.

  14. Neutron activation analysis as applied to instrumental analysis of trace elements from seawater

    International Nuclear Information System (INIS)

    Boniforti, R.; Moauro, A.; Madaro, M.

    1983-01-01

    Particulate matter collected from the coastal area delimited by the mouth of the river Volturno and the Sabaudia lake has been analyzed by instrumental neutron activation analysis for its content of twenty-two trace elements. The results for surface water and bottom water are reported separately, thus evidencing the effect of sampling depth on the concentration of many elements. The necessity of accurately 'cleaning' the filters before use is stressed

  15. Can Link Analysis Be Applied to Identify Behavioral Patterns in Train Recorder Data?

    Science.gov (United States)

    Strathie, Ailsa; Walker, Guy H

    2016-03-01

    A proof-of-concept analysis was conducted to establish whether link analysis could be applied to data from on-train recorders to detect patterns of behavior that could act as leading indicators of potential safety issues. On-train data recorders capture data about driving behavior on thousands of routine journeys every day and offer a source of untapped data that could be used to offer insights into human behavior. Data from 17 journeys undertaken by six drivers on the same route over a 16-hr period were analyzed using link analysis, and four key metrics were examined: number of links, network density, diameter, and sociometric status. The results established that link analysis can be usefully applied to data captured from on-vehicle recorders. The four metrics revealed key differences in normal driver behavior. These differences have promising construct validity as leading indicators. Link analysis is one method that could be usefully applied to exploit data routinely gathered by on-vehicle data recorders. It facilitates a proactive approach to safety based on leading indicators, offers a clearer understanding of what constitutes normal driving behavior, and identifies trends at the interface of people and systems, which is currently a key area of strategic risk. These research findings have direct applications in the field of transport data monitoring. They offer a means of automatically detecting patterns in driver behavior that could act as leading indicators of problems during operation and that could be used in the proactive monitoring of driver competence, risk management, and even infrastructure design. © 2015, Human Factors and Ergonomics Society.

  16. Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments.

    Science.gov (United States)

    Bi, Ran; Liu, Peng

    2016-03-31

    RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of differential expression analysis with RNA-seq data. One challenge is that there are no closed-form formulae to calculate power for the popularly applied tests for differential expression analysis. In addition, false discovery rate (FDR), instead of family-wise type I error rate, is controlled for the multiple testing error in RNA-seq data analysis. So far, there are very few proposals on sample size calculation for RNA-seq experiments. In this paper, we propose a procedure for sample size calculation while controlling FDR for RNA-seq experimental design. Our procedure is based on the weighted linear model analysis facilitated by the voom method which has been shown to have competitive performance in terms of power and FDR control for RNA-seq differential expression analysis. We derive a method that approximates the average power across the differentially expressed genes, and then calculate the sample size to achieve a desired average power while controlling FDR. Simulation results demonstrate that the actual power of several popularly applied tests for differential expression is achieved and is close to the desired power for RNA-seq data with sample size calculated based on our method. Our proposed method provides an efficient algorithm to calculate sample size while controlling FDR for RNA-seq experimental design. We also provide an R package ssizeRNA that implements our proposed method and can be downloaded from the Comprehensive R Archive Network ( http://cran.r-project.org ).

  17. Criticality analysis of thermal reactors for two energy groups applying Monte Carlo and neutron Albedo method

    International Nuclear Information System (INIS)

    Terra, Andre Miguel Barge Pontes Torres

    2005-01-01

    The Albedo method applied to criticality calculations to nuclear reactors is characterized by following the neutron currents, allowing to make detailed analyses of the physics phenomena about interactions of the neutrons with the core-reflector set, by the determination of the probabilities of reflection, absorption, and transmission. Then, allowing to make detailed appreciations of the variation of the effective neutron multiplication factor, keff. In the present work, motivated for excellent results presented in dissertations applied to thermal reactors and shieldings, was described the methodology to Albedo method for the analysis criticality of thermal reactors by using two energy groups admitting variable core coefficients to each re-entrant current. By using the Monte Carlo KENO IV code was analyzed relation between the total fraction of neutrons absorbed in the core reactor and the fraction of neutrons that never have stayed into the reflector but were absorbed into the core. As parameters of comparison and analysis of the results obtained by the Albedo method were used one dimensional deterministic code ANISN (ANIsotropic SN transport code) and Diffusion method. The keff results determined by the Albedo method, to the type of analyzed reactor, showed excellent agreement. Thus were obtained relative errors of keff values smaller than 0,78% between the Albedo method and code ANISN. In relation to the Diffusion method were obtained errors smaller than 0,35%, showing the effectiveness of the Albedo method applied to criticality analysis. The easiness of application, simplicity and clarity of the Albedo method constitute a valuable instrument to neutronic calculations applied to nonmultiplying and multiplying media. (author)

  18. 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...

  19. 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

  20. Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa.

    Directory of Open Access Journals (Sweden)

    Xiangshu Dong

    Full Text Available Genome-wide dissection of the heat stress response (HSR is necessary to overcome problems in crop production caused by global warming. To identify HSR genes, we profiled gene expression in two Chinese cabbage inbred lines with different thermotolerances, Chiifu and Kenshin. Many genes exhibited >2-fold changes in expression upon exposure to 0.5- 4 h at 45°C (high temperature, HT: 5.2% (2,142 genes in Chiifu and 3.7% (1,535 genes in Kenshin. The most enriched GO (Gene Ontology items included 'response to heat', 'response to reactive oxygen species (ROS', 'response to temperature stimulus', 'response to abiotic stimulus', and 'MAPKKK cascade'. In both lines, the genes most highly induced by HT encoded small heat shock proteins (Hsps and heat shock factor (Hsf-like proteins such as HsfB2A (Bra029292, whereas high-molecular weight Hsps were constitutively expressed. Other upstream HSR components were also up-regulated: ROS-scavenging genes like glutathione peroxidase 2 (BrGPX2, Bra022853, protein kinases, and phosphatases. Among heat stress (HS marker genes in Arabidopsis, only exportin 1A (XPO1A (Bra008580, Bra006382 can be applied to B. rapa for basal thermotolerance (BT and short-term acquired thermotolerance (SAT gene. CYP707A3 (Bra025083, Bra021965, which is involved in the dehydration response in Arabidopsis, was associated with membrane leakage in both lines following HS. Although many transcription factors (TF genes, including DREB2A (Bra005852, were involved in HS tolerance in both lines, Bra024224 (MYB41 and Bra021735 (a bZIP/AIR1 [Anthocyanin-Impaired-Response-1] were specific to Kenshin. Several candidate TFs involved in thermotolerance were confirmed as HSR genes by real-time PCR, and these assignments were further supported by promoter analysis. Although some of our findings are similar to those obtained using other plant species, clear differences in Brassica rapa reveal a distinct HSR in this species. Our data could also provide a

  1. Dimensional analysis and extended hydrodynamic theory applied to long-rod penetration of ceramics

    Directory of Open Access Journals (Sweden)

    J.D. Clayton

    2016-08-01

    Full Text Available Principles of dimensional analysis are applied in a new interpretation of penetration of ceramic targets subjected to hypervelocity impact. The analysis results in a power series representation – in terms of inverse velocity – of normalized depth of penetration that reduces to the hydrodynamic solution at high impact velocities. Specifically considered are test data from four literature sources involving penetration of confined thick ceramic targets by tungsten long rod projectiles. The ceramics are AD-995 alumina, aluminum nitride, silicon carbide, and boron carbide. Test data can be accurately represented by the linear form of the power series, whereby the same value of a single fitting parameter applies remarkably well for all four ceramics. Comparison of the present model with others in the literature (e.g., Tate's theory demonstrates a target resistance stress that depends on impact velocity, linearly in the limiting case. Comparison of the present analysis with recent research involving penetration of thin ceramic tiles at lower typical impact velocities confirms the importance of target properties related to fracture and shear strength at the Hugoniot Elastic Limit (HEL only in the latter. In contrast, in the former (i.e., hypervelocity and thick target experiments, the current analysis demonstrates dominant dependence of penetration depth only by target mass density. Such comparisons suggest transitions from microstructure-controlled to density-controlled penetration resistance with increasing impact velocity and ceramic target thickness.

  2. Statistical Techniques Applied to Aerial Radiometric Surveys (STAARS): cluster analysis. National Uranium Resource Evaluation

    International Nuclear Information System (INIS)

    Pirkle, F.L.; Stablein, N.K.; Howell, J.A.; Wecksung, G.W.; Duran, B.S.

    1982-11-01

    One objective of the aerial radiometric surveys flown as part of the US Department of Energy's National Uranium Resource Evaluation (NURE) program was to ascertain the regional distribution of near-surface radioelement abundances. Some method for identifying groups of observations with similar radioelement values was therefore required. It is shown in this report that cluster analysis can identify such groups even when no a priori knowledge of the geology of an area exists. A method of convergent k-means cluster analysis coupled with a hierarchical cluster analysis is used to classify 6991 observations (three radiometric variables at each observation location) from the Precambrian rocks of the Copper Mountain, Wyoming, area. Another method, one that combines a principal components analysis with a convergent k-means analysis, is applied to the same data. These two methods are compared with a convergent k-means analysis that utilizes available geologic knowledge. All three methods identify four clusters. Three of the clusters represent background values for the Precambrian rocks of the area, and one represents outliers (anomalously high 214 Bi). A segmentation of the data corresponding to geologic reality as discovered by other methods has been achieved based solely on analysis of aerial radiometric data. The techniques employed are composites of classical clustering methods designed to handle the special problems presented by large data sets. 20 figures, 7 tables

  3. Uncertainty and sensitivity analysis applied to coupled code calculations for a VVER plant transient

    International Nuclear Information System (INIS)

    Langenbuch, S.; Krzykacz-Hausmann, B.; Schmidt, K. D.

    2004-01-01

    The development of coupled codes, combining thermal-hydraulic system codes and 3D neutron kinetics, is an important step to perform best-estimate plant transient calculations. It is generally agreed that the application of best-estimate methods should be supplemented by an uncertainty and sensitivity analysis to quantify the uncertainty of the results. The paper presents results from the application of the GRS uncertainty and sensitivity method for a VVER-440 plant transient, which was already studied earlier for the validation of coupled codes. For this application, the main steps of the uncertainty method are described. Typical results of the method applied to the analysis of the plant transient by several working groups using different coupled codes are presented and discussed The results demonstrate the capability of an uncertainty and sensitivity analysis. (authors)

  4. An evaluation of an operating BWR piping system damping during earthquake by applying auto regressive analysis

    International Nuclear Information System (INIS)

    Kitada, Y.; Makiguchi, M.; Komori, A.; Ichiki, T.

    1985-01-01

    The records of three earthquakes which had induced significant earthquake response to the piping system were obtained with the earthquake observation system. In the present paper, first, the eigenvalue analysis results for the natural piping system based on the piping support (boundary) conditions are described and second, the frequency and the damping factor evaluation results for each vibrational mode are described. In the present study, the Auto Regressive (AR) analysis method is used in the evaluation of natural frequencies and damping factors. The AR analysis applied here has a capability of direct evaluation of natural frequencies and damping factors from earthquake records observed on a piping system without any information on the input motions to the system. (orig./HP)

  5. Applied Swarm-based medicine: collecting decision trees for patterns of algorithms analysis.

    Science.gov (United States)

    Panje, Cédric M; Glatzer, Markus; von Rappard, Joscha; Rothermundt, Christian; Hundsberger, Thomas; Zumstein, Valentin; Plasswilm, Ludwig; Putora, Paul Martin

    2017-08-16

    The objective consensus methodology has recently been applied in consensus finding in several studies on medical decision-making among clinical experts or guidelines. The main advantages of this method are an automated analysis and comparison of treatment algorithms of the participating centers which can be performed anonymously. Based on the experience from completed consensus analyses, the main steps for the successful implementation of the objective consensus methodology were identified and discussed among the main investigators. The following steps for the successful collection and conversion of decision trees were identified and defined in detail: problem definition, population selection, draft input collection, tree conversion, criteria adaptation, problem re-evaluation, results distribution and refinement, tree finalisation, and analysis. This manuscript provides information on the main steps for successful collection of decision trees and summarizes important aspects at each point of the analysis.

  6. The fundamental parameter method applied to X-ray fluorescence analysis with synchrotron radiation

    Science.gov (United States)

    Pantenburg, F. J.; Beier, T.; Hennrich, F.; Mommsen, H.

    1992-05-01

    Quantitative X-ray fluorescence analysis applying the fundamental parameter method is usually restricted to monochromatic excitation sources. It is shown here, that such analyses can be performed as well with a white synchrotron radiation spectrum. To determine absolute elemental concentration values it is necessary to know the spectral distribution of this spectrum. A newly designed and tested experimental setup, which uses the synchrotron radiation emitted from electrons in a bending magnet of ELSA (electron stretcher accelerator of the university of Bonn) is presented. The determination of the exciting spectrum, described by the given electron beam parameters, is limited due to uncertainties in the vertical electron beam size and divergence. We describe a method which allows us to determine the relative and absolute spectral distributions needed for accurate analysis. First test measurements of different alloys and standards of known composition demonstrate that it is possible to determine exact concentration values in bulk and trace element analysis.

  7. Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis

    Directory of Open Access Journals (Sweden)

    Botman Daniel

    2012-10-01

    Full Text Available Abstract Background Spatial gene expression quantification is required for modeling gene regulation in developing organisms. The fruit fly Drosophila melanogaster is the model system most widely applied for spatial gene expression analysis due to its unique embryonic properties: the shape does not change significantly during its early cleavage cycles and most genes are differentially expressed along a straight axis. This system of development is quite exceptional in the animal kingdom. In the sea anemone Nematostella vectensis the embryo changes its shape during early development; there are cell divisions and cell movement, like in most other metazoans. Nematostella is an attractive case study for spatial gene expression since its transparent body wall makes it accessible to various imaging techniques. Findings Our new quantification method produces standardized gene expression profiles from raw or annotated Nematostella in situ hybridizations by measuring the expression intensity along its cell layer. The procedure is based on digital morphologies derived from high-resolution fluorescence pictures. Additionally, complete descriptions of nonsymmetric expression patterns have been constructed by transforming the gene expression images into a three-dimensional representation. Conclusions We created a standard format for gene expression data, which enables quantitative analysis of in situ hybridizations from embryos with various shapes in different developmental stages. The obtained expression profiles are suitable as input for optimization of gene regulatory network models, and for correlation analysis of genes from dissimilar Nematostella morphologies. This approach is potentially applicable to many other metazoan model organisms and may also be suitable for processing data from three-dimensional imaging techniques.

  8. Applied statistical training to strengthen analysis and health research capacity in Rwanda.

    Science.gov (United States)

    Thomson, Dana R; Semakula, Muhammed; Hirschhorn, Lisa R; Murray, Megan; Ndahindwa, Vedaste; Manzi, Anatole; Mukabutera, Assumpta; Karema, Corine; Condo, Jeanine; Hedt-Gauthier, Bethany

    2016-09-29

    To guide efficient investment of limited health resources in sub-Saharan Africa, local researchers need to be involved in, and guide, health system and policy research. While extensive survey and census data are available to health researchers and program officers in resource-limited countries, local involvement and leadership in research is limited due to inadequate experience, lack of dedicated research time and weak interagency connections, among other challenges. Many research-strengthening initiatives host prolonged fellowships out-of-country, yet their approaches have not been evaluated for effectiveness in involvement and development of local leadership in research. We developed, implemented and evaluated a multi-month, deliverable-driven, survey analysis training based in Rwanda to strengthen skills of five local research leaders, 15 statisticians, and a PhD candidate. Research leaders applied with a specific research question relevant to country challenges and committed to leading an analysis to publication. Statisticians with prerequisite statistical training and experience with a statistical software applied to participate in class-based trainings and complete an assigned analysis. Both statisticians and research leaders were provided ongoing in-country mentoring for analysis and manuscript writing. Participants reported a high level of skill, knowledge and collaborator development from class-based trainings and out-of-class mentorship that were sustained 1 year later. Five of six manuscripts were authored by multi-institution teams and submitted to international peer-reviewed scientific journals, and three-quarters of the participants mentored others in survey data analysis or conducted an additional survey analysis in the year following the training. Our model was effective in utilizing existing survey data and strengthening skills among full-time working professionals without disrupting ongoing work commitments and using few resources. Critical to our

  9. Applied Behavior Analysis, Autism, and Occupational Therapy: A Search for Understanding.

    Science.gov (United States)

    Welch, Christie D; Polatajko, H J

    2016-01-01

    Occupational therapists strive to be mindful, competent practitioners and continuously look for ways to improve practice. Applied behavior analysis (ABA) has strong evidence of effectiveness in helping people with autism achieve goals, yet it does not seem to be implemented in occupational therapy practice. To better understand whether ABA could be an evidence-based option to expand occupational therapy practice, the authors conducted an iterative, multiphase investigation of relevant literature. Findings suggest that occupational therapists apply developmental and sensory approaches to autism treatment. The occupational therapy literature does not reflect any use of ABA despite its strong evidence base. Occupational therapists may currently avoid using ABA principles because of a perception that ABA is not client centered. ABA principles and occupational therapy are compatible, and the two could work synergistically. Copyright © 2016 by the American Occupational Therapy Association, Inc.

  10. A formal concept analysis approach to consensus clustering of multi-experiment expression data

    Science.gov (United States)

    2014-01-01

    Background Presently, with the increasing number and complexity of available gene expression datasets, the combination of data from multiple microarray studies addressing a similar biological question is gaining importance. The analysis and integration of multiple datasets are expected to yield more reliable and robust results since they are based on a larger number of samples and the effects of the individual study-specific biases are diminished. This is supported by recent studies suggesting that important biological signals are often preserved or enhanced by multiple experiments. An approach to combining data from different experiments is the aggregation of their clusterings into a consensus or representative clustering solution which increases the confidence in the common features of all the datasets and reveals the important differences among them. Results We propose a novel generic consensus clustering technique that applies Formal Concept Analysis (FCA) approach for the consolidation and analysis of clustering solutions derived from several microarray datasets. These datasets are initially divided into groups of related experiments with respect to a predefined criterion. Subsequently, a consensus clustering algorithm is applied to each group resulting in a clustering solution per group. These solutions are pooled together and further analysed by employing FCA which allows extracting valuable insights from the data and generating a gene partition over all the experiments. In order to validate the FCA-enhanced approach two consensus clustering algorithms are adapted to incorporate the FCA analysis. Their performance is evaluated on gene expression data from multi-experiment study examining the global cell-cycle control of fission yeast. The FCA results derived from both methods demonstrate that, although both algorithms optimize different clustering characteristics, FCA is able to overcome and diminish these differences and preserve some relevant biological

  11. Multivariat least-squares methods applied to the quantitative spectral analysis of multicomponent samples

    International Nuclear Information System (INIS)

    Haaland, D.M.; Easterling, R.G.; Vopicka, D.A.

