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Sample records for microarray facilities selected

  1. SLIMarray: Lightweight software for microarray facility management

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    Marzolf Bruz

    2006-10-01

    Full Text Available Abstract Background Microarray core facilities are commonplace in biological research organizations, and need systems for accurately tracking various logistical aspects of their operation. Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors. Results We present SLIMarray (System for Lab Information Management of Microarrays, an open source, modular database web application capable of managing microarray inventories, sample processing and usage charges. The software allows modular configuration and is well suited for further development, providing users the flexibility to adapt it to their needs. SLIMarray Lite, a version of the software that is especially easy to install and run, is also available. Conclusion SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

  2. Detection of selected plant viruses by microarrays

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    HRABÁKOVÁ, Lenka

    2013-01-01

    The main aim of this master thesis was the simultaneous detection of four selected plant viruses ? Apple mosaic virus, Plum pox virus, Prunus necrotic ringspot virus and Prune harf virus, by microarrays. The intermediate step in the process of the detection was optimizing of multiplex polymerase chain reaction (PCR).

  3. Probe Selection for DNA Microarrays using OligoWiz

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    Wernersson, Rasmus; Juncker, Agnieszka; Nielsen, Henrik Bjørn

    2007-01-01

    Nucleotide abundance measurements using DNA microarray technology are possible only if appropriate probes complementary to the target nucleotides can be identified. Here we present a protocol for selecting DNA probes for microarrays using the OligoWiz application. OligoWiz is a client-server appl......Nucleotide abundance measurements using DNA microarray technology are possible only if appropriate probes complementary to the target nucleotides can be identified. Here we present a protocol for selecting DNA probes for microarrays using the OligoWiz application. OligoWiz is a client......-server application that offers a detailed graphical interface and real-time user interaction on the client side, and massive computer power and a large collection of species databases (400, summer 2007) on the server side. Probes are selected according to five weighted scores: cross-hybridization, deltaT(m), folding...... computer skills and can be executed from any Internet-connected computer. The probe selection procedure for a standard microarray design targeting all yeast transcripts can be completed in 1 h....

  4. MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies

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    Beaudoing Emmanuel

    2006-09-01

    Full Text Available Abstract Background High throughput gene expression profiling (GEP is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. Results MAF (MicroArray Facility is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking, data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. Conclusion MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for

  5. Gene selection for microarray data classification via subspace learning and manifold regularization.

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    Tang, Chang; Cao, Lijuan; Zheng, Xiao; Wang, Minhui

    2017-12-19

    With the rapid development of DNA microarray technology, large amount of genomic data has been generated. Classification of these microarray data is a challenge task since gene expression data are often with thousands of genes but a small number of samples. In this paper, an effective gene selection method is proposed to select the best subset of genes for microarray data with the irrelevant and redundant genes removed. Compared with original data, the selected gene subset can benefit the classification task. We formulate the gene selection task as a manifold regularized subspace learning problem. In detail, a projection matrix is used to project the original high dimensional microarray data into a lower dimensional subspace, with the constraint that the original genes can be well represented by the selected genes. Meanwhile, the local manifold structure of original data is preserved by a Laplacian graph regularization term on the low-dimensional data space. The projection matrix can serve as an importance indicator of different genes. An iterative update algorithm is developed for solving the problem. Experimental results on six publicly available microarray datasets and one clinical dataset demonstrate that the proposed method performs better when compared with other state-of-the-art methods in terms of microarray data classification. Graphical Abstract The graphical abstract of this work.