    1985-01-01

    In an extension of earlier work, weighted multivariate least-squares methods of quantitative FT-IR analysis have been developed. A linear least-squares approximation to nonlinearities in the Beer-Lambert law is made by allowing the reference spectra to be a set of known mixtures, The incorporation of nonzero intercepts in the relation between absorbance and concentration further improves the approximation of nonlinearities while simultaneously accounting for nonzero spectra baselines. Pathlength variations are also accommodated in the analysis, and under certain conditions, unknown sample pathlengths can be determined. All spectral data are used to improve the precision and accuracy of the estimated concentrations. During the calibration phase of the analysis, pure component spectra are estimated from the standard mixture spectra. These can be compared with the measured pure component spectra to determine which vibrations experience nonlinear behavior. In the predictive phase of the analysis, the calculated spectra are used in our previous least-squares analysis to estimate sample component concentrations. These methods were applied to the analysis of the IR spectra of binary mixtures of esters. Even with severely overlapping spectral bands and nonlinearities in the Beer-Lambert law, the average relative error in the estimated concentration was <1%

  12. Analysis of the Nevada-Applied-Ecology-Group model of transuranic radionuclide transport and dose

    International Nuclear Information System (INIS)

    Kercher, J.R.; Anspaugh, L.R.

    1991-01-01

    The authors analyze the model for estimating the dose from 239 Pu developed for the Nevada Applied Ecology Group (NAEG) by using sensitivity analysis and uncertainty analysis. Sensitivity analysis results suggest that the inhalation pathway is the critical pathway for the organs receiving the highest dose. Soil concentration and the factors controlling air concentration are the most important parameters. The only organ whose dose is sensitive to parameters in the ingestion pathway is the GI tract. The inhalation pathway accounts for 100% of the dose to lung, upper respiratory tract and thoracic lymph nodes; and 95% of the dose to liver, bone, kidney and total body. The GI tract receives 99% of its dose via ingestion. Leafy vegetable ingestion accounts for 70% of the dose from the ingestion pathway regardless of organ, peeled vegetables 20%; accidental soil ingestion 5% ingestion of beef liver 4%; beef muscle 1%. Uncertainty analysis indicates that choosing a uniform distribution for the input parameters produces a lognormal distribution of the dose. The ratio of the square root of the variance to the mean is three times greater for the doses than it is for the individual parameters. As found by the sensitivity analysis, the uncertainty analysis suggests that only a few parameters control the dose for each organ. All organs have similar distributions and variance to mean ratios except for the lymph nodes. (author)

  13. IAEA-ASSET's root cause analysis method applied to sodium leakage incident at Monju

    International Nuclear Information System (INIS)

    Watanabe, Norio; Hirano, Masashi

    1997-08-01

    The present study applied the ASSET (Analysis and Screening of Safety Events Team) methodology (This method identifies occurrences such as component failures and operator errors, identifies their respective direct/root causes and determines corrective actions.) to the analysis of the sodium leakage incident at Monju, based on the published reports by mainly the Science and Technology Agency, aiming at systematic identification of direct/root causes and corrective actions, and discussed the effectiveness and problems of the ASSET methodology. The results revealed the following seven occurrences and showed the direct/root causes and contributing factors for the individual occurrences: failure of thermometer well tube, delayed reactor manual trip, inadequate continuous monitoring of leakage, misjudgment of leak rate, non-required operator action (turbine trip), retarded emergency sodium drainage, and retarded securing of ventilation system. Most of the occurrences stemmed from deficiencies in emergency operating procedures (EOPs), which were mainly caused by defects in the EOP preparation process and operator training programs. The corrective actions already proposed in the published reports were reviewed, identifying issues to be further studied. Possible corrective actions were discussed for these issues. The present study also demonstrated the effectiveness of the ASSET methodology and pointed out some problems, for example, in delineating causal relations among occurrences, for applying it to the detail and systematic analysis of event direct/root causes and determination of concrete measures. (J.P.N.)

  14. IAEA-ASSET`s root cause analysis method applied to sodium leakage incident at Monju

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Norio; Hirano, Masashi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1997-08-01

    The present study applied the ASSET (Analysis and Screening of Safety Events Team) methodology (This method identifies occurrences such as component failures and operator errors, identifies their respective direct/root causes and determines corrective actions.) to the analysis of the sodium leakage incident at Monju, based on the published reports by mainly the Science and Technology Agency, aiming at systematic identification of direct/root causes and corrective actions, and discussed the effectiveness and problems of the ASSET methodology. The results revealed the following seven occurrences and showed the direct/root causes and contributing factors for the individual occurrences: failure of thermometer well tube, delayed reactor manual trip, inadequate continuous monitoring of leakage, misjudgment of leak rate, non-required operator action (turbine trip), retarded emergency sodium drainage, and retarded securing of ventilation system. Most of the occurrences stemmed from deficiencies in emergency operating procedures (EOPs), which were mainly caused by defects in the EOP preparation process and operator training programs. The corrective actions already proposed in the published reports were reviewed, identifying issues to be further studied. Possible corrective actions were discussed for these issues. The present study also demonstrated the effectiveness of the ASSET methodology and pointed out some problems, for example, in delineating causal relations among occurrences, for applying it to the detail and systematic analysis of event direct/root causes and determination of concrete measures. (J.P.N.)

  15. Expression and Activity Analysis of Fructosyltransferase from Aspergillus oryzae.

    Science.gov (United States)

    Guan, Lihong; Chen, Liping; Chen, Yongsen; Zhang, Nu; Han, Yawei

    2017-08-01

    The fructosyltransferase gene was isolated and cloned from Aspergillus oryzae. The gene was 1368 bp, which encoded a protein of 455 amino acids. To analyze the activity of the expressed fructosyltransferase, the pET32a-fructosyltransferase recombined plasmid was transformed into Escherichia coli BL21. The fructosyltransferase gene was successfully expressed by Isopropyl-β-d-thiogalactoside (IPTG) induction. The molecular weight of the expression protein was about 45 kDa. The optimal conditions of protein expression were 25 °C, 0.1 mM IPTG, and 8 h of inducing time. The optimal concentration of urea dealing with inclusion body was 2.5 M. The expressed protein exhibited a strong fructosyl transfer activity. These results showed that the expressed fructosyltransferas owned transferase activity, and could catalyze the synthesis of sucrose-6-acetate.

  16. Planarian homeobox genes: cloning, sequence analysis, and expression.

    Science.gov (United States)

    Garcia-Fernàndez, J; Baguñà, J; Saló, E

    1991-01-01

    Freshwater planarians (Platyhelminthes, Turbellaria, and Tricladida) are acoelomate, triploblastic, unsegmented, and bilaterally symmetrical organisms that are mainly known for their ample power to regenerate a complete organism from a small piece of their body. To identify potential pattern-control genes in planarian regeneration, we have isolated two homeobox-containing genes, Dth-1 and Dth-2 [Dugesia (Girardia) tigrina homeobox], by using degenerate oligonucleotides corresponding to the most conserved amino acid sequence from helix-3 of the homeodomain. Dth-1 and Dth-2 homeodomains are closely related (68% at the nucleotide level and 78% at the protein level) and show the conserved residues characteristic of the homeodomains identified to data. Similarity with most homeobox sequences is low (30-50%), except with Drosophila NK homeodomains (80-82% with NK-2) and the rodent TTF-1 homeodomain (77-87%). Some unusual amino acid residues specific to NK-2, TTF-1, Dth-1, and Dth-2 can be observed in the recognition helix (helix-3) and may define a family of homeodomains. The deduced amino acid sequences from the cDNAs contain, in addition to the homeodomain, other domains also present in various homeobox-containing genes. The expression of both genes, detected by Northern blot analysis, appear slightly higher in cephalic regions than in the rest of the intact organism, while a slight increase is detected in the central period (5 days) or regeneration. Images PMID:1714599

  17. Analysis of expressed sequence tags from the Ulva prolifera (Chlorophyta)

    Science.gov (United States)

    Niu, Jianfeng; Hu, Haiyan; Hu, Songnian; Wang, Guangce; Peng, Guang; Sun, Song

    2010-01-01

    In 2008, a green tide broke out before the sailing competition of the 29th Olympic Games in Qingdao. The causative species was determined to be Enteromorpha prolifera ( Ulva prolifera O. F. Müller), a familiar green macroalga along the coastline of China. Rapid accumulation of a large biomass of floating U. prolifera prompted research on different aspects of this species. In this study, we constructed a nonnormalized cDNA library from the thalli of U. prolifera and acquired 10 072 high-quality expressed sequence tags (ESTs). These ESTs were assembled into 3 519 nonredundant gene groups, including 1 446 clusters and 2 073 singletons. After annotation with the nr database, a large number of genes were found to be related with chloroplast and ribosomal protein, GO functional classification showed 1 418 ESTs participated in photosynthesis and 1 359 ESTs were responsible for the generation of precursor metabolites and energy. In addition, rather comprehensive carbon fixation pathways were found in U. prolifera using KEGG. Some stress-related and signal transduction-related genes were also found in this study. All the evidences displayed that U. prolifera had substance and energy foundation for the intense photosynthesis and the rapid proliferation. Phylogenetic analysis of cytochrome c oxidase subunit I revealed that this green-tide causative species is most closely affiliated to Pseudendoclonium akinetum (Ulvophyceae).

  18. Shaped 3D Singular Spectrum Analysis for Quantifying Gene Expression, with Application to the Early Zebrafish Embryo

    Directory of Open Access Journals (Sweden)

    Alex Shlemov

    2015-01-01

    Full Text Available Recent progress in microscopy technologies, biological markers, and automated processing methods is making possible the development of gene expression atlases at cellular-level resolution over whole embryos. Raw data on gene expression is usually very noisy. This noise comes from both experimental (technical/methodological and true biological sources (from stochastic biochemical processes. In addition, the cells or nuclei being imaged are irregularly arranged in 3D space. This makes the processing, extraction, and study of expression signals and intrinsic biological noise a serious challenge for 3D data, requiring new computational approaches. Here, we present a new approach for studying gene expression in nuclei located in a thick layer around a spherical surface. The method includes depth equalization on the sphere, flattening, interpolation to a regular grid, pattern extraction by Shaped 3D singular spectrum analysis (SSA, and interpolation back to original nuclear positions. The approach is demonstrated on several examples of gene expression in the zebrafish egg (a model system in vertebrate development. The method is tested on several different data geometries (e.g., nuclear positions and different forms of gene expression patterns. Fully 3D datasets for developmental gene expression are becoming increasingly available; we discuss the prospects of applying 3D-SSA to data processing and analysis in this growing field.

  19. Analysis of multiplex gene expression maps obtained by voxelation

    OpenAIRE

    An, L; Xie, H; Chin, MH; Obradovic, Z; Smith, DJ; Megalooikonomou, V

    2009-01-01

    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 presen...

  20. Applying HAZOP analysis in assessing remote handling compatibility of ITER port plugs

    International Nuclear Information System (INIS)

    Duisings, L.P.M.; Til, S. van; Magielsen, A.J.; Ronden, D.M.S.; Elzendoorn, B.S.Q.; Heemskerk, C.J.M.

    2013-01-01

    Highlights: ► We applied HAZOP analysis to assess the criticality of remote handling maintenance activities on port plugs in the ITER Hot Cell facility. ► We identified several weak points in the general upper port plug maintenance concept. ► We made clear recommendations on redesign in port plug design, operational sequence and Hot Cell equipment. ► The use of a HAZOP approach for the ECH UL port can also be applied to ITER port plugs in general. -- Abstract: This paper describes the application of a Hazard and Operability Analysis (HAZOP) methodology in assessing the criticality of remote handling maintenance activities on port plugs in the ITER Hot Cell facility. As part of the ECHUL consortium, the remote handling team at the DIFFER Institute is developing maintenance tools and procedures for critical components of the ECH Upper launcher (UL). Based on NRG's experience with nuclear risk analysis and Hot Cell procedures, early versions of these tool concepts and maintenance procedures were subjected to a HAZOP analysis. The analysis identified several weak points in the general upper port plug maintenance concept and led to clear recommendations on redesigns in port plug design, the operational sequence and ITER Hot Cell equipment. The paper describes the HAZOP methodology and illustrates its application with specific procedures: the Steering Mirror Assembly (SMA) replacement and the exchange of the Mid Shield Optics (MSO) in the ECH UPL. A selection of recommended changes to the launcher design associated with the accessibility, maintainability and manageability of replaceable components are presented

  1. A comparative analysis of three metaheuristic methods applied to fuzzy cognitive maps learning

    Directory of Open Access Journals (Sweden)

    Bruno A. Angélico

    2013-12-01

    Full Text Available This work analyses the performance of three different population-based metaheuristic approaches applied to Fuzzy cognitive maps (FCM learning in qualitative control of processes. Fuzzy cognitive maps permit to include the previous specialist knowledge in the control rule. Particularly, Particle Swarm Optimization (PSO, Genetic Algorithm (GA and an Ant Colony Optimization (ACO are considered for obtaining appropriate weight matrices for learning the FCM. A statistical convergence analysis within 10000 simulations of each algorithm is presented. In order to validate the proposed approach, two industrial control process problems previously described in the literature are considered in this work.

  2. A risk analysis approach applied to field surveillance in utility meters in legal metrology

    Science.gov (United States)

    Rodrigues Filho, B. A.; Nonato, N. S.; Carvalho, A. D.

    2018-03-01

    Field surveillance represents the level of control in metrological supervision responsible for checking the conformity of measuring instruments in-service. Utility meters represent the majority of measuring instruments produced by notified bodies due to self-verification in Brazil. They play a major role in the economy once electricity, gas and water are the main inputs to industries in their production processes. Then, to optimize the resources allocated to control these devices, the present study applied a risk analysis in order to identify among the 11 manufacturers notified to self-verification, the instruments that demand field surveillance.

  3. cDNA-SRAP and Its Application in Differential Gene Expression Analysis: A Case Study in Erianthus arundinaceum

    Directory of Open Access Journals (Sweden)

    Youxiong Que

    2012-01-01

    Full Text Available Erianthus arundinaceum is a wild relative species of sugarcane. The aim of this research was to demonstrate the feasibility of cDNA-SRAP for differential gene expression and to explore the molecular mechanism of drought resistance in E. arundinaceum. cDNA-SRAP technique, for the first time, was applied in the analysis of differential gene expression in E. arundinaceum under drought stress. In total, eight differentially expressed genes with length of 185–427 bp were successfully isolated (GenBank Accession numbers: EU071770, EU071772, EU071774, EU071776, EU071777, EU071779, EU071780, and EU071781. Based on their homologies with genes in GenBank, these genes were assumed to encode ribonuclease III, vacuolar protein, ethylene insensitive protein, aerobactin biosynthesis protein, photosystem II protein, glucose transporter, leucine-rich repeat protein, and ammonia monooxygenase. Real-time PCR analysis on the expression profiling of gene (EU071774 encoding ethylene-insensitive protein and gene (EU071781 encoding ammonia monooxygenase revealed that the expression of these two genes was upregulated both by PEG and ABA treatments, suggesting that they may involve in the drought resistance of E. arundinaceum. This study constitutes the first report of genes activated in E. arundinaceum by drought stress and opens up the application of cDNA-SRAP in differential gene expression analysis in E. arundinaceum under certain stress conditions.

  4. 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

  5. Feasibility evaluation of two solar cooling systems applied to a cuban hotel. Comparative analysis

    International Nuclear Information System (INIS)

    Díaz Torres, Yamile; Valdivia Nodal, Yarelis; Monteagudo Yanes, José Pedro; Miranda Torres, Yudit

    2016-01-01

    The article presents an analysis of technical and economic feasibility of using two configurations of solar cooling in a Cuban hotel. HVAC hybrid schemes are: a cooler of ice water vapor compression (chiller) interconnected in parallel with a smaller capacity chiller, first with a solar-powered absorption cooling system (SACS), and then with a photovoltaic cooling system(PSC). Both were simulated taking into account the weather conditions in the region, thermodynamic calculation methodologies and principles that govern these technologies. The results show that the use of these alternatives contributes to reducing energy consumption and the environmental impact of heating, ventilation and air conditioning systems (HVAC). Economic analysis highlights that PCS is more favorable than the SACS taking into account the cooling cost generation (CCG) but energy assessment indicates that SACS has higher thermal performance for the case study to which it is applied. (author)

  6. Applying reliability analysis to design electric power systems for More-electric aircraft

    Science.gov (United States)

    Zhang, Baozhu

    The More-Electric Aircraft (MEA) is a type of aircraft that replaces conventional hydraulic and pneumatic systems with electrically powered components. These changes have significantly challenged the aircraft electric power system design. This thesis investigates how reliability analysis can be applied to automatically generate system topologies for the MEA electric power system. We first use a traditional method of reliability block diagrams to analyze the reliability level on different system topologies. We next propose a new methodology in which system topologies, constrained by a set reliability level, are automatically generated. The path-set method is used for analysis. Finally, we interface these sets of system topologies with control synthesis tools to automatically create correct-by-construction control logic for the electric power system.

  7. An Appraisal of Social Network Theory and Analysis as Applied to Public Health: Challenges and Opportunities.

    Science.gov (United States)

    Valente, Thomas W; Pitts, Stephanie R

    2017-03-20

    The use of social network theory and analysis methods as applied to public health has expanded greatly in the past decade, yielding a significant academic literature that spans almost every conceivable health issue. This review identifies several important theoretical challenges that confront the field but also provides opportunities for new research. These challenges include (a) measuring network influences, (b) identifying appropriate influence mechanisms, (c) the impact of social media and computerized communications, (d) the role of networks in evaluating public health interventions, and (e) ethics. Next steps for the field are outlined and the need for funding is emphasized. Recently developed network analysis techniques, technological innovations in communication, and changes in theoretical perspectives to include a focus on social and environmental behavioral influences have created opportunities for new theory and ever broader application of social networks to public health topics.

  8. Escalation research: Providing new frontiers for applying behavior analysis to organizational behavior

    Science.gov (United States)

    Goltz, Sonia M.

    2000-01-01

    Decision fiascoes such as escalation of commitment, the tendency of decision makers to “throw good money after bad,” can have serious consequences for organizations and are therefore of great interest in applied research. This paper discusses the use of behavior analysis in organizational behavior research on escalation. Among the most significant aspects of behavior-analytic research on escalation is that it has indicated that both the patterns of outcomes that decision makers have experienced for past decisions and the patterns of responses that they make are critical for understanding escalation. This research has also stimulated the refinement of methods by researchers to better assess decision making and the role reinforcement plays in it. Finally, behavior-analytic escalation research has not only indicated the utility of reinforcement principles for predicting more complex human behavior but has also suggested some additional areas for future exploration of decision making using behavior analysis. PMID:22478347

  9. Digital image analysis applied to industrial nondestructive evaluation and automated parts assembly

    International Nuclear Information System (INIS)

    Janney, D.H.; Kruger, R.P.

    1979-01-01

    Many ideas of image enhancement and analysis are relevant to the needs of the nondestructive testing engineer. These ideas not only aid the engineer in the performance of his current responsibilities, they also open to him new areas of industrial development and automation which are logical extensions of classical testing problems. The paper begins with a tutorial on the fundamentals of computerized image enhancement as applied to nondestructive testing, then progresses through pattern recognition and automated inspection to automated, or robotic, assembly procedures. It is believed that such procedures are cost-effective in many instances, and are but the logical extension of those techniques now commonly used, but often limited to analysis of data from quality-assurance images. Many references are given in order to help the reader who wishes to pursue a given idea further

  10. Selection of Forklift Unit for Warehouse Operation by Applying Multi-Criteria Analysis

    Directory of Open Access Journals (Sweden)

    Predrag Atanasković

    2013-07-01

    Full Text Available This paper presents research related to the choice of the criteria that can be used to perform an optimal selection of the forklift unit for warehouse operation. The analysis has been done with the aim of exploring the requirements and defining relevant criteria that are important when investment decision is made for forklift procurement, and based on the conducted research by applying multi-criteria analysis, to determine the appropriate parameters and their relative weights that form the input data and database for selection of the optimal handling unit. This paper presents an example of choosing the optimal forklift based on the selected criteria for the purpose of making the relevant investment decision.

  11. Functional analysis and applied optimization in Banach spaces applications to non-convex variational models

    CERN Document Server

    Botelho, Fabio

    2014-01-01

    This book introduces the basic concepts of real and functional analysis. It presents the fundamentals of the calculus of variations, convex analysis, duality, and optimization that are necessary to develop applications to physics and engineering problems. The book includes introductory and advanced concepts in measure and integration, as well as an introduction to Sobolev spaces. The problems presented are nonlinear, with non-convex variational formulation. Notably, the primal global minima may not be attained in some situations, in which cases the solution of the dual problem corresponds to an appropriate weak cluster point of minimizing sequences for the primal one. Indeed, the dual approach more readily facilitates numerical computations for some of the selected models. While intended primarily for applied mathematicians, the text will also be of interest to engineers, physicists, and other researchers in related fields.

  12. Analysis of the concept of nursing educational technology applied to the patient

    Directory of Open Access Journals (Sweden)

    Aline Cruz Esmeraldo Áfio

    2014-04-01

    Full Text Available It is aimed at analyzing the concept of educational technology, produced by nursing, applied to the patient. Rodgers´ Evolutionary Method of Concept Analysis was used, identifying background, attributes and consequential damages. 13 articles were selected for analysis in which the background was identified: knowledge deficiency, shortage of nursing professionals' time, to optimize nursing work, the need to achieve the goals of the patients. Attributes: tool, strategy, innovative approach, pedagogical approach, mediator of knowledge, creative way to encourage the acquisition of skills, health production instrument. Consequences: to improve the quality of life, encouraging healthy behavior, empowerment, reflection and link. It emphasizes the importance of educational technologies for the care in nursing, to boost health education activities.

  13. Immunohistochemical Analysis of P63 Expression in Odontogenic Lesions

    Science.gov (United States)

    Atarbashi Moghadam, Saede; Atarbashi Moghadam, Fazele; Eini, Ebrahim

    2013-01-01

    P63 may have a role in tumorigenesis and cytodifferentiation of odontogenic lesions. We investigated the immunohistochemical expression of P63 in a total of 30 cases of odontogenic cysts and tumors. The percentage of positive cells was calculated in the lining of odontogenic cysts and islands of ameloblastoma. P63 expression was evident in all types of odontogenic lesions. P63 was expressed throughout the lining epithelium of odontogenic keratocyst except surface parakeratinized layer. In addition, calcifying odontogenic cyst showed P63 expression in all layers. In almost all radicular and dentigerous cysts, the basal and parabasal layers were immunoreactive. Peripheral cells of ameloblastoma expressed P63; however, stellate reticulum had weaker immunostaining. No significant difference in P63 expression was observed between studied lesions (P = 0.86). Expression of P63 in odontogenic lesions suggests that this protein is important in differentiation and proliferation of odontogenic epithelial cells. However, it seems that it could not be a useful marker to differentiate between aggressive and nonaggressive lesions. P63 also represents a progenitor or basal cell marker, and it is not expressed in mature differentiated cells. PMID:24350278

  14. Meta-Analysis of the First Facial Expression Recognition Challenge

    NARCIS (Netherlands)

    Valstar, M.F.; Mehu, M.; Jiang, Bihan; Pantic, Maja; Scherer, K.

    Automatic facial expression recognition has been an active topic in computer science for over two decades, in particular facial action coding system action unit (AU) detection and classification of a number of discrete emotion states from facial expressive imagery. Standardization and comparability

  15. Immunohistochemical Analysis of P63 Expression in Odontogenic Lesions

    Directory of Open Access Journals (Sweden)

    Saede Atarbashi Moghadam

    2013-01-01

    Full Text Available P63 may have a role in tumorigenesis and cytodifferentiation of odontogenic lesions. We investigated the immunohistochemical expression of P63 in a total of 30 cases of odontogenic cysts and tumors. The percentage of positive cells was calculated in the lining of odontogenic cysts and islands of ameloblastoma. P63 expression was evident in all types of odontogenic lesions. P63 was expressed throughout the lining epithelium of odontogenic keratocyst except surface parakeratinized layer. In addition, calcifying odontogenic cyst showed P63 expression in all layers. In almost all radicular and dentigerous cysts, the basal and parabasal layers were immunoreactive. Peripheral cells of ameloblastoma expressed P63; however, stellate reticulum had weaker immunostaining. No significant difference in P63 expression was observed between studied lesions (. Expression of P63 in odontogenic lesions suggests that this protein is important in differentiation and proliferation of odontogenic epithelial cells. However, it seems that it could not be a useful marker to differentiate between aggressive and nonaggressive lesions. P63 also represents a progenitor or basal cell marker, and it is not expressed in mature differentiated cells.

  16. Expression Analysis of CB2-GFP BAC Transgenic Mice.

    Science.gov (United States)

    Schmöle, Anne-Caroline; Lundt, Ramona; Gennequin, Benjamin; Schrage, Hanna; Beins, Eva; Krämer, Alexandra; Zimmer, Till; Limmer, Andreas; Zimmer, Andreas; Otte, David-Marian

    2015-01-01

    The endocannabinoid system (ECS) is a retrograde messenger system, consisting of lipid signaling molecules that bind to at least two G-protein-coupled receptors, Cannabinoid receptor 1 and 2 (CB1 and 2). As CB2 is primarily expressed on immune cells such as B cells, T cells, macrophages, dendritic cells, and microglia, it is of great interest how CB2 contributes to immune cell development and function in health and disease. Here, understanding the mechanisms of CB2 involvement in immune-cell function as well as the trafficking and regulation of CB2 expressing cells are crucial issues. Up to now, CB2 antibodies produce unclear results, especially those targeting the murine protein. Therefore, we have generated BAC transgenic GFP reporter mice (CB2-GFPTg) to trace CB2 expression in vitro and in situ. Those mice express GFP under the CB2 promoter and display GFP expression paralleling CB2 expression on the transcript level in spleen, thymus and brain tissue. Furthermore, by using fluorescence techniques we show that the major sources for GFP-CB2 expression are B cells in spleen and blood and microglia in the brain. This novel CB2-GFP transgenic reporter mouse line represents a powerful resource to study CB2 expression in different cell types. Furthermore, it could be used for analyzing CB2-mediated mobilization and trafficking of immune cells as well as studying the fate of recruited immune cells in models of acute and chronic inflammation.

  17. Expression Analysis of CB2-GFP BAC Transgenic Mice.

    Directory of Open Access Journals (Sweden)

    Anne-Caroline Schmöle

    Full Text Available The endocannabinoid system (ECS is a retrograde messenger system, consisting of lipid signaling molecules that bind to at least two G-protein-coupled receptors, Cannabinoid receptor 1 and 2 (CB1 and 2. As CB2 is primarily expressed on immune cells such as B cells, T cells, macrophages, dendritic cells, and microglia, it is of great interest how CB2 contributes to immune cell development and function in health and disease. Here, understanding the mechanisms of CB2 involvement in immune-cell function as well as the trafficking and regulation of CB2 expressing cells are crucial issues. Up to now, CB2 antibodies produce unclear results, especially those targeting the murine protein. Therefore, we have generated BAC transgenic GFP reporter mice (CB2-GFPTg to trace CB2 expression in vitro and in situ. Those mice express GFP under the CB2 promoter and display GFP expression paralleling CB2 expression on the transcript level in spleen, thymus and brain tissue. Furthermore, by using fluorescence techniques we show that the major sources for GFP-CB2 expression are B cells in spleen and blood and microglia in the brain. This novel CB2-GFP transgenic reporter mouse line represents a powerful resource to study CB2 expression in different cell types. Furthermore, it could be used for analyzing CB2-mediated mobilization and trafficking of immune cells as well as studying the fate of recruited immune cells in models of acute and chronic inflammation.

  18. Expression analysis revealing destabilizing mutations in phosphomannomutase 2 deficiency (PMM2-CDG): expression analysis of PMM2-CDG mutations.

    Science.gov (United States)

    Vega, Ana Isabel; Pérez-Cerdá, Celia; Abia, David; Gámez, Alejandra; Briones, Paz; Artuch, Rafael; Desviat, Lourdes R; Ugarte, Magdalena; Pérez, Belén

    2011-08-01

    Deficiency of phosphomannomutase (PMM2, MIM#601785) is the most common congenital disorder of glycosylation. Herein we report the genetic analysis of 22 Spanish PMM2 deficient patients and the functional analysis of 14 nucleotide changes in a prokaryotic expression system in order to elucidate their molecular pathogenesis. PMM2 activity assay revealed the presence of six protein changes with no enzymatic activities (p.R123Q, p.R141H, p.F157S, p.P184T, p.F207S and p.D209G) and seven mild protein changes with residual activities ranging from 16 to 54% (p.L32R, p.V44A p.D65Y, p.P113L p.T118S, p.T237M and p.C241S) and also one variant change with normal activity (p.E197A). The results obtained from Western blot analysis, degradation time courses of 11 protein changes and structural analysis of the PMM2 protein, suggest that the loss-of-function of most mutant proteins is based on their increased susceptibility to degradation or aggregation compared to the wild type protein, considering PMM2 deficiency as a conformational disease. We have identified exclusively catalytic protein change (p.D209G), catalytic protein changes affecting protein stability (p.R123Q and p.R141H), two protein changes disrupting the dimer interface (p.P113L and p.T118S) and several misfolding changes (p.L32R, p.V44A, p.D65Y, p.F157S, p.P184T, p.F207S, p.T237M and p.C241S). Our current work opens a promising therapeutic option using pharmacological chaperones to revert the effect of the characterized misfolding mutations identified in a wide range of PMM2 deficient patients.

  19. Adding value in oil and gas by applying decision analysis methodologies: case history

    Energy Technology Data Exchange (ETDEWEB)

    Marot, Nicolas [Petro Andina Resources Inc., Alberta (Canada); Francese, Gaston [Tandem Decision Solutions, Buenos Aires (Argentina)

    2008-07-01

    Petro Andina Resources Ltd. together with Tandem Decision Solutions developed a strategic long range plan applying decision analysis methodology. The objective was to build a robust and fully integrated strategic plan that accomplishes company growth goals to set the strategic directions for the long range. The stochastic methodology and the Integrated Decision Management (IDM{sup TM}) staged approach allowed the company to visualize the associated value and risk of the different strategies while achieving organizational alignment, clarity of action and confidence in the path forward. A decision team involving jointly PAR representatives and Tandem consultants was established to carry out this four month project. Discovery and framing sessions allow the team to disrupt the status quo, discuss near and far reaching ideas and gather the building blocks from which creative strategic alternatives were developed. A comprehensive stochastic valuation model was developed to assess the potential value of each strategy applying simulation tools, sensitivity analysis tools and contingency planning techniques. Final insights and results have been used to populate the final strategic plan presented to the company board providing confidence to the team, assuring that the work embodies the best available ideas, data and expertise, and that the proposed strategy was ready to be elaborated into an optimized course of action. (author)

  20. TRICARE Applied Behavior Analysis (ABA) Benefit: Comparison with Medicaid and Commercial Benefits.

    Science.gov (United States)

    Maglione, Margaret; Kadiyala, Srikanth; Kress, Amii; Hastings, Jaime L; O'Hanlon, Claire E

    2017-01-01

    This study compared the Applied Behavior Analysis (ABA) benefit provided by TRICARE as an early intervention for autism spectrum disorder with similar benefits in Medicaid and commercial health insurance plans. The sponsor, the Office of the Under Secretary of Defense for Personnel and Readiness, was particularly interested in how a proposed TRICARE reimbursement rate decrease from $125 per hour to $68 per hour for ABA services performed by a Board Certified Behavior Analyst compared with reimbursement rates (defined as third-party payment to the service provider) in Medicaid and commercial health insurance plans. Information on ABA coverage in state Medicaid programs was collected from Medicaid state waiver databases; subsequently, Medicaid provider reimbursement data were collected from state Medicaid fee schedules. Applied Behavior Analysis provider reimbursement in the commercial health insurance system was estimated using Truven Health MarketScan® data. A weighted mean U.S. reimbursement rate was calculated for several services using cross-state information on the number of children diagnosed with autism spectrum disorder. Locations of potential provider shortages were also identified. Medicaid and commercial insurance reimbursement rates varied considerably across the United States. This project concluded that the proposed $68-per-hour reimbursement rate for services provided by a board certified analyst was more than 25 percent below the U.S. mean.

  1. 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.

  2. Topological data analysis (TDA) applied to reveal pedogenetic principles of European topsoil system.

    Science.gov (United States)

    Savic, Aleksandar; Toth, Gergely; Duponchel, Ludovic

    2017-05-15

    Recent developments in applied mathematics are bringing new tools that are capable to synthesize knowledge in various disciplines, and help in finding hidden relationships between variables. One such technique is topological data analysis (TDA), a fusion of classical exploration techniques such as principal component analysis (PCA), and a topological point of view applied to clustering of results. Various phenomena have already received new interpretations thanks to TDA, from the proper choice of sport teams to cancer treatments. For the first time, this technique has been applied in soil science, to show the interaction between physical and chemical soil attributes and main soil-forming factors, such as climate and land use. The topsoil data set of the Land Use/Land Cover Area Frame survey (LUCAS) was used as a comprehensive database that consists of approximately 20,000 samples, each described by 12 physical and chemical parameters. After the application of TDA, results obtained were cross-checked against known grouping parameters including five types of land cover, nine types of climate and the organic carbon content of soil. Some of the grouping characteristics observed using standard approaches were confirmed by TDA (e.g., organic carbon content) but novel subtle relationships (e.g., magnitude of anthropogenic effect in soil formation), were discovered as well. The importance of this finding is that TDA is a unique mathematical technique capable of extracting complex relations hidden in soil science data sets, giving the opportunity to see the influence of physicochemical, biotic and abiotic factors on topsoil formation through fresh eyes. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A novel joint analysis framework improves identification of differentially expressed genes in cross disease transcriptomic analysis

    Directory of Open Access Journals (Sweden)

    Wenyi Qin

    2018-02-01

    Full Text Available Abstract Motivation Detecting differentially expressed (DE genes between disease and normal control group is one of the most common analyses in genome-wide transcriptomic data. Since most studies don’t have a lot of samples, researchers have used meta-analysis to group different datasets for the same disease. Even then, in many cases the statistical power is still not enough. Taking into account the fact that many diseases share the same disease genes, it is desirable to design a statistical framework that can identify diseases’ common and specific DE genes simultaneously to improve the identification power. Results We developed a novel empirical Bayes based mixture model to identify DE genes in specific study by leveraging the shared information across multiple different disease expression data sets. The effectiveness of joint analysis was demonstrated through comprehensive simulation studies and two real data applications. The simulation results showed that our method consistently outperformed single data set analysis and two other meta-analysis methods in identification power. In real data analysis, overall our method demonstrated better identification power in detecting DE genes and prioritized more disease related genes and disease related pathways than single data set analysis. Over 150% more disease related genes are identified by our method in application to Huntington’s disease. We expect that our method would provide researchers a new way of utilizing available data sets from different diseases when sample size of the focused disease is limited.

  4. Clinical usefulness of the clock drawing test applying rasch analysis in predicting of cognitive impairment.

    Science.gov (United States)

    Yoo, Doo Han; Lee, Jae Shin

    2016-07-01

    [Purpose] This study examined the clinical usefulness of the clock drawing test applying Rasch analysis for predicting the level of cognitive impairment. [Subjects and Methods] A total of 187 stroke patients with cognitive impairment were enrolled in this study. The 187 patients were evaluated by the clock drawing test developed through Rasch analysis along with the mini-mental state examination of cognitive evaluation tool. An analysis of the variance was performed to examine the significance of the mini-mental state examination and the clock drawing test according to the general characteristics of the subjects. Receiver operating characteristic analysis was performed to determine the cutoff point for cognitive impairment and to calculate the sensitivity and specificity values. [Results] The results of comparison of the clock drawing test with the mini-mental state showed significant differences in according to gender, age, education, and affected side. A total CDT of 10.5, which was selected as the cutoff point to identify cognitive impairement, showed a sensitivity, specificity, Youden index, positive predictive, and negative predicive values of 86.4%, 91.5%, 0.8, 95%, and 88.2%. [Conclusion] The clock drawing test is believed to be useful in assessments and interventions based on its excellent ability to identify cognitive disorders.

  5. The Investigation of NPP Control and Monitoring Functional Analysis Applied to Functional Displays’ Implementation

    International Nuclear Information System (INIS)

    Yan, J.

    2015-01-01

    NPP Control and Monitoring System has been recognised as extreme and safe as well as large scale product, thus it was one of the most major design activities that fully, accurately and operationally functional analysis. The results of functional analysis would be employed as initial instruction through the whole lifecycle of NPP Control and Monitoring System. In this paper, it was discovered that several disadvantages of present functional analysis methods included FAST, The Subtract and Operate Procedure and Functional Procedure Method; owing to the identity methods enveloped here was the combination of Functional Tree and System Structure, as well as its decomposition steps; and RCS Inventory Control function which is defined as one of the most significant control functions in Advanced Light Water Reactor Utility Requirement Document has been employed to demonstrate the feasibility of this method; the analysis results of RCS Inventory function has been applied to direct the design and implementation of related displays, here the functional display of RCS Inventory Control function has been implemented on NuCON which is originated by SNPAS. Owing to the analyzing results, it would be ensured that the accuracy of information displayed to operators, thus the operator would be aware the condition of systems and then make the proper move to ensure the safety and productivity of NPP based on the received data. (author)

  6. Cloud Computing and Internet of Things Concepts Applied on Buildings Data Analysis

    Directory of Open Access Journals (Sweden)

    Hebean Florin-Adrian

    2017-12-01

    Full Text Available Used and developed initially for the IT industry, the Cloud computing and Internet of Things concepts are found at this moment in a lot of sectors of activity, building industry being one of them. These are defined like a global computing, monitoring and analyze network, which is composed of hardware and software resources, with the feature of allocating and dynamically relocating the shared resources, in accordance with user requirements. Data analysis and process optimization techniques based on these new concepts are used increasingly more in the buildings industry area, especially for an optimal operations of the buildings installations and also for increasing occupants comfort. The multitude of building data taken from HVAC sensor, from automation and control systems and from the other systems connected to the network are optimally managed by these new analysis techniques. Through analysis techniques can be identified and manage the issues the arise in operation of building installations like critical alarms, nonfunctional equipment, issues regarding the occupants comfort, for example the upper and lower temperature deviation to the set point and other issues related to equipment maintenance. In this study, a new approach regarding building control is presented and also a generalized methodology for applying data analysis to building services data is described. This methodology is then demonstrated using two case studies.