  6. FiGS: a filter-based gene selection workbench for microarray data

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    Yun Taegyun

    2010-01-01

    Full Text Available Abstract Background The selection of genes that discriminate disease classes from microarray data is widely used for the identification of diagnostic biomarkers. Although various gene selection methods are currently available and some of them have shown excellent performance, no single method can retain the best performance for all types of microarray datasets. It is desirable to use a comparative approach to find the best gene selection result after rigorous test of different methodological strategies for a given microarray dataset. Results FiGS is a web-based workbench that automatically compares various gene selection procedures and provides the optimal gene selection result for an input microarray dataset. FiGS builds up diverse gene selection procedures by aligning different feature selection techniques and classifiers. In addition to the highly reputed techniques, FiGS diversifies the gene selection procedures by incorporating gene clustering options in the feature selection step and different data pre-processing options in classifier training step. All candidate gene selection procedures are evaluated by the .632+ bootstrap errors and listed with their classification accuracies and selected gene sets. FiGS runs on parallelized computing nodes that capacitate heavy computations. FiGS is freely accessible at http://gexp.kaist.ac.kr/figs. Conclusion FiGS is an web-based application that automates an extensive search for the optimized gene selection analysis for a microarray dataset in a parallel computing environment. FiGS will provide both an efficient and comprehensive means of acquiring optimal gene sets that discriminate disease states from microarray datasets.

  7. A study of metaheuristic algorithms for high dimensional feature selection on microarray data

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    Dankolo, Muhammad Nasiru; Radzi, Nor Haizan Mohamed; Sallehuddin, Roselina; Mustaffa, Noorfa Haszlinna

    2017-11-01

    Microarray systems enable experts to examine gene profile at molecular level using machine learning algorithms. It increases the potentials of classification and diagnosis of many diseases at gene expression level. Though, numerous difficulties may affect the efficiency of machine learning algorithms which includes vast number of genes features comprised in the original data. Many of these features may be unrelated to the intended analysis. Therefore, feature selection is necessary to be performed in the data pre-processing. Many feature selection algorithms are developed and applied on microarray which including the metaheuristic optimization algorithms. This paper discusses the application of the metaheuristics algorithms for feature selection in microarray dataset. This study reveals that, the algorithms have yield an interesting result with limited resources thereby saving computational expenses of machine learning algorithms.

  8. Robust Feature Selection from Microarray Data Based on Cooperative Game Theory and Qualitative Mutual Information

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    Atiyeh Mortazavi

    2016-01-01

    Full Text Available High dimensionality of microarray data sets may lead to low efficiency and overfitting. In this paper, a multiphase cooperative game theoretic feature selection approach is proposed for microarray data classification. In the first phase, due to high dimension of microarray data sets, the features are reduced using one of the two filter-based feature selection methods, namely, mutual information and Fisher ratio. In the second phase, Shapley index is used to evaluate the power of each feature. The main innovation of the proposed approach is to employ Qualitative Mutual Information (QMI for this purpose. The idea of Qualitative Mutual Information causes the selected features to have more stability and this stability helps to deal with the problem of data imbalance and scarcity. In the third phase, a forward selection scheme is applied which uses a scoring function to weight each feature. The performance of the proposed method is compared with other popular feature selection algorithms such as Fisher ratio, minimum redundancy maximum relevance, and previous works on cooperative game based feature selection. The average classification accuracy on eleven microarray data sets shows that the proposed method improves both average accuracy and average stability compared to other approaches.

  9. Multi-task feature selection in microarray data by binary integer programming.

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    Lan, Liang; Vucetic, Slobodan

    2013-12-20

    A major challenge in microarray classification is that the number of features is typically orders of magnitude larger than the number of examples. In this paper, we propose a novel feature filter algorithm to select the feature subset with maximal discriminative power and minimal redundancy by solving a quadratic objective function with binary integer constraints. To improve the computational efficiency, the binary integer constraints are relaxed and a low-rank approximation to the quadratic term is applied. The proposed feature selection algorithm was extended to solve multi-task microarray classification problems. We compared the single-task version of the proposed feature selection algorithm with 9 existing feature selection methods on 4 benchmark microarray data sets. The empirical results show that the proposed method achieved the most accurate predictions overall. We also evaluated the multi-task version of the proposed algorithm on 8 multi-task microarray datasets. The multi-task feature selection algorithm resulted in significantly higher accuracy than when using the single-task feature selection methods.