  7. Gene expression analysis in human breast cancer associated blood vessels.

    Directory of Open Access Journals (Sweden)

    Dylan T Jones

    Full Text Available Angiogenesis is essential for solid tumour growth, whilst the molecular profiles of tumour blood vessels have been reported to be different between cancer types. Although presently available anti-angiogenic strategies are providing some promise for the treatment of some cancers it is perhaps not surprisingly that, none of the anti-angiogenic agents available work on all tumours. Thus, the discovery of novel anti-angiogenic targets, relevant to individual cancer types, is required. Using Affymetrix microarray analysis of laser-captured, CD31-positive blood vessels we have identified 63 genes that are upregulated significantly (5-72 fold in angiogenic blood vessels associated with human invasive ductal carcinoma (IDC of the breast as compared with blood vessels in normal human breast. We tested the angiogenic capacity of a subset of these genes. Genes were selected based on either their known cellular functions, their enriched expression in endothelial cells and/or their sensitivity to anti-VEGF treatment; all features implicating their involvement in angiogenesis. For example, RRM2, a ribonucleotide reductase involved in DNA synthesis, was upregulated 32-fold in IDC-associated blood vessels; ATF1, a nuclear activating transcription factor involved in cellular growth and survival was upregulated 23-fold in IDC-associated blood vessels and HEX-B, a hexosaminidase involved in the breakdown of GM2 gangliosides, was upregulated 8-fold in IDC-associated blood vessels. Furthermore, in silico analysis confirmed that AFT1 and HEX-B also were enriched in endothelial cells when compared with non-endothelial cells. None of these genes have been reported previously to be involved in neovascularisation. However, our data establish that siRNA depletion of Rrm2, Atf1 or Hex-B had significant anti-angiogenic effects in VEGF-stimulated ex vivo mouse aortic ring assays. Overall, our results provide proof-of-principle that our approach can identify a cohort of

  8. Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers.

    Science.gov (United States)

    Labaj, Wojciech; Papiez, Anna; Polanski, Andrzej; Polanska, Joanna

    2017-03-01

    Large collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction. In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set. Three analyses are accomplished, each for gaining a deeper understanding of the processes underlying leukaemia types and subtypes. First, the main disease groups are tested for differential expression against the healthy control as in a standard case-control study. Here, the basic knowledge on molecular mechanisms is confirmed quantitatively and by literature references. Second, pairwise comparison testing is performed for juxtaposing the main leukaemia types among each other. In this case by means of the Dice coefficient similarity measure the general relations are pointed out. Moreover, lists of candidate main leukaemia group biomarkers are proposed. Finally, with this approach being successful, the third analysis provides insight into all of the studied subtypes, followed by the emergence of four leukaemia subtype biomarkers. In addition, the class enhanced DEG signature obtained on the basis of novel pipeline processing leads to significantly better classification power of multi-class data classifiers. The developed methodology consisting of batch effect adjustment, adaptive noise and feature filtration coupled with adequate statistical testing and biomarker definition proves to be an effective approach towards knowledge discovery in high-throughput molecular biology experiments.

  9. General theory for integrated analysis of growth, gene, and protein expression in biofilms.

    Science.gov (United States)

    Zhang, Tianyu; Pabst, Breana; Klapper, Isaac; Stewart, Philip S

    2013-01-01

    A theory for analysis and prediction of spatial and temporal patterns of gene and protein expression within microbial biofilms is derived. The theory integrates phenomena of solute reaction and diffusion, microbial growth, mRNA or protein synthesis, biomass advection, and gene transcript or protein turnover. Case studies illustrate the capacity of the theory to simulate heterogeneous spatial patterns and predict microbial activities in biofilms that are qualitatively different from those of planktonic cells. Specific scenarios analyzed include an inducible GFP or fluorescent protein reporter, a denitrification gene repressed by oxygen, an acid stress response gene, and a quorum sensing circuit. It is shown that the patterns of activity revealed by inducible stable fluorescent proteins or reporter unstable proteins overestimate the region of activity. This is due to advective spreading and finite protein turnover rates. In the cases of a gene induced by either limitation for a metabolic substrate or accumulation of a metabolic product, maximal expression is predicted in an internal stratum of the biofilm. A quorum sensing system that includes an oxygen-responsive negative regulator exhibits behavior that is distinct from any stage of a batch planktonic culture. Though here the analyses have been limited to simultaneous interactions of up to two substrates and two genes, the framework applies to arbitrarily large networks of genes and metabolites. Extension of reaction-diffusion modeling in biofilms to the analysis of individual genes and gene networks is an important advance that dovetails with the growing toolkit of molecular and genetic experimental techniques.

  10. Automated Diatom Analysis Applied to Traditional Light Microscopy: A Proof-of-Concept Study

    Science.gov (United States)

    Little, Z. H. L.; Bishop, I.; Spaulding, S. A.; Nelson, H.; Mahoney, C.

    2017-12-01

    Diatom identification and enumeration by high resolution light microscopy is required for many areas of research and water quality assessment. Such analyses, however, are both expertise and labor-intensive. These challenges motivate the need for an automated process to efficiently and accurately identify and enumerate diatoms. Improvements in particle analysis software have increased the likelihood that diatom enumeration can be automated. VisualSpreadsheet software provides a possible solution for automated particle analysis of high-resolution light microscope diatom images. We applied the software, independent of its complementary FlowCam hardware, to automated analysis of light microscope images containing diatoms. Through numerous trials, we arrived at threshold settings to correctly segment 67% of the total possible diatom valves and fragments from broad fields of view. (183 light microscope images were examined containing 255 diatom particles. Of the 255 diatom particles present, 216 diatoms valves and fragments of valves were processed, with 170 properly analyzed and focused upon by the software). Manual analysis of the images yielded 255 particles in 400 seconds, whereas the software yielded a total of 216 particles in 68 seconds, thus highlighting that the software has an approximate five-fold efficiency advantage in particle analysis time. As in past efforts, incomplete or incorrect recognition was found for images with multiple valves in contact or valves with little contrast. The software has potential to be an effective tool in assisting taxonomists with diatom enumeration by completing a large portion of analyses. Benefits and limitations of the approach are presented to allow for development of future work in image analysis and automated enumeration of traditional light microscope images containing diatoms.

  11. Super-delta: a new differential gene expression analysis procedure with robust data normalization.

    Science.gov (United States)

    Liu, Yuhang; Zhang, Jinfeng; Qiu, Xing

    2017-12-21

    Normalization is an important data preparation step in gene expression analyses, designed to remove various systematic noise. Sample variance is greatly reduced after normalization, hence the power of subsequent statistical analyses is likely to increase. On the other hand, variance reduction is made possible by borrowing information across all genes, including differentially expressed genes (DEGs) and outliers, which will inevitably introduce some bias. This bias typically inflates type I error; and can reduce statistical power in certain situations. In this study we propose a new differential expression analysis pipeline, dubbed as super-delta, that consists of a multivariate extension of the global normalization and a modified t-test. A robust procedure is designed to minimize the bias introduced by DEGs in the normalization step. The modified t-test is derived based on asymptotic theory for hypothesis testing that suitably pairs with the proposed robust normalization. We first compared super-delta with four commonly used normalization methods: global, median-IQR, quantile, and cyclic loess normalization in simulation studies. Super-delta was shown to have better statistical power with tighter control of type I error rate than its competitors. In many cases, the performance of super-delta is close to that of an oracle test in which datasets without technical noise were used. We then applied all methods to a collection of gene expression datasets on breast cancer patients who received neoadjuvant chemotherapy. While there is a substantial overlap of the DEGs identified by all of them, super-delta were able to identify comparatively more DEGs than its competitors. Downstream gene set enrichment analysis confirmed that all these methods selected largely consistent pathways. Detailed investigations on the relatively small differences showed that pathways identified by super-delta have better connections to breast cancer than other methods. As a new pipeline, super

  12. Analysis of combustion turbine inlet air cooling systems applied to an operating cogeneration power plant

    International Nuclear Information System (INIS)

    Chacartegui, R.; Jimenez-Espadafor, F.; Sanchez, D.; Sanchez, T.

    2008-01-01

    In this work, combustion turbine inlet air cooling (CTIAC) systems are analyzed from an economic outlook, their effects on the global performance parameters and the economic results of the power plant. The study has been carried out on a combined cogeneration system, composed of a General Electric PG 6541 gas turbine and a heat recovery steam generator. The work has been divided into three parts. First, a revision of the present CTIAC technologies is shown, their effects on power plant performance and evaluation of the associated investment and maintenance costs. In a second phase of the work, the cogeneration plant was modelled with the objective of evaluating the power increase and the effects on the generated steam and the thermal oil. The cogeneration power plant model was developed, departing from the recorded operational data of the plant in 2005 and the gas turbine model offered by General Electric, to take into consideration that, in 2000, the gas turbine had been remodelled and the original performance curves should be corrected. The final objective of this model was to express the power plant main variables as a function of the gas turbine intake temperature, pressure and relative humidity. Finally, this model was applied to analyze the economic interest of different intake cooling systems, in different operative ranges and with different cooling capacities

  13. IMPORTANCE OF APPLYING DATA ENVELOPMENT ANALYSIS IN CASE OF HIGHER EDUCATIONAL INSTITUTIONS

    Directory of Open Access Journals (Sweden)

    Labas Istvan

    2015-07-01

    Full Text Available Today, the saying predominates better and better according to which a strong target rationalism has to characterize the higher educational institutions due to the scarce resources and the limitlessness of user demands. Now in Hungary, the funding of higher educational system goes through a total transformation thus the leadership has continuously to reckon with the changes of environment and, in tune with these ones, has to modify the goals existing already. Nowadays, it becomes more and more important to measure the effectiveness of the organizations – organizational units pursuing the same or similar activities relative to each other. Benchmarking helps this procedure. Benchmarking is none other than such a tool of analysis and planning which allows comparing the organizations with the best of the competitors. Applying the method with regard to the higher educational institutions is really nothing but a procedure which focuses on comparing processes and results of the institutions’ different functional areas in order to bring to light the opportunities for the rationality as well as the quality and performance improvement. Those benefits could be managed and used as breakthrough possibilities which have been already developed/applied by other organizations and are given by the way leading to a more effective management.The main goal of my monograph is to show a kind of application of Data Envelopment Analysis (DEA method in the higher education. DEA itself is a performance measuring methodology which is a part of benchmarking and uses the linear programming as a method. By means of its application, the effectiveness of different decision-making units can be compared numerically. In our forcefully varying environment, the managerial decision making can be largely supported in each case by such information that is numerically able to identify which organizational units and activities are effective or less effective. Its advantage is that

  14. Applying Signature Extraction and Classification Algorithms on Express on Profiles of CD Markers and Toll Like Receptors to Classify and Predict Exposures to Various Pathogens

    Science.gov (United States)

    2016-02-10

    various time points  in more than three  replicates  each.    Host gene expression in vitro: Microarray analysis was carried out at 3‐6 time periods post...Bibliography 1. Gibb TR, Norwood DA, Jr., Woollen N, Henchal EA: Viral replication and host gene expression in alveolar macrophages...infected with Ebola virus (Zaire strain). Clin Diagn Lab Immunol 2002, 9:19-27. 2. Henchal EA, Teska JD, Ludwig GV, Shoemaker DR, Ezzell JW: Current

  15. Global analysis of differential expressed genes in ECV304 ...

    African Journals Online (AJOL)

    EB

    Abstract. Background: Human cytomegalovirus (HCMV) is a virus which has the potential to alter cellular gene expression through .... and (reverse: 5'-CAG CAC CAT CCT CCT CTT. CCT CT ..... acute respiratory syndrome (SARS) coronavirus.

  16. Spatial and temporal expression analysis of D- myo -inositol 3 ...

    African Journals Online (AJOL)

    1á (eukaryotic elongation factor 1-alpha) using SYBER-Green. ... expression in the developing seed tissues and can be targeted using the dsRNA induced sequence specific RNA degradation mechanism for reduction of phytate levels without ...

  17. Global analysis of differential expressed genes in ECV304 ...

    African Journals Online (AJOL)

    EB

    Methods: Changes in mRNA expression levels of human endothelial-like ... recognized as a risk factor for vascular diseases, like ..... and JUN kinase signaling pathways and transform ... protein accumulates at the G1-S phase boundary and.

  18. An information-theoretic machine learning approach to expression QTL analysis.

    Directory of Open Access Journals (Sweden)

    Tao Huang

    Full Text Available Expression Quantitative Trait Locus (eQTL analysis is a powerful tool to study the biological mechanisms linking the genotype with gene expression. Such analyses can identify genomic locations where genotypic variants influence the expression of genes, both in close proximity to the variant (cis-eQTL, and on other chromosomes (trans-eQTL. Many traditional eQTL methods are based on a linear regression model. In this study, we propose a novel method by which to identify eQTL associations with information theory and machine learning approaches. Mutual Information (MI is used to describe the association between genetic marker and gene expression. MI can detect both linear and non-linear associations. What's more, it can capture the heterogeneity of the population. Advanced feature selection methods, Maximum Relevance Minimum Redundancy (mRMR and Incremental Feature Selection (IFS, were applied to optimize the selection of the affected genes by the genetic marker. When we applied our method to a study of apoE-deficient mice, it was found that the cis-acting eQTLs are stronger than trans-acting eQTLs but there are more trans-acting eQTLs than cis-acting eQTLs. We compared our results (mRMR.eQTL with R/qtl, and MatrixEQTL (modelLINEAR and modelANOVA. In female mice, 67.9% of mRMR.eQTL results can be confirmed by at least two other methods while only 14.4% of R/qtl result can be confirmed by at least two other methods. In male mice, 74.1% of mRMR.eQTL results can be confirmed by at least two other methods while only 18.2% of R/qtl result can be confirmed by at least two other methods. Our methods provide a new way to identify the association between genetic markers and gene expression. Our software is available from supporting information.

  19. Gene Expression Analysis of Four Radiation-resistant Bacteria

    OpenAIRE

    Gao, Na; Ma, Bin-Guang; Zhang, Yu-Sheng; Song, Qin; Chen, Ling-Ling; Zhang, Hong-Yu

    2009-01-01

    To investigate the general radiation-resistant mechanisms of bacteria, bioinformatic method was employed to predict highly expressed genes for four radiation-resistant bacteria, i.e. Deinococcus geothermalis (D. geo), Deinococcus radiodurans (D. rad), Kineococcus radiotolerans (K. rad) and Rubrobacter xylanophilus (R. xyl). It is revealed that most of the three reference gene sets, i.e. ribosomal proteins, transcription factors and major chaperones, are generally highly expressed in the four ...

  20. Host Gene Expression Analysis in Sri Lankan Melioidosis Patients

    Science.gov (United States)

    2017-06-19

    CCL5 Chemokine (C-C motif) ligand 5 /RANTES. IFNγ Interferon gamma TNFα Tumor necrosis factor alpha HMGB1 High mobility group box 1 protein /high...aim of this study was to analyze gene expression levels of human host factors in melioidosis patients and establish useful correlation with disease...PBMC’s) of study subjects. Gene expression profiles of 25 gene targets including 19 immune response genes and 6 epigenetic factors were analyzed by

  1. UNCERT: geostatistics, uncertainty analysis and visualization software applied to groundwater flow and contaminant transport modeling

    International Nuclear Information System (INIS)

    Wingle, W.L.; Poeter, E.P.; McKenna, S.A.

    1999-01-01

    UNCERT is a 2D and 3D geostatistics, uncertainty analysis and visualization software package applied to ground water flow and contaminant transport modeling. It is a collection of modules that provides tools for linear regression, univariate statistics, semivariogram analysis, inverse-distance gridding, trend-surface analysis, simple and ordinary kriging and discrete conditional indicator simulation. Graphical user interfaces for MODFLOW and MT3D, ground water flow and contaminant transport models, are provided for streamlined data input and result analysis. Visualization tools are included for displaying data input and output. These include, but are not limited to, 2D and 3D scatter plots, histograms, box and whisker plots, 2D contour maps, surface renderings of 2D gridded data and 3D views of gridded data. By design, UNCERT's graphical user interface and visualization tools facilitate model design and analysis. There are few built in restrictions on data set sizes and each module (with two exceptions) can be run in either graphical or batch mode. UNCERT is in the public domain and is available from the World Wide Web with complete on-line and printable (PDF) documentation. UNCERT is written in ANSI-C with a small amount of FORTRAN77, for UNIX workstations running X-Windows and Motif (or Lesstif). This article discusses the features of each module and demonstrates how they can be used individually and in combination. The tools are applicable to a wide range of fields and are currently used by researchers in the ground water, mining, mathematics, chemistry and geophysics, to name a few disciplines. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  2. LOGICAL CONDITIONS ANALYSIS METHOD FOR DIAGNOSTIC TEST RESULTS DECODING APPLIED TO COMPETENCE ELEMENTS PROFICIENCY

    Directory of Open Access Journals (Sweden)

    V. I. Freyman

    2015-11-01

    Full Text Available Subject of Research.Representation features of education results for competence-based educational programs are analyzed. Solution importance of decoding and proficiency estimation for elements and components of discipline parts of competences is shown. The purpose and objectives of research are formulated. Methods. The paper deals with methods of mathematical logic, Boolean algebra, and parametrical analysis of complex diagnostic test results, that controls proficiency of some discipline competence elements. Results. The method of logical conditions analysis is created. It will give the possibility to formulate logical conditions for proficiency determination of each discipline competence element, controlled by complex diagnostic test. Normalized test result is divided into noncrossing zones; a logical condition about controlled elements proficiency is formulated for each of them. Summarized characteristics for test result zones are imposed. An example of logical conditions forming for diagnostic test with preset features is provided. Practical Relevance. The proposed method of logical conditions analysis is applied in the decoding algorithm of proficiency test diagnosis for discipline competence elements. It will give the possibility to automate the search procedure for elements with insufficient proficiency, and is also usable for estimation of education results of a discipline or a component of competence-based educational program.

  3. Experimental design technique applied to the validation of an instrumental Neutron Activation Analysis procedure

    International Nuclear Information System (INIS)

    Santos, Uanda Paula de M. dos; Moreira, Edson Gonçalves

    2017-01-01

    In this study optimization of procedures and standardization of Instrumental Neutron Activation Analysis (INAA) method were carried out for the determination of the elements bromine, chlorine, magnesium, manganese, potassium, sodium and vanadium in biological matrix materials using short irradiations at a pneumatic system. 2 k experimental designs were applied for evaluation of the individual contribution of selected variables of the analytical procedure in the final mass fraction result. The chosen experimental designs were the 2 3 and the 2 4 , depending on the radionuclide half life. Different certified reference materials and multi-element comparators were analyzed considering the following variables: sample decay time, irradiation time, counting time and sample distance to detector. Comparator concentration, sample mass and irradiation time were maintained constant in this procedure. By means of the statistical analysis and theoretical and experimental considerations, it was determined the optimized experimental conditions for the analytical methods that will be adopted for the validation procedure of INAA methods in the Neutron Activation Analysis Laboratory (LAN) of the Research Reactor Center (CRPq) at the Nuclear and Energy Research Institute (IPEN /CNEN-SP). Optimized conditions were estimated based on the results of z-score tests, main effect, interaction effects and better irradiation conditions. (author)

  4. On the Formal-Logical Analysis of the Foundations of Mathematics Applied to Problems in Physics

    Science.gov (United States)

    Kalanov, Temur Z.

    2016-03-01

    Analysis of the foundations of mathematics applied to problems in physics was proposed. The unity of formal logic and of rational dialectics is methodological basis of the analysis. It is shown that critical analysis of the concept of mathematical quantity - central concept of mathematics - leads to the following conclusion: (1) The concept of ``mathematical quantity'' is the result of the following mental operations: (a) abstraction of the ``quantitative determinacy of physical quantity'' from the ``physical quantity'' at that the ``quantitative determinacy of physical quantity'' is an independent object of thought; (b) abstraction of the ``amount (i.e., abstract number)'' from the ``quantitative determinacy of physical quantity'' at that the ``amount (i.e., abstract number)'' is an independent object of thought. In this case, unnamed, abstract numbers are the only sign of the ``mathematical quantity''. This sign is not an essential sign of the material objects. (2) The concept of mathematical quantity is meaningless, erroneous, and inadmissible concept in science because it represents the following formal-logical and dialectical-materialistic error: negation of the existence of the essential sign of the concept (i.e., negation of the existence of the essence of the concept) and negation of the existence of measure of material object.

  5. Experimental design technique applied to the validation of an instrumental Neutron Activation Analysis procedure

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Uanda Paula de M. dos; Moreira, Edson Gonçalves, E-mail: uandapaula@gmail.com, E-mail: emoreira@ipen.br [Instituto de Pesquisas Energéticas e Nucleares (IPEN/CNEN-SP), São Paulo, SP (Brazil)

    2017-07-01

    In this study optimization of procedures and standardization of Instrumental Neutron Activation Analysis (INAA) method were carried out for the determination of the elements bromine, chlorine, magnesium, manganese, potassium, sodium and vanadium in biological matrix materials using short irradiations at a pneumatic system. 2{sup k} experimental designs were applied for evaluation of the individual contribution of selected variables of the analytical procedure in the final mass fraction result. The chosen experimental designs were the 2{sup 3} and the 2{sup 4}, depending on the radionuclide half life. Different certified reference materials and multi-element comparators were analyzed considering the following variables: sample decay time, irradiation time, counting time and sample distance to detector. Comparator concentration, sample mass and irradiation time were maintained constant in this procedure. By means of the statistical analysis and theoretical and experimental considerations, it was determined the optimized experimental conditions for the analytical methods that will be adopted for the validation procedure of INAA methods in the Neutron Activation Analysis Laboratory (LAN) of the Research Reactor Center (CRPq) at the Nuclear and Energy Research Institute (IPEN /CNEN-SP). Optimized conditions were estimated based on the results of z-score tests, main effect, interaction effects and better irradiation conditions. (author)

  6. Reflections of the social environment in chimpanzee memory: applying rational analysis beyond humans.

    Science.gov (United States)

    Stevens, Jeffrey R; Marewski, Julian N; Schooler, Lael J; Gilby, Ian C

    2016-08-01

    In cognitive science, the rational analysis framework allows modelling of how physical and social environments impose information-processing demands onto cognitive systems. In humans, for example, past social contact among individuals predicts their future contact with linear and power functions. These features of the human environment constrain the optimal way to remember information and probably shape how memory records are retained and retrieved. We offer a primer on how biologists can apply rational analysis to study animal behaviour. Using chimpanzees ( Pan troglodytes ) as a case study, we modelled 19 years of observational data on their social contact patterns. Much like humans, the frequency of past encounters in chimpanzees linearly predicted future encounters, and the recency of past encounters predicted future encounters with a power function. Consistent with the rational analyses carried out for human memory, these findings suggest that chimpanzee memory performance should reflect those environmental regularities. In re-analysing existing chimpanzee memory data, we found that chimpanzee memory patterns mirrored their social contact patterns. Our findings hint that human and chimpanzee memory systems may have evolved to solve similar information-processing problems. Overall, rational analysis offers novel theoretical and methodological avenues for the comparative study of cognition.

  7. A Monte Carlo error simulation applied to calibration-free X-ray diffraction phase analysis

    International Nuclear Information System (INIS)

    Braun, G.E.

    1986-01-01

    Quantitative phase analysis of a system of n phases can be effected without the need for calibration standards provided at least n different mixtures of these phases are available. A series of linear equations relating diffracted X-ray intensities, weight fractions and quantitation factors coupled with mass balance relationships can be solved for the unknown weight fractions and factors. Uncertainties associated with the measured X-ray intensities, owing to counting of random X-ray quanta, are used to estimate the errors in the calculated parameters utilizing a Monte Carlo simulation. The Monte Carlo approach can be generalized and applied to any quantitative X-ray diffraction phase analysis method. Two examples utilizing mixtures of CaCO 3 , Fe 2 O 3 and CaF 2 with an α-SiO 2 (quartz) internal standard illustrate the quantitative method and corresponding error analysis. One example is well conditioned; the other is poorly conditioned and, therefore, very sensitive to errors in the measured intensities. (orig.)

  8. Reflections of the social environment in chimpanzee memory: applying rational analysis beyond humans

    Science.gov (United States)

    Marewski, Julian N.; Schooler, Lael J.; Gilby, Ian C.

    2016-01-01

    In cognitive science, the rational analysis framework allows modelling of how physical and social environments impose information-processing demands onto cognitive systems. In humans, for example, past social contact among individuals predicts their future contact with linear and power functions. These features of the human environment constrain the optimal way to remember information and probably shape how memory records are retained and retrieved. We offer a primer on how biologists can apply rational analysis to study animal behaviour. Using chimpanzees (Pan troglodytes) as a case study, we modelled 19 years of observational data on their social contact patterns. Much like humans, the frequency of past encounters in chimpanzees linearly predicted future encounters, and the recency of past encounters predicted future encounters with a power function. Consistent with the rational analyses carried out for human memory, these findings suggest that chimpanzee memory performance should reflect those environmental regularities. In re-analysing existing chimpanzee memory data, we found that chimpanzee memory patterns mirrored their social contact patterns. Our findings hint that human and chimpanzee memory systems may have evolved to solve similar information-processing problems. Overall, rational analysis offers novel theoretical and methodological avenues for the comparative study of cognition. PMID:27853606

  9. Global Appearance Applied to Visual Map Building and Path Estimation Using Multiscale Analysis

    Directory of Open Access Journals (Sweden)

    Francisco Amorós

    2014-01-01

    Full Text Available In this work we present a topological map building and localization system for mobile robots based on global appearance of visual information. We include a comparison and analysis of global-appearance techniques applied to wide-angle scenes in retrieval tasks. Next, we define multiscale analysis, which permits improving the association between images and extracting topological distances. Then, a topological map-building algorithm is proposed. At first, the algorithm has information only of some isolated positions of the navigation area in the form of nodes. Each node is composed of a collection of images that covers the complete field of view from a certain position. The algorithm solves the node retrieval and estimates their spatial arrangement. With these aims, it uses the visual information captured along some routes that cover the navigation area. As a result, the algorithm builds a graph that reflects the distribution and adjacency relations between nodes (map. After the map building, we also propose a route path estimation system. This algorithm takes advantage of the multiscale analysis. The accuracy in the pose estimation is not reduced to the nodes locations but also to intermediate positions between them. The algorithms have been tested using two different databases captured in real indoor environments under dynamic conditions.

  10. Multilayers quantitative X-ray fluorescence analysis applied to easel paintings.

    Science.gov (United States)

    de Viguerie, Laurence; Sole, V Armando; Walter, Philippe

    2009-12-01

    X-ray fluorescence spectrometry (XRF) allows a rapid and simple determination of the elemental composition of a material. As a non-destructive tool, it has been extensively used for analysis in art and archaeology since the early 1970s. Whereas it is commonly used for qualitative analysis, recent efforts have been made to develop quantitative treatment even with portable systems. However, the interpretation of the results obtained with this technique can turn out to be problematic in the case of layered structures such as easel paintings. The use of differential X-ray attenuation enables modelling of the various layers: indeed, the absorption of X-rays through different layers will result in modification of intensity ratio between the different characteristic lines. This work focuses on the possibility to use XRF with the fundamental parameters method to reconstruct the composition and thickness of the layers. This method was tested on several multilayers standards and gives a maximum error of 15% for thicknesses and errors of 10% for concentrations. On a painting test sample that was rather inhomogeneous, the XRF analysis provides an average value. This method was applied in situ to estimate the thickness of the layers a painting from Marco d'Oggiono, pupil of Leonardo da Vinci.

  11. Practical considerations for sensitivity analysis after multiple imputation applied to epidemiological studies with incomplete data

    Science.gov (United States)

    2012-01-01

    Background Multiple Imputation as usually implemented assumes that data are Missing At Random (MAR), meaning that the underlying missing data mechanism, given the observed data, is independent of the unobserved data. To explore the sensitivity of the inferences to departures from the MAR assumption, we applied the method proposed by Carpenter et al. (2007). This approach aims to approximate inferences under a Missing Not At random (MNAR) mechanism by reweighting estimates obtained after multiple imputation where the weights depend on the assumed degree of departure from the MAR assumption. Methods The method is illustrated with epidemiological data from a surveillance system of hepatitis C virus (HCV) infection in France during the 2001–2007 period. The subpopulation studied included 4343 HCV infected patients who reported drug use. Risk factors for severe liver disease were assessed. After performing complete-case and multiple imputation analyses, we applied the sensitivity analysis to 3 risk factors of severe liver disease: past excessive alcohol consumption, HIV co-infection and infection with HCV genotype 3. Results In these data, the association between severe liver disease and HIV was underestimated, if given the observed data the chance of observing HIV status is high when this is positive. Inference for two other risk factors were robust to plausible local departures from the MAR assumption. Conclusions We have demonstrated the practical utility of, and advocate, a pragmatic widely applicable approach to exploring plausible departures from the MAR assumption post multiple imputation. We have developed guidelines for applying this approach to epidemiological studies. PMID:22681630

  12. EXPRESS

    International Nuclear Information System (INIS)

    Ancelin, C.; Le, P.; DeSaint-Quentin, S.; Villatte, N.

    1987-01-01

    This paper presents EXPRESS, an expert system developed for the automation of reliability studies. The first part consists in the description of the method for static thermohydraulic systems. In this step, the authors define the knowledge representation based on the two inference engines - ALOUETTE and LCR developed by EDF. They explain all the process to construct a fault tree from a topological and functional description of the system. Numerous examples are exhibited in illustration of the method. This is followed by the lessons derived from the studies performed on some safety systems of the PALUEL nuclear plant. The development of the same approach for electric power systems is described, insisting on the difference resulting from the sequential nature of these systems. Finally, they show the main advantages identified during the studies

  13. ABCG2 in peptic ulcer: gene expression and mutation analysis.

    Science.gov (United States)

    Salagacka-Kubiak, Aleksandra; Żebrowska, Marta; Wosiak, Agnieszka; Balcerczak, Mariusz; Mirowski, Marek; Balcerczak, Ewa

    2016-08-01

    The aim of this study was to evaluate the participation of polymorphism at position C421A and mRNA expression of the ABCG2 gene in the development of peptic ulcers, which is a very common and severe disease. ABCG2, encoded by the ABCG2 gene, has been found inter alia in the gastrointestinal tract, where it plays a protective role eliminating xenobiotics from cells into the extracellular environment. The materials for the study were biopsies of gastric mucosa taken during a routine endoscopy. For genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) at position C421A, DNA was isolated from 201 samples, while for the mRNA expression level by real-time PCR, RNA was isolated from 60 patients. The control group of healthy individuals consisted of 97 blood donors. The dominant genotype in the group of peptic ulcer patients and healthy individuals was homozygous CC. No statistically significant differences between healthy individuals and the whole group of peptic ulcer patients and, likewise, between the subgroups of peptic ulcer patients (infected and uninfected with Helicobacter pylori) were found. ABCG2 expression relative to GAPDH expression was found in 38 of the 60 gastric mucosa samples. The expression level of the gene varies greatly among cases. The statistically significant differences between the intensity (p = 0.0375) of H. pylori infection and ABCG2 gene expression have been shown. It was observed that the more intense the infection, the higher the level of ABCG2 expression.

  14. Applying Different Independent Component Analysis Algorithms and Support Vector Regression for IT Chain Store Sales Forecasting

    Science.gov (United States)

    Dai, Wensheng

    2014-01-01

    Sales forecasting is one of the most important issues in managing information technology (IT) chain store sales since an IT chain store has many branches. Integrating feature extraction method and prediction tool, such as support vector regression (SVR), is a useful method for constructing an effective sales forecasting scheme. Independent component analysis (ICA) is a novel feature extraction technique and has been widely applied to deal with various forecasting problems. But, up to now, only the basic ICA method (i.e., temporal ICA model) was applied to sale forecasting problem. In this paper, we utilize three different ICA methods including spatial ICA (sICA), temporal ICA (tICA), and spatiotemporal ICA (stICA) to extract features from the sales data and compare their performance in sales forecasting of IT chain store. Experimental results from a real sales data show that the sales forecasting scheme by integrating stICA and SVR outperforms the comparison models in terms of forecasting error. The stICA is a promising tool for extracting effective features from branch sales data and the extracted features can improve the prediction performance of SVR for sales forecasting. PMID:25165740

  15. Applying different independent component analysis algorithms and support vector regression for IT chain store sales forecasting.

    Science.gov (United States)

    Dai, Wensheng; Wu, Jui-Yu; Lu, Chi-Jie

    2014-01-01

    Sales forecasting is one of the most important issues in managing information technology (IT) chain store sales since an IT chain store has many branches. Integrating feature extraction method and prediction tool, such as support vector regression (SVR), is a useful method for constructing an effective sales forecasting scheme. Independent component analysis (ICA) is a novel feature extraction technique and has been widely applied to deal with various forecasting problems. But, up to now, only the basic ICA method (i.e., temporal ICA model) was applied to sale forecasting problem. In this paper, we utilize three different ICA methods including spatial ICA (sICA), temporal ICA (tICA), and spatiotemporal ICA (stICA) to extract features from the sales data and compare their performance in sales forecasting of IT chain store. Experimental results from a real sales data show that the sales forecasting scheme by integrating stICA and SVR outperforms the comparison models in terms of forecasting error. The stICA is a promising tool for extracting effective features from branch sales data and the extracted features can improve the prediction performance of SVR for sales forecasting.

  16. The Private Lives of Minerals: Social Network Analysis Applied to Mineralogy and Petrology

    Science.gov (United States)

    Hazen, R. M.; Morrison, S. M.; Fox, P. A.; Golden, J. J.; Downs, R. T.; Eleish, A.; Prabhu, A.; Li, C.; Liu, C.

    2016-12-01

    Comprehensive databases of mineral species (rruff.info/ima) and their geographic localities and co-existing mineral assemblages (mindat.org) reveal patterns of mineral association and distribution that mimic social networks, as commonly applied to such varied topics as social media interactions, the spread of disease, terrorism networks, and research collaborations. Applying social network analysis (SNA) to common assemblages of rock-forming igneous and regional metamorphic mineral species, we find patterns of cohesion, segregation, density, and cliques that are similar to those of human social networks. These patterns highlight classic trends in lithologic evolution and are illustrated with sociograms, in which mineral species are the "nodes" and co-existing species form "links." Filters based on chemistry, age, structural group, and other parameters highlight visually both familiar and new aspects of mineralogy and petrology. We quantify sociograms with SNA metrics, including connectivity (based on the frequency of co-occurrence of mineral pairs), homophily (the extent to which co-existing mineral species share compositional and other characteristics), network closure (based on the degree of network interconnectivity), and segmentation (as revealed by isolated "cliques" of mineral species). Exploitation of large and growing mineral data resources with SNA offers promising avenues for discovering previously hidden trends in mineral diversity-distribution systematics, as well as providing new pedagogical approaches to teaching mineralogy and petrology.

  17. Applying a social network analysis (SNA) approach to understanding radiologists' performance in reading mammograms

    Science.gov (United States)

    Tavakoli Taba, Seyedamir; Hossain, Liaquat; Heard, Robert; Brennan, Patrick; Lee, Warwick; Lewis, Sarah

    2017-03-01

    Rationale and objectives: Observer performance has been widely studied through examining the characteristics of individuals. Applying a systems perspective, while understanding of the system's output, requires a study of the interactions between observers. This research explains a mixed methods approach to applying a social network analysis (SNA), together with a more traditional approach of examining personal/ individual characteristics in understanding observer performance in mammography. Materials and Methods: Using social networks theories and measures in order to understand observer performance, we designed a social networks survey instrument for collecting personal and network data about observers involved in mammography performance studies. We present the results of a study by our group where 31 Australian breast radiologists originally reviewed 60 mammographic cases (comprising of 20 abnormal and 40 normal cases) and then completed an online questionnaire about their social networks and personal characteristics. A jackknife free response operating characteristic (JAFROC) method was used to measure performance of radiologists. JAFROC was tested against various personal and network measures to verify the theoretical model. Results: The results from this study suggest a strong association between social networks and observer performance for Australian radiologists. Network factors accounted for 48% of variance in observer performance, in comparison to 15.5% for the personal characteristics for this study group. Conclusion: This study suggest a strong new direction for research into improving observer performance. Future studies in observer performance should consider social networks' influence as part of their research paradigm, with equal or greater vigour than traditional constructs of personal characteristics.