  10. Evaluation of gene importance in microarray data based upon probability of selection

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    Fu Li M

    2005-03-01

    Full Text Available Abstract Background Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking to metabolic characteristics that contribute to disease development and progression. The microarray approach offers an expedited solution to this problem. However, it has posed a challenging issue to recognize disease-related genes expression patterns embedded in the microarray data. In selecting a small set of biologically significant genes for classifier design, the nature of high data dimensionality inherent in this problem creates substantial amount of uncertainty. Results Here we present a model for probability analysis of selected genes in order to determine their importance. Our contribution is that we show how to derive the P value of each selected gene in multiple gene selection trials based on different combinations of data samples and how to conduct a reliability analysis accordingly. The importance of a gene is indicated by its associated P value in that a smaller value implies higher information content from information theory. On the microarray data concerning the subtype classification of small round blue cell tumors, we demonstrate that the method is capable of finding the smallest set of genes (19 genes with optimal classification performance, compared with results reported in the literature. Conclusion In classifier design based on microarray data, the probability value derived from gene selection based on multiple combinations of data samples enables an effective mechanism for reducing the tendency of fitting local data particularities.

  11. A Combinatory Approach for Selecting Prognostic Genes in Microarray Studies of Tumour Survivals

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    Qihua Tan

    2009-01-01

    Full Text Available Different from significant gene expression analysis which looks for genes that are differentially regulated, feature selection in the microarray-based prognostic gene expression analysis aims at finding a subset of marker genes that are not only differentially expressed but also informative for prediction. Unfortunately feature selection in literature of microarray study is predominated by the simple heuristic univariate gene filter paradigm that selects differentially expressed genes according to their statistical significances. We introduce a combinatory feature selection strategy that integrates differential gene expression analysis with the Gram-Schmidt process to identify prognostic genes that are both statistically significant and highly informative for predicting tumour survival outcomes. Empirical application to leukemia and ovarian cancer survival data through-within- and cross-study validations shows that the feature space can be largely reduced while achieving improved testing performances.

  12. Statistical Redundancy Testing for Improved Gene Selection in Cancer Classification Using Microarray Data

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    J. Sunil Rao

    2007-01-01

    Full Text Available In gene selection for cancer classifi cation using microarray data, we define an eigenvalue-ratio statistic to measure a gene’s contribution to the joint discriminability when this gene is included into a set of genes. Based on this eigenvalueratio statistic, we define a novel hypothesis testing for gene statistical redundancy and propose two gene selection methods. Simulation studies illustrate the agreement between statistical redundancy testing and gene selection methods. Real data examples show the proposed gene selection methods can select a compact gene subset which can not only be used to build high quality cancer classifiers but also show biological relevance.

  13. Focused Screening of ECM-Selective Adhesion Peptides on Cellulose-Bound Peptide Microarrays.

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    Kanie, Kei; Kondo, Yuto; Owaki, Junki; Ikeda, Yurika; Narita, Yuji; Kato, Ryuji; Honda, Hiroyuki

    2016-11-19

    The coating of surfaces with bio-functional proteins is a promising strategy for the creation of highly biocompatible medical implants. Bio-functional proteins from the extracellular matrix (ECM) provide effective surface functions for controlling cellular behavior. We have previously screened bio-functional tripeptides for feasibility of mass production with the aim of identifying those that are medically useful, such as cell-selective peptides. In this work, we focused on the screening of tripeptides that selectively accumulate collagen type IV (Col IV), an ECM protein that accelerates the re-endothelialization of medical implants. A SPOT peptide microarray was selected for screening owing to its unique cellulose membrane platform, which can mimic fibrous scaffolds used in regenerative medicine. However, since the library size on the SPOT microarray was limited, physicochemical clustering was used to provide broader variation than that of random peptide selection. Using the custom focused microarray of 500 selected peptides, we assayed the relative binding rates of tripeptides to Col IV, collagen type I (Col I), and albumin. We discovered a cluster of Col IV-selective adhesion peptides that exhibit bio-safety with endothelial cells. The results from this study can be used to improve the screening of regeneration-enhancing peptides.