  18. Raman spectroscopy and capillary electrophoresis applied to forensic colour inkjet printer inks analysis.

    Science.gov (United States)

    Król, Małgorzata; Karoly, Agnes; Kościelniak, Paweł

    2014-09-01

    Forensic laboratories are increasingly engaged in the examination of fraudulent documents, and what is important, in many cases these are inkjet-printed documents. That is why systematic approaches to inkjet printer inks comparison and identification have been carried out by both non-destructive and destructive methods. In this study, micro-Raman spectroscopy and capillary electrophoresis (CE) were applied to the analysis of colour inkjet printer inks. Micro-Raman spectroscopy was used to study the chemical composition of colour inks in situ on a paper surface. It helps to characterize and differentiate inkjet inks, and can be used to create a spectra database of inks taken from different cartridge brands and cartridge numbers. Capillary electrophoresis in micellar electrophoretic capillary chromatography mode was applied to separate colour and colourless components of inks, enabling group identification of those components which occur in a sufficient concentration (giving intensive peaks). Finally, on the basis of the obtained results, differentiation of the analysed inks was performed. Twenty-three samples of inkjet printer inks were examined and the discriminating power (DP) values for both presented methods were established in the routine work of experts during the result interpretation step. DP was found to be 94.0% (Raman) and 95.6% (CE) when all the analysed ink samples were taken into account, and it was 96.7% (Raman) and 98.4% (CE), when only cartridges with different index numbers were considered. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  19. Essays on environmental policy analysis: Computable general equilibrium approaches applied to Sweden

    International Nuclear Information System (INIS)

    Hill, M.

    2001-01-01

    This thesis consists of three essays within the field of applied environmental economics, with the common basic aim of analyzing effects of Swedish environmental policy. Starting out from Swedish environmental goals, the thesis assesses a range of policy-related questions. The objective is to quantify policy outcomes by constructing and applying numerical models especially designed for environmental policy analysis. Static and dynamic multi-sectoral computable general equilibrium models are developed in order to analyze the following issues. The costs and benefits of a domestic carbon dioxide (CO 2 ) tax reform. Special attention is given to how these costs and benefits depend on the structure of the tax system and, furthermore, how they depend on policy-induced changes in 'secondary' pollutants. The effects of allowing for emission permit trading through time when the domestic long-term domestic environmental goal is specified in CO 2 stock terms. The effects on long-term projected economic growth and welfare that are due to damages from emission flow and accumulation of 'local' pollutants (nitrogen oxides and sulfur dioxide), as well as the outcome of environmental policy when costs and benefits are considered in an integrated environmental-economic framework

  20. Applying Different Independent Component Analysis Algorithms and Support Vector Regression for IT Chain Store Sales Forecasting

    Directory of Open Access Journals (Sweden)

    Wensheng Dai

    2014-01-01

    Full Text Available Sales forecasting is one of the most important issues in managing information technology (IT chain store sales since an IT chain store has many branches. Integrating feature extraction method and prediction tool, such as support vector regression (SVR, is a useful method for constructing an effective sales forecasting scheme. Independent component analysis (ICA is a novel feature extraction technique and has been widely applied to deal with various forecasting problems. But, up to now, only the basic ICA method (i.e., temporal ICA model was applied to sale forecasting problem. In this paper, we utilize three different ICA methods including spatial ICA (sICA, temporal ICA (tICA, and spatiotemporal ICA (stICA to extract features from the sales data and compare their performance in sales forecasting of IT chain store. Experimental results from a real sales data show that the sales forecasting scheme by integrating stICA and SVR outperforms the comparison models in terms of forecasting error. The stICA is a promising tool for extracting effective features from branch sales data and the extracted features can improve the prediction performance of SVR for sales forecasting.

  1. Some remarks concerning the Cost/Benefit Analysis applied to LHC at CERN

    CERN Document Server

    Schopper, Herwig

    2016-01-01

    The cost/benefit analysis originally developed for infrastructures in the economic sector has recently been extended by Florio et al to infrastructures of basic research. As a case study the large accelerator LHC at CERN and its experiments have been selected since as a paradigmatic example of frontier research they offer an excellent case to test the CBA model. It will be shown that in spite of this improved method the LHC poses serious difficulties for such an analysis. Some principle difficulties are due to the special character of scientific projects. Their main result is the production of new basic scientific knowledge whose net social value cannot be easily expressed in monetary terms. Other problems are related to the very strong integration of LHC into the general activities of CERN providing however, interesting observations concerning a new management style for global projects. Finally the mission of CERN (including LHC) is unique since it was founded with two tasks - promote science and bring natio...

  2. De-biasing the dynamic mode decomposition for applied Koopman spectral analysis of noisy datasets

    Science.gov (United States)

    Hemati, Maziar S.; Rowley, Clarence W.; Deem, Eric A.; Cattafesta, Louis N.

    2017-08-01

    The dynamic mode decomposition (DMD)—a popular method for performing data-driven Koopman spectral analysis—has gained increased popularity for extracting dynamically meaningful spatiotemporal descriptions of fluid flows from snapshot measurements. Often times, DMD descriptions can be used for predictive purposes as well, which enables informed decision-making based on DMD model forecasts. Despite its widespread use and utility, DMD can fail to yield accurate dynamical descriptions when the measured snapshot data are imprecise due to, e.g., sensor noise. Here, we express DMD as a two-stage algorithm in order to isolate a source of systematic error. We show that DMD's first stage, a subspace projection step, systematically introduces bias errors by processing snapshots asymmetrically. To remove this systematic error, we propose utilizing an augmented snapshot matrix in a subspace projection step, as in problems of total least-squares, in order to account for the error present in all snapshots. The resulting unbiased and noise-aware total DMD (TDMD) formulation reduces to standard DMD in the absence of snapshot errors, while the two-stage perspective generalizes the de-biasing framework to other related methods as well. TDMD's performance is demonstrated in numerical and experimental fluids examples. In particular, in the analysis of time-resolved particle image velocimetry data for a separated flow, TDMD outperforms standard DMD by providing dynamical interpretations that are consistent with alternative analysis techniques. Further, TDMD extracts modes that reveal detailed spatial structures missed by standard DMD.

  3. Methods of economic analysis applied to fusion research. Fourth annual report

    International Nuclear Information System (INIS)

    Hazelrigg, G.A. Jr.

    1980-01-01

    The current study reported here has involved three separate tasks. The first task deals with the development of expected utility analysis techniques for economic evaluation of fusion research. A decision analytic model is developed for the incorporation of market uncertainties, as well as technological uncertainties in an economic evaluation of long-range energy research. The model is applied to the case of fusion research. The second task deals with the potential effects of long-range energy RD and D on fossil fuel prices. ECON's previous fossil fuel price model is extended to incorporate a dynamic demand function. The dynamic demand function supports price fluctuations such as those observed in the marketplace. The third task examines alternative uses of fusion technologies, specifically superconducting technologies and first wall materials to determine the potential for alternative, nonfusion use of these technologies. In both cases, numerous alternative uses are found

  4. [Methodological novelties applied to the anthropology of food: agent-based models and social networks analysis].

    Science.gov (United States)

    Díaz Córdova, Diego

    2016-01-01

    The aim of this article is to introduce two methodological strategies that have not often been utilized in the anthropology of food: agent-based models and social networks analysis. In order to illustrate these methods in action, two cases based in materials typical of the anthropology of food are presented. For the first strategy, fieldwork carried out in Quebrada de Humahuaca (province of Jujuy, Argentina) regarding meal recall was used, and for the second, elements of the concept of "domestic consumption strategies" applied by Aguirre were employed. The underlying idea is that, given that eating is recognized as a "total social fact" and, therefore, as a complex phenomenon, the methodological approach must also be characterized by complexity. The greater the number of methods utilized (with the appropriate rigor), the better able we will be to understand the dynamics of feeding in the social environment.

  5. Graph theory applied to noise and vibration control in statistical energy analysis models.

    Science.gov (United States)

    Guasch, Oriol; Cortés, Lluís

    2009-06-01

    A fundamental aspect of noise and vibration control in statistical energy analysis (SEA) models consists in first identifying and then reducing the energy flow paths between subsystems. In this work, it is proposed to make use of some results from graph theory to address both issues. On the one hand, linear and path algebras applied to adjacency matrices of SEA graphs are used to determine the existence of any order paths between subsystems, counting and labeling them, finding extremal paths, or determining the power flow contributions from groups of paths. On the other hand, a strategy is presented that makes use of graph cut algorithms to reduce the energy flow from a source subsystem to a receiver one, modifying as few internal and coupling loss factors as possible.

  6. Econometrics analysis of consumer behaviour: a linear expenditure system applied to energy

    International Nuclear Information System (INIS)

    Giansante, C.; Ferrari, V.

    1996-12-01

    In economics literature the expenditure system specification is a well known subject. The problem is to define a coherent representation of consumer behaviour through functional forms easy to calculate. In this work it is used the Stone-Geary Linear Expenditure System and its multi-level decision process version. The Linear Expenditure system is characterized by an easy calculating estimation procedure, and its multi-level specification allows substitution and complementary relations between goods. Moreover, the utility function separability condition on which the Utility Tree Approach is based, justifies to use an estimation procedure in two or more steps. This allows to use an high degree of expenditure categories disaggregation, impossible to reach the Linear Expediture System. The analysis is applied to energy sectors

  7. A Numerical Procedure for Model Identifiability Analysis Applied to Enzyme Kinetics

    DEFF Research Database (Denmark)

    Daele, Timothy, Van; Van Hoey, Stijn; Gernaey, Krist

    2015-01-01

    The proper calibration of models describing enzyme kinetics can be quite challenging. In the literature, different procedures are available to calibrate these enzymatic models in an efficient way. However, in most cases the model structure is already decided on prior to the actual calibration...... and Pronzato (1997) and which can be easily set up for any type of model. In this paper the proposed approach is applied to the forward reaction rate of the enzyme kinetics proposed by Shin and Kim(1998). Structural identifiability analysis showed that no local structural model problems were occurring......) identifiability problems. By using the presented approach it is possible to detect potential identifiability problems and avoid pointless calibration (and experimental!) effort....

  8. Pretreatment procedures applied to samples to be analysed by neutron activation analysis at CDTN/CNEN

    International Nuclear Information System (INIS)

    Francisco, Dovenir; Menezes, Maria Angela de Barros Correia

    2009-01-01

    The neutron activation technique - using several methods - has been applied in 80% of the analytical demand of Division for Reactor and Analytical Techniques at CDTN/CNEN, Belo Horizonte, Minas Gerais. This scenario emphasizes the responsibility of the Laboratory to provide and assure the quality of the measurements. The first step to assure the results quality is the preparation of the samples. Therefore, this paper describes the experimental procedures adopted at CDTN/CNEN in order to uniform conditions of analysis and to avoid contaminations by elements present everywhere. Some of the procedures are based on methods described in the literature; others are based on many years of experience preparing samples from many kinds of matrices. The procedures described are related to geological material - soil, sediment, rock, gems, clay, archaeological ceramics and ore - biological materials - hair, fish, plants, food - water, etc. Analytical results in sediment samples are shown as n example pointing out the efficiency of the experimental procedure. (author)

  9. Common faults in turbines and applying neural networks in order to fault diagnostic by vibration analysis

    International Nuclear Information System (INIS)

    Masoudifar, M.; AghaAmini, M.

    2001-01-01

    Today the fault diagnostic of the rotating machinery based on the vibration analysis is an effective method in designing predictive maintenance programs. In this method, vibration level of the turbines is monitored and if it is higher than the allowable limit, vibrational data will be analyzed and the growing faults will be detected. But because of the high complexity of the system monitoring, the interpretation of the measured data is more difficult. Therefore, design of the fault diagnostic expert systems by using the expert's technical experiences and knowledge; seem to be the best solution. In this paper,at first several common faults in turbines are studied and the how applying the neural networks to interpret the vibrational data for fault diagnostic is explained

  10. Applied behavior analysis programs for autism: sibling psychosocial adjustment during and following intervention use.

    Science.gov (United States)

    Cebula, Katie R

    2012-05-01

    Psychosocial adjustment in siblings of children with autism whose families were using a home-based, applied behavior analysis (ABA) program was compared to that of siblings in families who were not using any intensive autism intervention. Data gathered from parents, siblings and teachers indicated that siblings in ABA families experienced neither significant drawbacks nor benefits in terms of their behavioral adjustment, sibling relationship quality and self-concept compared to control group siblings, either during or following intervention use. Parents and siblings perceived improvements in sibling interaction since the outset of ABA, with parents somewhat more positive in their views than were siblings. Social support was associated with better sibling outcomes in all groups. Implications for supporting families using ABA are considered.

  11. [Matrix analysis of the client's voice: QFD applied to healthcare management].

    Science.gov (United States)

    Lorenzo, Susana; Mira, José; Olarte, Mayerly; Guerrero, Johana; Guerrero, Johann; Moyano, Silvia

    2004-01-01

    To apply quality function deployment (QFD) methodology to identify clients' needs by relating complaints with perceived quality domains. A hospital within the Public Health Service of Madrid. Matrix analysis based on the QFD model was performed, using the surveys (1998-2002) conducted in the hospital with the Servqhos questionnaire and a sample of 363 complaints made in 2002. The complaints analyzed were selected using a non-probabilistic sampling method. QFD methodology was highly useful, allowing complaints to be related to the results of a perceived quality questionnaire and identification of the attributes with the greatest influence on patient satisfaction. It also allowed us to identify areas for improvement according to clients' needs.

  12. Gene Expression Analysis of Plum pox virus (Sharka Susceptibility/Resistance in Apricot (Prunus armeniaca L..

    Directory of Open Access Journals (Sweden)

    Manuel Rubio

    Full Text Available RNA-Seq has proven to be a very powerful tool in the analysis of the Plum pox virus (PPV, sharka disease/Prunus interaction. This technique is an important complementary tool to other means of studying genomics. In this work an analysis of gene expression of resistance/susceptibility to PPV in apricot is performed. RNA-Seq has been applied to analyse the gene expression changes induced by PPV infection in leaves from two full-sib apricot genotypes, "Rojo Pasión" and "Z506-7", resistant and susceptible to PPV, respectively. Transcriptomic analyses revealed the existence of more than 2,000 genes related to the pathogen response and resistance to PPV in apricot. These results showed that the response to infection by the virus in the susceptible genotype is associated with an induction of genes involved in pathogen resistance such as the allene oxide synthase, S-adenosylmethionine synthetase 2 and the major MLP-like protein 423. Over-expression of the Dicer protein 2a may indicate the suppression of a gene silencing mechanism of the plant by PPV HCPro and P1 PPV proteins. On the other hand, there were 164 genes involved in resistance mechanisms that have been identified in apricot, 49 of which are located in the PPVres region (scaffold 1 positions from 8,050,804 to 8,244,925, which is responsible for PPV resistance in apricot. Among these genes in apricot there are several MATH domain-containing genes, although other genes inside (Pleiotropic drug resistance 9 gene or outside (CAP, Cysteine-rich secretory proteins, Antigen 5 and Pathogenesis-related 1 protein; and LEA, Late embryogenesis abundant protein PPVres region could also be involved in the resistance.

  13. Gene Expression Analysis of Plum pox virus (Sharka) Susceptibility/Resistance in Apricot (Prunus armeniaca L.).

    Science.gov (United States)

    Rubio, Manuel; Ballester, Ana Rosa; Olivares, Pedro Manuel; Castro de Moura, Manuel; Dicenta, Federico; Martínez-Gómez, Pedro

    2015-01-01

    RNA-Seq has proven to be a very powerful tool in the analysis of the Plum pox virus (PPV, sharka disease)/Prunus interaction. This technique is an important complementary tool to other means of studying genomics. In this work an analysis of gene expression of resistance/susceptibility to PPV in apricot is performed. RNA-Seq has been applied to analyse the gene expression changes induced by PPV infection in leaves from two full-sib apricot genotypes, "Rojo Pasión" and "Z506-7", resistant and susceptible to PPV, respectively. Transcriptomic analyses revealed the existence of more than 2,000 genes related to the pathogen response and resistance to PPV in apricot. These results showed that the response to infection by the virus in the susceptible genotype is associated with an induction of genes involved in pathogen resistance such as the allene oxide synthase, S-adenosylmethionine synthetase 2 and the major MLP-like protein 423. Over-expression of the Dicer protein 2a may indicate the suppression of a gene silencing mechanism of the plant by PPV HCPro and P1 PPV proteins. On the other hand, there were 164 genes involved in resistance mechanisms that have been identified in apricot, 49 of which are located in the PPVres region (scaffold 1 positions from 8,050,804 to 8,244,925), which is responsible for PPV resistance in apricot. Among these genes in apricot there are several MATH domain-containing genes, although other genes inside (Pleiotropic drug resistance 9 gene) or outside (CAP, Cysteine-rich secretory proteins, Antigen 5 and Pathogenesis-related 1 protein; and LEA, Late embryogenesis abundant protein) PPVres region could also be involved in the resistance.

  14. Challenges in the implementation of a quality management system applied to radiometric analysis

    Energy Technology Data Exchange (ETDEWEB)

    Dias, Danila C.S.; Bonifacio, Rodrigo L.; Nascimento, Marcos R.L.; Silva, Nivaldo C. da; Taddei, Maria Helena T., E-mail: danilacdias@gmail.com [Comissao Nacional de Energia Nuclear (LAPOC/CNEN-MG), Pocos de Caldas, MG (Brazil). Laboratorio de Pocos de Caldas

    2015-07-01

    The concept of quality in laboratories has been well established as an essential factor in the search for reliable results. Since its first version published (1999), the ISO/IEC 17025 has been applied in the industrial and research fields, in a wide range of laboratorial analyses. However, the implementation of a Quality Management System still poses great challenges to institutions and companies. The purpose of this work is to expose the constraints related to the implementation of ISO/IEC 17025 applied to analytical assays of radionuclides, accomplished by studying the case of the Pocos de Caldas Laboratory of the Brazilian Commission for Nuclear Energy. In this lab, a project of accreditation of techniques involving determination of radionuclides in water, soil, sediment and food samples has been conducted since 2011. The challenges presented by this project arise from the administrative view, where the governmental nature of the institution translates into unlevelled availability resources and the organizational view, whereas QMS requires inevitable changes in the organizational culture. It is important to point out that when it comes to accreditation of analysis involving radioactive elements, many aspects must be treated carefully due to the their very particular nature. Among these concerns are the determination of analysis uncertainties, accessibility to international proficiency studies, international radioactive samples and CRM transportation, the study of parameters on the validation of analytical methods and the lack of documentation and specialized personnel regarding quality at radiometric measurements. Through an effective management system, the institution is overcoming these challenges, moving toward the ISO/IEC 17025 accreditation. (author)

  15. Challenges in the implementation of a quality management system applied to radiometric analysis

    International Nuclear Information System (INIS)

    Dias, Danila C.S.; Bonifacio, Rodrigo L.; Nascimento, Marcos R.L.; Silva, Nivaldo C. da; Taddei, Maria Helena T.

    2015-01-01

    The concept of quality in laboratories has been well established as an essential factor in the search for reliable results. Since its first version published (1999), the ISO/IEC 17025 has been applied in the industrial and research fields, in a wide range of laboratorial analyses. However, the implementation of a Quality Management System still poses great challenges to institutions and companies. The purpose of this work is to expose the constraints related to the implementation of ISO/IEC 17025 applied to analytical assays of radionuclides, accomplished by studying the case of the Pocos de Caldas Laboratory of the Brazilian Commission for Nuclear Energy. In this lab, a project of accreditation of techniques involving determination of radionuclides in water, soil, sediment and food samples has been conducted since 2011. The challenges presented by this project arise from the administrative view, where the governmental nature of the institution translates into unlevelled availability resources and the organizational view, whereas QMS requires inevitable changes in the organizational culture. It is important to point out that when it comes to accreditation of analysis involving radioactive elements, many aspects must be treated carefully due to the their very particular nature. Among these concerns are the determination of analysis uncertainties, accessibility to international proficiency studies, international radioactive samples and CRM transportation, the study of parameters on the validation of analytical methods and the lack of documentation and specialized personnel regarding quality at radiometric measurements. Through an effective management system, the institution is overcoming these challenges, moving toward the ISO/IEC 17025 accreditation. (author)

  16. Gene expression analysis in calcific tendinopathy of the rotator cuff

    Directory of Open Access Journals (Sweden)

    F Oliva

    2011-06-01

    Full Text Available We evaluated the expression of several genes involved in tissue remodelling and bone development in patients with calcific tendinopathy of the rotator cuff. Biopsies from calcified and non-calcified areas were obtained from 10 patients (8 women and 2 men; average age: 55 years; range: 40-68 with calcific tendinopathy of the rotator cuff. To evaluate the expression of selected genes, RNA extraction, cDNA synthesis and quantitative polymerase chain reaction (PCR were performed. A significantly increased expression of tissue transglutaminase (tTG2 and its substrate, osteopontin, was detected in the calcific areas compared to the levels observed in the normal tissue from the same subject with calcific tendinopathy, whereas a modest increase was observed for catepsin K. There was also a significant decrease in mRNA expression of Bone Morphogenetic Protein (BMP4 and BMP6 in the calcific area. BMP-2, collagen V and vascular endothelial growth factor (VEGF did not show significant differences. Collagen X and matrix metalloproteinase (MMP-9 were not detectable. A variation in expression of these genes could be characteristic of this form tendinopathy, since an increased level of these genes has not been detected in other forms of tendon lesions.

  17. Bayesian statistics applied to neutron activation data for reactor flux spectrum analysis

    International Nuclear Information System (INIS)

    Chiesa, Davide; Previtali, Ezio; Sisti, Monica

    2014-01-01

    Highlights: • Bayesian statistics to analyze the neutron flux spectrum from activation data. • Rigorous statistical approach for accurate evaluation of the neutron flux groups. • Cross section and activation data uncertainties included for the problem solution. • Flexible methodology applied to analyze different nuclear reactor flux spectra. • The results are in good agreement with the MCNP simulations of neutron fluxes. - Abstract: In this paper, we present a statistical method, based on Bayesian statistics, to analyze the neutron flux spectrum from the activation data of different isotopes. The experimental data were acquired during a neutron activation experiment performed at the TRIGA Mark II reactor of Pavia University (Italy) in four irradiation positions characterized by different neutron spectra. In order to evaluate the neutron flux spectrum, subdivided in energy groups, a system of linear equations, containing the group effective cross sections and the activation rate data, has to be solved. However, since the system’s coefficients are experimental data affected by uncertainties, a rigorous statistical approach is fundamental for an accurate evaluation of the neutron flux groups. For this purpose, we applied the Bayesian statistical analysis, that allows to include the uncertainties of the coefficients and the a priori information about the neutron flux. A program for the analysis of Bayesian hierarchical models, based on Markov Chain Monte Carlo (MCMC) simulations, was used to define the problem statistical model and solve it. The first analysis involved the determination of the thermal, resonance-intermediate and fast flux components and the dependence of the results on the Prior distribution choice was investigated to confirm the reliability of the Bayesian analysis. After that, the main resonances of the activation cross sections were analyzed to implement multi-group models with finer energy subdivisions that would allow to determine the

  18. Simplification and Shift in Cognition of Political Difference: Applying the Geometric Modeling to the Analysis of Semantic Similarity Judgment

    Science.gov (United States)

    Kato, Junko; Okada, Kensuke

    2011-01-01

    Perceiving differences by means of spatial analogies is intrinsic to human cognition. Multi-dimensional scaling (MDS) analysis based on Minkowski geometry has been used primarily on data on sensory similarity judgments, leaving judgments on abstractive differences unanalyzed. Indeed, analysts have failed to find appropriate experimental or real-life data in this regard. Our MDS analysis used survey data on political scientists' judgments of the similarities and differences between political positions expressed in terms of distance. Both distance smoothing and majorization techniques were applied to a three-way dataset of similarity judgments provided by at least seven experts on at least five parties' positions on at least seven policies (i.e., originally yielding 245 dimensions) to substantially reduce the risk of local minima. The analysis found two dimensions, which were sufficient for mapping differences, and fit the city-block dimensions better than the Euclidean metric in all datasets obtained from 13 countries. Most city-block dimensions were highly correlated with the simplified criterion (i.e., the left–right ideology) for differences that are actually used in real politics. The isometry of the city-block and dominance metrics in two-dimensional space carries further implications. More specifically, individuals may pay attention to two dimensions (if represented in the city-block metric) or focus on a single dimension (if represented in the dominance metric) when judging differences between the same objects. Switching between metrics may be expected to occur during cognitive processing as frequently as the apparent discontinuities and shifts in human attention that may underlie changing judgments in real situations occur. Consequently, the result has extended strong support for the validity of the geometric models to represent an important social cognition, i.e., the one of political differences, which is deeply rooted in human nature. PMID:21673959

  19. Spectral Analysis on Time-Course Expression Data: Detecting Periodic Genes Using a Real-Valued Iterative Adaptive Approach

    Directory of Open Access Journals (Sweden)

    Kwadwo S. Agyepong

    2013-01-01

    Full Text Available Time-course expression profiles and methods for spectrum analysis have been applied for detecting transcriptional periodicities, which are valuable patterns to unravel genes associated with cell cycle and circadian rhythm regulation. However, most of the proposed methods suffer from restrictions and large false positives to a certain extent. Additionally, in some experiments, arbitrarily irregular sampling times as well as the presence of high noise and small sample sizes make accurate detection a challenging task. A novel scheme for detecting periodicities in time-course expression data is proposed, in which a real-valued iterative adaptive approach (RIAA, originally proposed for signal processing, is applied for periodogram estimation. The inferred spectrum is then analyzed using Fisher’s hypothesis test. With a proper -value threshold, periodic genes can be detected. A periodic signal, two nonperiodic signals, and four sampling strategies were considered in the simulations, including both bursts and drops. In addition, two yeast real datasets were applied for validation. The simulations and real data analysis reveal that RIAA can perform competitively with the existing algorithms. The advantage of RIAA is manifested when the expression data are highly irregularly sampled, and when the number of cycles covered by the sampling time points is very reduced.

  20. Contribution of the CEC in structural analysis applied to LMFBR problems

    International Nuclear Information System (INIS)

    Larsson, L.H.; Terzaghi, A.

    1983-01-01

    This paper presents both the activity of DG XII in field of Codes and Standards (harmonization) and the research activity carried out at the JRC in Ispra. The first part describes the activity performed in the field of structural analysis by the Fast Reactor Coordinating Committee of the CEC and its Working Group Codes and Standards. This activity, which is aimed at resolving difficulties encountered in using design procedures based on ASME Code Case N-47, has made good progress in most areas. Results from recent inelastic and seismic benchmark calculations are presented as well as future computational exercises and investigations related to piping analysis, defect analysis, material behaviour and life prediction at elevated temperature. In the second part of the paper results of recent research and future plans in the area of structural mechanics at the JRC Ispra are discussed. In the past years, a large effort was devoted to the COVA (code validation) program intended to validate dynamic fluid/structure codes necessary for predicting the response of LMFBR containments. The main conclusions that can be drawn from COVA which finishes this year are presented, and some still open questions related to the prediction of containment response to an HCDA are discussed. The paper then describes the identification technique which is applied for the determination of constitutive equations for the dynamic behaviour of materials. In the field of fracture mechanics JRC has mostly concentrated its efforts on the elastic-plastic fracture toughness properties of irradiated austenitic steels. In the future, also dynamic ductile fracture problems will be investigated, for these a large dynamic test facility with a max. force of 5 MN will be used. The numerical analysis methods associated with these tests are discussed. (author)

  1. Success Factors of European Syndromic Surveillance Systems: A Worked Example of Applying Qualitative Comparative Analysis.

    Science.gov (United States)

    Ziemann, Alexandra; Fouillet, Anne; Brand, Helmut; Krafft, Thomas

    2016-01-01

    Syndromic surveillance aims at augmenting traditional public health surveillance with timely information. To gain a head start, it mainly analyses existing data such as from web searches or patient records. Despite the setup of many syndromic surveillance systems, there is still much doubt about the benefit of the approach. There are diverse interactions between performance indicators such as timeliness and various system characteristics. This makes the performance assessment of syndromic surveillance systems a complex endeavour. We assessed if the comparison of several syndromic surveillance systems through Qualitative Comparative Analysis helps to evaluate performance and identify key success factors. We compiled case-based, mixed data on performance and characteristics of 19 syndromic surveillance systems in Europe from scientific and grey literature and from site visits. We identified success factors by applying crisp-set Qualitative Comparative Analysis. We focused on two main areas of syndromic surveillance application: seasonal influenza surveillance and situational awareness during different types of potentially health threatening events. We found that syndromic surveillance systems might detect the onset or peak of seasonal influenza earlier if they analyse non-clinical data sources. Timely situational awareness during different types of events is supported by an automated syndromic surveillance system capable of analysing multiple syndromes. To our surprise, the analysis of multiple data sources was no key success factor for situational awareness. We suggest to consider these key success factors when designing or further developing syndromic surveillance systems. Qualitative Comparative Analysis helped interpreting complex, mixed data on small-N cases and resulted in concrete and practically relevant findings.

  2. Applied Electromagnetics

    Energy Technology Data Exchange (ETDEWEB)

    Yamashita, H; Marinova, I; Cingoski, V [eds.

    2002-07-01

    These proceedings contain papers relating to the 3rd Japanese-Bulgarian-Macedonian Joint Seminar on Applied Electromagnetics. Included are the following groups: Numerical Methods I; Electrical and Mechanical System Analysis and Simulations; Inverse Problems and Optimizations; Software Methodology; Numerical Methods II; Applied Electromagnetics.

  3. Applied Electromagnetics

    International Nuclear Information System (INIS)

    Yamashita, H.; Marinova, I.; Cingoski, V.

    2002-01-01

    These proceedings contain papers relating to the 3rd Japanese-Bulgarian-Macedonian Joint Seminar on Applied Electromagnetics. Included are the following groups: Numerical Methods I; Electrical and Mechanical System Analysis and Simulations; Inverse Problems and Optimizations; Software Methodology; Numerical Methods II; Applied Electromagnetics

  4. Analysis of meniscal degeneration and meniscal gene expression

    Directory of Open Access Journals (Sweden)

    Norton James H

    2010-01-01

    Full Text Available Abstract Background Menisci play a vital role in load transmission, shock absorption and joint stability. There is increasing evidence suggesting that OA menisci may not merely be bystanders in the disease process of OA. This study sought: 1 to determine the prevalence of meniscal degeneration in OA patients, and 2 to examine gene expression in OA meniscal cells compared to normal meniscal cells. Methods Studies were approved by our human subjects Institutional Review Board. Menisci and articular cartilage were collected during joint replacement surgery for OA patients and lower limb amputation surgery for osteosarcoma patients (normal control specimens, and graded. Meniscal cells were prepared from these meniscal tissues and expanded in monolayer culture. Differential gene expression in OA meniscal cells and normal meniscal cells was examined using Affymetrix microarray and real time RT-PCR. Results The grades of meniscal degeneration correlated with the grades of articular cartilage degeneration (r = 0.672; P HLA-DPA1, integrin, beta 2 (ITGB2, ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1, ankylosis, progressive homolog (ANKH and fibroblast growth factor 7 (FGF7, were expressed at significantly higher levels in OA meniscal cells compared to normal meniscal cells. Importantly, many of the genes that have been shown to be differentially expressed in other OA cell types/tissues, including ADAM metallopeptidase with thrombospondin type 1 motif 5 (ADAMTS5 and prostaglandin E synthase (PTGES, were found to be expressed at significantly higher levels in OA meniscal cells. This consistency suggests that many of the genes detected in our study are disease-specific. Conclusion Our findings suggest that OA is a whole joint disease. Meniscal cells may play an active role in the development of OA. Investigation of the gene expression profiles of OA meniscal cells may reveal new therapeutic targets for OA therapy and also may uncover novel

  5. School-Wide PBIS: Extending the Impact of Applied Behavior Analysis. Why is This Important to Behavior Analysts?

    Science.gov (United States)

    Putnam, Robert F; Kincaid, Donald

    2015-05-01

    Horner and Sugai (2015) recently wrote a manuscript providing an overview of school-wide positive behavioral interventions and supports (PBIS) and why it is an example of applied behavior analysis at the scale of social importance. This paper will describe why school-wide PBIS is important to behavior analysts, how it helps promote applied behavior analysis in schools and other organizations, and how behavior analysts can use this framework to assist them in the promotion and implementation of applied behavior analysis at both at the school and organizational level, as well as, the classroom and individual level.

  6. 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.

  7. Analysis of coupled neutron-gamma radiations, applied to shieldings in multigroup albedo method

    International Nuclear Information System (INIS)

    Dunley, Leonardo Souza

    2002-01-01

    The principal mathematical tools frequently available for calculations in Nuclear Engineering, including coupled neutron-gamma radiations shielding problems, involve the full Transport Theory or the Monte Carlo techniques. The Multigroup Albedo Method applied to shieldings is characterized by following the radiations through distinct layers of materials, allowing the determination of the neutron and gamma fractions reflected from, transmitted through and absorbed in the irradiated media when a neutronic stream hits the first layer of material, independently of flux calculations. Then, the method is a complementary tool of great didactic value due to its clarity and simplicity in solving neutron and/or gamma shielding problems. The outstanding results achieved in previous works motivated the elaboration and the development of this study that is presented in this dissertation. The radiation balance resulting from the incidence of a neutronic stream into a shielding composed by 'm' non-multiplying slab layers for neutrons was determined by the Albedo method, considering 'n' energy groups for neutrons and 'g' energy groups for gammas. It was taken into account there is no upscattering of neutrons and gammas. However, it was considered that neutrons from any energy groups are able to produce gammas of all energy groups. The ANISN code, for an angular quadrature order S 2 , was used as a standard for comparison of the results obtained by the Albedo method. So, it was necessary to choose an identical system configuration, both for ANISN and Albedo methods. This configuration was six neutron energy groups and eight gamma energy groups, using three slab layers (iron aluminum - manganese). The excellent results expressed in comparative tables show great agreement between the values determined by the deterministic code adopted as standard and, the values determined by the computational program created using the Albedo method and the algorithm developed for coupled neutron

  8. Acquaintance Rape: Applying Crime Scene Analysis to the Prediction of Sexual Recidivism.

    Science.gov (United States)

    Lehmann, Robert J B; Goodwill, Alasdair M; Hanson, R Karl; Dahle, Klaus-Peter

    2016-10-01

    The aim of the current study was to enhance the assessment and predictive accuracy of risk assessments for sexual offenders by utilizing detailed crime scene analysis (CSA). CSA was conducted on a sample of 247 male acquaintance rapists from Berlin (Germany) using a nonmetric, multidimensional scaling (MDS) Behavioral Thematic Analysis (BTA) approach. The age of the offenders at the time of the index offense ranged from 14 to 64 years (M = 32.3; SD = 11.4). The BTA procedure revealed three behavioral themes of hostility, criminality, and pseudo-intimacy, consistent with previous CSA research on stranger rape. The construct validity of the three themes was demonstrated through correlational analyses with known sexual offending measures and criminal histories. The themes of hostility and pseudo-intimacy were significant predictors of sexual recidivism. In addition, the pseudo-intimacy theme led to a significant increase in the incremental validity of the Static-99 actuarial risk assessment instrument for the prediction of sexual recidivism. The results indicate the potential utility and validity of crime scene behaviors in the applied risk assessment of sexual offenders. © The Author(s) 2015.

  9. Failure Bounding And Sensitivity Analysis Applied To Monte Carlo Entry, Descent, And Landing Simulations

    Science.gov (United States)

    Gaebler, John A.; Tolson, Robert H.

    2010-01-01

    In the study of entry, descent, and landing, Monte Carlo sampling methods are often employed to study the uncertainty in the designed trajectory. The large number of uncertain inputs and outputs, coupled with complicated non-linear models, can make interpretation of the results difficult. Three methods that provide statistical insights are applied to an entry, descent, and landing simulation. The advantages and disadvantages of each method are discussed in terms of the insights gained versus the computational cost. The first method investigated was failure domain bounding which aims to reduce the computational cost of assessing the failure probability. Next a variance-based sensitivity analysis was studied for the ability to identify which input variable uncertainty has the greatest impact on the uncertainty of an output. Finally, probabilistic sensitivity analysis is used to calculate certain sensitivities at a reduced computational cost. These methods produce valuable information that identifies critical mission parameters and needs for new technology, but generally at a significant computational cost.

  10. Analysis of Phoenix Anomalies and IV & V Findings Applied to the GRAIL Mission

    Science.gov (United States)

    Larson, Steve

    2012-01-01

    NASA IV&V was established in 1993 to improve safety and cost-effectiveness of mission critical software. Since its inception the tools and strategies employed by IV&V have evolved. This paper examines how lessons learned from the Phoenix project were developed and applied to the GRAIL project. Shortly after selection, the GRAIL project initiated a review of the issues documented by IV&V for Phoenix. The motivation was twofold: the learn as much as possible about the types of issues that arose from the flight software product line slated for use on GRAIL, and to identify opportunities for improving the effectiveness of IV&V on GRAIL. The IV&V Facility provided a database dump containing 893 issues. These were categorized into 16 bins, and then analyzed according to whether the project responded by changing the affected artifacts or using as-is. The results of this analysis were compared to a similar assessment of post-launch anomalies documented by the project. Results of the analysis were discussed with the IV&V team assigned to GRAIL. These discussions led to changes in the way both the project and IV&V approached the IV&V task, and improved the efficiency of the activity.

  11. How can social network analysis contribute to social behavior research in applied ethology?

    Science.gov (United States)

    Makagon, Maja M; McCowan, Brenda; Mench, Joy A

    2012-05-01

    Social network analysis is increasingly used by behavioral ecologists and primatologists to describe the patterns and quality of interactions among individuals. We provide an overview of this methodology, with examples illustrating how it can be used to study social behavior in applied contexts. Like most kinds of social interaction analyses, social network analysis provides information about direct relationships (e.g. dominant-subordinate relationships). However, it also generates a more global model of social organization that determines how individual patterns of social interaction relate to individual and group characteristics. A particular strength of this approach is that it provides standardized mathematical methods for calculating metrics of sociality across levels of social organization, from the population and group levels to the individual level. At the group level these metrics can be used to track changes in social network structures over time, evaluate the effect of the environment on social network structure, or compare social structures across groups, populations or species. At the individual level, the metrics allow quantification of the heterogeneity of social experience within groups and identification of individuals who may play especially important roles in maintaining social stability or information flow throughout the network.

  12. Independent component analysis applied to long bunch beams in the Los Alamos Proton Storage Ring

    Science.gov (United States)

    Kolski, Jeffrey S.; Macek, Robert J.; McCrady, Rodney C.; Pang, Xiaoying

    2012-11-01

    Independent component analysis (ICA) is a powerful blind source separation (BSS) method. Compared to the typical BSS method, principal component analysis, ICA is more robust to noise, coupling, and nonlinearity. The conventional ICA application to turn-by-turn position data from multiple beam position monitors (BPMs) yields information about cross-BPM correlations. With this scheme, multi-BPM ICA has been used to measure the transverse betatron phase and amplitude functions, dispersion function, linear coupling, sextupole strength, and nonlinear beam dynamics. We apply ICA in a new way to slices along the bunch revealing correlations of particle motion within the beam bunch. We digitize beam signals of the long bunch at the Los Alamos Proton Storage Ring with a single device (BPM or fast current monitor) for an entire injection-extraction cycle. ICA of the digitized beam signals results in source signals, which we identify to describe varying betatron motion along the bunch, locations of transverse resonances along the bunch, measurement noise, characteristic frequencies of the digitizing oscilloscopes, and longitudinal beam structure.

  13. Independent component analysis applied to long bunch beams in the Los Alamos Proton Storage Ring

    Directory of Open Access Journals (Sweden)

    Jeffrey S. Kolski

    2012-11-01

    Full Text Available Independent component analysis (ICA is a powerful blind source separation (BSS method. Compared to the typical BSS method, principal component analysis, ICA is more robust to noise, coupling, and nonlinearity. The conventional ICA application to turn-by-turn position data from multiple beam position monitors (BPMs yields information about cross-BPM correlations. With this scheme, multi-BPM ICA has been used to measure the transverse betatron phase and amplitude functions, dispersion function, linear coupling, sextupole strength, and nonlinear beam dynamics. We apply ICA in a new way to slices along the bunch revealing correlations of particle motion within the beam bunch. We digitize beam signals of the long bunch at the Los Alamos Proton Storage Ring with a single device (BPM or fast current monitor for an entire injection-extraction cycle. ICA of the digitized beam signals results in source signals, which we identify to describe varying betatron motion along the bunch, locations of transverse resonances along the bunch, measurement noise, characteristic frequencies of the digitizing oscilloscopes, and longitudinal beam structure.

  14. Molecular cloning, structural analysis and expression of a zinc ...

    African Journals Online (AJOL)

    The results of prokaryotic expression of ZnBP and overexpression of the ZnBP gene in A. thaliana improve our understanding of the function of this gene. Future studies should investigate the molecular mechanisms involved in gland morphogenesis in cotton. Key words: Gossypium hirsutum, pigment gland, zinc binding ...

  15. Identification and expression analysis of zebrafish glypicans during embryonic development.

    Directory of Open Access Journals (Sweden)

    Mansi Gupta

    Full Text Available Heparan sulfate Proteoglycans (HSPG are ubiquitous molecules with indispensable functions in various biological processes. Glypicans are a family of HSPG's, characterized by a Gpi-anchor which directs them to the cell surface and/or extracellular matrix where they regulate growth factor signaling during development and disease. We report the identification and expression pattern of glypican genes from zebrafish. The zebrafish genome contains 10 glypican homologs, as opposed to six in mammals, which are highly conserved and are phylogenetically related to the mammalian genes. Some of the fish glypicans like Gpc1a, Gpc3, Gpc4, Gpc6a and Gpc6b show conserved synteny with their mammalian cognate genes. Many glypicans are expressed during the gastrulation stage, but their expression becomes more tissue specific and defined during somitogenesis stages, particularly in the developing central nervous system. Existence of multiple glypican orthologs in fish with diverse expression pattern suggests highly specialized and/or redundant function of these genes during embryonic development.

  16. Expression analysis of OsbZIP transcription factors in resistance ...

    African Journals Online (AJOL)

    zino

    2013-08-21

    Aug 21, 2013 ... Plant basic leucine zipper (bZIP) proteins play an essential role in the genes expression and regulation in higher plants. They have been shown to regulate diverse plant specific phenomena, including germination, floral induction and development, seed maturation, photomorphogenesis, biotic and.

  17. Isolation and expression analysis of LEA genes in peanut

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Late embryogenesis abundant (LEA) protein family is a large protein family that includes proteins accumulated at late stages of seed development or in vegetative tissues in response to drought, salinity, cold stress and exogenous application of abscisic acid. In order to isolate peanut genes, an expressed ...

  18. Cloning, expression and functional analysis of MAP30 from ...

    African Journals Online (AJOL)

    use

    2011-12-07

    Dec 7, 2011 ... gene was cloned and expressed and the induction of the recombinant MAP30 protein on .... RNA reverse transcription was carried out by RevertAidTM First ... volume of Premix Ex Taq™ (Takara Bio Inc, Japan), PCR cycling.

  19. Cloning and expression analysis of a blue copperbinding protein ...

    African Journals Online (AJOL)

    Adifferentially expressed fragment EST145 was isolated by suppression subtractive hybridization (SSH) method. Using EST145 as the probe, a blue copper-binding protein gene designated as DvBCB was screened from Dasypyrum villosum cDNA Library. The DvBCB gene was 845 bp in length with an open reading frame ...

  20. DNA sequence and prokaryotic expression analysis of vitellogenin ...

    African Journals Online (AJOL)

    In this study, the DNA sequence of vitellogenin from Antheraea pernyi (Ap-Vg) was identified and its functional domain (30-740 aa, Ap-Vg-1) was expressed in Escherichia coli BL21 (DE3) cells. The recombinant Ap-Vg-1 proteins were purified and used for antibody preparation. The results showed that the intact DNA ...

  1. Gene expression analysis identifies global gene dosage sensitivity in cancer

    DEFF Research Database (Denmark)

    Fehrmann, Rudolf S. N.; Karjalainen, Juha M.; Krajewska, Malgorzata

    2015-01-01

    Many cancer-associated somatic copy number alterations (SCNAs) are known. Currently, one of the challenges is to identify the molecular downstream effects of these variants. Although several SCNAs are known to change gene expression levels, it is not clear whether each individual SCNA affects gen...

  2. Molecular characterization and expression analysis of a hepcidin ...

    African Journals Online (AJOL)

    After challenged with Aeromonas hydrophila infection or iron-dextran stimulation, the hepcidin transcript levels were analyzed by RT-PCR. The results revealed that the expression of hepcidin dramatically increased at 24 h post-infection of the pathogen injection. Moreover, hepcidin mRNAs in the liver, intestine and brain ...

  3. Analysis and visualization of gene expression data using ...

    African Journals Online (AJOL)

    Several clustering and biclustering methods have been introduced to analyze the gene expression data by identifying the similar patterns and grouping genes into subsets that share biological significance. However, it is not clear how the different methods compare with each other with respect to the biological relevance of ...

  4. Expression profiling of human renal carcinomas with functional taxonomic analysis

    Science.gov (United States)

    2002-01-01

    Background Molecular characterization has contributed to the understanding of the inception, progression, treatment and prognosis of cancer. Nucleic acid array-based technologies extend molecular characterization of tumors to thousands of gene products. To effectively discriminate between tumor sub-types, reliable laboratory techniques and analytic methods are required. Results We derived mRNA expression profiles from 21 human tissue samples (eight normal kidneys and 13 kidney tumors) and two pooled samples using the Affymetrix GeneChip platform. A panel of ten clustering algorithms combined with four data pre-processing methods identified a consensus cluster dendrogram in 18 of 40 analyses and of these 16 used a logarithmic transformation. Within the consensus dendrogram the expression profiles of the samples grouped according to tissue type; clear cell and chromophobe carcinomas displayed distinctly different gene expression patterns. By using a rigorous statistical selection based method we identified 355 genes that showed significant (p Matrix Organization and Adhesion. Conclusions Affymetrix GeneChip profiling differentiated clear cell and chromophobe carcinomas from one another and from normal kidney cortex. Clustering methods that used logarithmic transformation of data sets produced dendrograms consistent with the sample biology. Functional taxonomy provided a practical approach to the interpretation of gene expression data. PMID:12356337

  5. Expression profiling of human renal carcinomas with functional taxonomic analysis

    Directory of Open Access Journals (Sweden)

    Madore Steven J

    2002-09-01

    Full Text Available Abstract Background Molecular characterization has contributed to the understanding of the inception, progression, treatment and prognosis of cancer. Nucleic acid array-based technologies extend molecular characterization of tumors to thousands of gene products. To effectively discriminate between tumor sub-types, reliable laboratory techniques and analytic methods are required. Results We derived mRNA expression profiles from 21 human tissue samples (eight normal kidneys and 13 kidney tumors and two pooled samples using the Affymetrix GeneChip platform. A panel of ten clustering algorithms combined with four data pre-processing methods identified a consensus cluster dendrogram in 18 of 40 analyses and of these 16 used a logarithmic transformation. Within the consensus dendrogram the expression profiles of the samples grouped according to tissue type; clear cell and chromophobe carcinomas displayed distinctly different gene expression patterns. By using a rigorous statistical selection based method we identified 355 genes that showed significant (p Conclusions Affymetrix GeneChip profiling differentiated clear cell and chromophobe carcinomas from one another and from normal kidney cortex. Clustering methods that used logarithmic transformation of data sets produced dendrograms consistent with the sample biology. Functional taxonomy provided a practical approach to the interpretation of gene expression data.

  6. Cloning and mRNA expression pattern analysis under low ...

    African Journals Online (AJOL)

    This research cloned endochitinase-antifreeze protein precursor (EAPP) gene of Dong-mu 70 rye (Secale cereale) by designing special primers according to Genbank's EAPP gene sequence, and analyzing the influence of low temperature stress on the expression of mRNA with RT-PCR. The results indicated that the ...

  7. Molecular characters and expression analysis of a new isoform of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-10-20

    Oct 20, 2008 ... isoform of the myocyte enhancer factor 2 gene from the silkworm, Bombyx mori. Qing-zhi Ling1, 2, ... BMEF2B mRNA content in the brain was measured using the combined method of quantitative RT-PCR and Southern ... specific cofactors to control gene expression in pheno- typically different muscles.

  8. Molecular cloning, sequence analysis and tissue expression of ...

    African Journals Online (AJOL)

    Proofreader

    2017-10-01

    Oct 1, 2017 ... p-distance model for amino acid substitutions. A bootstrap .... These were a thymine/cytosine (T/C) SNP and a thymine/adenine (T/A) SNP. ..... Two rat homologues of Drosophila achaete–scute specifically expressed in ...

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

    African Journals Online (AJOL)

    Haloxylon ammodendron (C.A Mey.) Bunge is a xero-halophytic desert shrub with excellent drought resistance and salt tolerance. To decipher the molecular responses involved in its drought resistance, the cDNA-AFLP (amplified fragment length polymorphism) technique was employed to identify genes expressed ...

  10. The application of DNA microarrays in gene expression analysis

    NARCIS (Netherlands)

    Hal, van N.L.W.; Vorst, O.; Houwelingen, van A.M.M.L.; Kok, E.J.; Peijnenburg, A.A.C.M.; Aharoni, A.; Tunen, van A.J.; Keijer, J.

    2000-01-01

    DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed.

  11. The time-course analysis of gene expression during wound healing in mouse skin.

    Science.gov (United States)

    Kagawa, Shinichiro; Matsuo, Aya; Yagi, Yoichi; Ikematsu, Kazuya; Tsuda, Ryouichi; Nakasono, Ichiro

    2009-03-01

    RNA analysis has been applied to forensic work to determine wound age. We investigated mRNA expression using quantitative RT-PCR of ten genes, including c-fos, fosB, mitogen-activated protein kinase phosphatase-1 (MKP-1), CD14, chemokine (C-C motif) ligand 9 (CCL9), placenta growth factor (PlGF), mast cell protease-5 (MCP-5), growth arrest specific 5 (Gas5), beta-2 microglobulin (B2M) and major urinary protein-1 (MUP-1), in terms of repair response in adult mice. The expression level of c-fos, fosB and MKP-1 transcripts increased drastically, peaked within 1h, and that of the CD14 and CCL9 transcripts peaked from 12 to 24h. An increase in PlGF and MCP-5 mRNA appeared on about day 5. Gas5, B2M and MUP-1 transcripts showed no significant change. Each gene had differentially expressional patterns with time-course. Our result implied that the observation of the 7 genes in wounded skin could serve to aid in the accurate diagnosis of wound age.

  12. Applying information network analysis to fire-prone landscapes: implications for community resilience

    Directory of Open Access Journals (Sweden)

    Derric B. Jacobs

    2017-03-01

    Full Text Available Resilient communities promote trust, have well-developed networks, and can adapt to change. For rural communities in fire-prone landscapes, current resilience strategies may prove insufficient in light of increasing wildfire risks due to climate change. It is argued that, given the complexity of climate change, adaptations are best addressed at local levels where specific social, cultural, political, and economic conditions are matched with local risks and opportunities. Despite the importance of social networks as key attributes of community resilience, research using social network analysis on coupled human and natural systems is scarce. Furthermore, the extent to which local communities in fire-prone areas understand climate change risks, accept the likelihood of potential changes, and have the capacity to develop collaborative mitigation strategies is underexamined, yet these factors are imperative to community resiliency. We apply a social network framework to examine information networks that affect perceptions of wildfire and climate change in Central Oregon. Data were collected using a mailed questionnaire. Analysis focused on the residents' information networks that are used to gain awareness of governmental activities and measures of community social capital. A two-mode network analysis was used to uncover information exchanges. Results suggest that the general public develops perceptions about climate change based on complex social and cultural systems rather than as patrons of scientific inquiry and understanding. It appears that perceptions about climate change itself may not be the limiting factor in these communities' adaptive capacity, but rather how they perceive local risks. We provide a novel methodological approach in understanding rural community adaptation and resilience in fire-prone landscapes and offer a framework for future studies.

  13. Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans

    Directory of Open Access Journals (Sweden)

    Benjamin Mayne

    2016-10-01

    Full Text Available The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analysed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes, followed by the heart (375 genes, kidney (224 genes, colon (218 genes and thyroid (163 genes. More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.

  14. Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set.

    Directory of Open Access Journals (Sweden)

    Clive H Glover

    2006-11-01

    Full Text Available Stem cell differentiation involves critical changes in gene expression. Identification of these should provide endpoints useful for optimizing stem cell propagation as well as potential clues about mechanisms governing stem cell maintenance. Here we describe the results of a new meta-analysis methodology applied to multiple gene expression datasets from three mouse embryonic stem cell (ESC lines obtained at specific time points during the course of their differentiation into various lineages. We developed methods to identify genes with expression changes that correlated with the altered frequency of functionally defined, undifferentiated ESC in culture. In each dataset, we computed a novel statistical confidence measure for every gene which captured the certainty that a particular gene exhibited an expression pattern of interest within that dataset. This permitted a joint analysis of the datasets, despite the different experimental designs. Using a ranking scheme that favored genes exhibiting patterns of interest, we focused on the top 88 genes whose expression was consistently changed when ESC were induced to differentiate. Seven of these (103728_at, 8430410A17Rik, Klf2, Nr0b1, Sox2, Tcl1, and Zfp42 showed a rapid decrease in expression concurrent with a decrease in frequency of undifferentiated cells and remained predictive when evaluated in additional maintenance and differentiating protocols. Through a novel meta-analysis, this study identifies a small set of genes whose expression is useful for identifying changes in stem cell frequencies in cultures of mouse ESC. The methods and findings have broader applicability to understanding the regulation of self-renewal of other stem cell types.

  15. Comparative analysis of lockout programs and procedures applied to industrial machines

    Energy Technology Data Exchange (ETDEWEB)

    Chinniah, Y.; Champoux, M.; Burlet-Vienney, D.; Daigle, R. [Institut de recherche Robert-Sauve en sante et en securite du travail, Montreal, PQ (Canada)

    2008-09-15

    In 2005, approximately 20 workers in Quebec were killed by dangerous machines. Approximately 13,000 accidents in the province were linked to the use of machines. The resulting cost associated with these accidents was estimated to be $70 million to the Quebec Occupational Health and Safety Commission (CSST) in compensation and salary replacement. According to article 185 of the Quebec Occupational Health and Safety Regulation (RSST), workers intervening in hazardous zones of machines and processes during maintenance, repairs, and unjamming activities must apply lockout procedures. Lockout is defined as the placement of a lock or tag on an energy-isolating device in accordance with an established procedure, indicating that the energy-isolating device is not to be operated until removal of the lock or tag in accordance with an established procedure. This report presented a comparative analysis of lockout programs and procedures applied to industrial machines. The study attempted to answer several questions regarding the concept of lockout and its definition in the literature; the differences between legal lockout requirements among provinces and countries; different standards on lockout; the contents of lockout programs as described by different documents; and the compliance of lockout programs in a sample of industries in Quebec in terms of Canadian standard on lockout, the CSA Z460-05 (2005). The report discussed the research objectives, methodology, and results of the study. It was concluded that the concept of lockout has different meanings or definitions in the literature, especially in regulations. However, definitions of lockout which are found in standards have certain similarities. 50 refs., 52 tabs., 2 appendices.

  16. A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma

    DEFF Research Database (Denmark)

    Sun, Xiangqing; Vengoechea, Jaime; Elston, Robert

    2012-01-01

    We propose a 2-step model-based approach, with correction for ascertainment, to linkage analysis of a binary trait with variable age of onset and apply it to a set of multiplex pedigrees segregating for adult glioma....

  17. Non-Linear Non Stationary Analysis of Two-Dimensional Time-Series Applied to GRACE Data, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovative two-dimensional (2D) empirical mode decomposition (EMD) analysis was applied to NASA's Gravity Recovery and Climate Experiment (GRACE)...

  18. A Pilot Study on the Combination of Applied Behavior Analysis and Bumetanide Treatment for Children with Autism

    NARCIS (Netherlands)

    Du, L.; Shan, L.; Wang, B.; Li, H.; Xu, Z.; Staal, W.G.; Jia, F.

    2015-01-01

    OBJECTIVE: The purpose of this study was to investigate the therapeutic effects of combined bumetanide and applied behavior analysis (ABA) treatment in children with autism. METHODS: Sixty children diagnosed with autism according to the International Classification of Diseases, Tenth Revision

  19. Molecular cloning, expression and computational analysis of a water ...

    African Journals Online (AJOL)

    User

    2012-11-06

    Nov 6, 2012 ... analysis of a water stress inducible copper-containing ... Although, in slico analysis of the protein have indicated its probable structure and functions, further ..... based on protein data bank (PDB) template c1ksiA which.

  20. 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.