  14. Focused Screening of ECM-Selective Adhesion Peptides on Cellulose-Bound Peptide Microarrays

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    Kei Kanie

    2016-11-01

    Full Text Available The coating of surfaces with bio-functional proteins is a promising strategy for the creation of highly biocompatible medical implants. Bio-functional proteins from the extracellular matrix (ECM provide effective surface functions for controlling cellular behavior. We have previously screened bio-functional tripeptides for feasibility of mass production with the aim of identifying those that are medically useful, such as cell-selective peptides. In this work, we focused on the screening of tripeptides that selectively accumulate collagen type IV (Col IV, an ECM protein that accelerates the re-endothelialization of medical implants. A SPOT peptide microarray was selected for screening owing to its unique cellulose membrane platform, which can mimic fibrous scaffolds used in regenerative medicine. However, since the library size on the SPOT microarray was limited, physicochemical clustering was used to provide broader variation than that of random peptide selection. Using the custom focused microarray of 500 selected peptides, we assayed the relative binding rates of tripeptides to Col IV, collagen type I (Col I, and albumin. We discovered a cluster of Col IV-selective adhesion peptides that exhibit bio-safety with endothelial cells. The results from this study can be used to improve the screening of regeneration-enhancing peptides.

  15. Robust gene selection methods using weighting schemes for microarray data analysis.

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    Kang, Suyeon; Song, Jongwoo

    2017-09-02

    A common task in microarray data analysis is to identify informative genes that are differentially expressed between two different states. Owing to the high-dimensional nature of microarray data, identification of significant genes has been essential in analyzing the data. However, the performances of many gene selection techniques are highly dependent on the experimental conditions, such as the presence of measurement error or a limited number of sample replicates. We have proposed new filter-based gene selection techniques, by applying a simple modification to significance analysis of microarrays (SAM). To prove the effectiveness of the proposed method, we considered a series of synthetic datasets with different noise levels and sample sizes along with two real datasets. The following findings were made. First, our proposed methods outperform conventional methods for all simulation set-ups. In particular, our methods are much better when the given data are noisy and sample size is small. They showed relatively robust performance regardless of noise level and sample size, whereas the performance of SAM became significantly worse as the noise level became high or sample size decreased. When sufficient sample replicates were available, SAM and our methods showed similar performance. Finally, our proposed methods are competitive with traditional methods in classification tasks for microarrays. The results of simulation study and real data analysis have demonstrated that our proposed methods are effective for detecting significant genes and classification tasks, especially when the given data are noisy or have few sample replicates. By employing weighting schemes, we can obtain robust and reliable results for microarray data analysis.

  16. Gene selection and classification for cancer microarray data based on machine learning and similarity measures

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    Liu Qingzhong

    2011-12-01

    Full Text Available Abstract Background Microarray data have a high dimension of variables and a small sample size. In microarray data analyses, two important issues are how to choose genes, which provide reliable and good prediction for disease status, and how to determine the final gene set that is best for classification. Associations among genetic markers mean one can exploit information redundancy to potentially reduce classification cost in terms of time and money. Results To deal with redundant information and improve classification, we propose a gene selection method, Recursive Feature Addition, which combines supervised learning and statistical similarity measures. To determine the final optimal gene set for prediction and classification, we propose an algorithm, Lagging Prediction Peephole Optimization. By using six benchmark microarray gene expression data sets, we compared Recursive Feature Addition with recently developed gene selection methods: Support Vector Machine Recursive Feature Elimination, Leave-One-Out Calculation Sequential Forward Selection and several others. Conclusions On average, with the use of popular learning machines including Nearest Mean Scaled Classifier, Support Vector Machine, Naive Bayes Classifier and Random Forest, Recursive Feature Addition outperformed other methods. Our studies also showed that Lagging Prediction Peephole Optimization is superior to random strategy; Recursive Feature Addition with Lagging Prediction Peephole Optimization obtained better testing accuracies than the gene selection method varSelRF.

  17. Empirical Bayes ranking and selection methods via semiparametric hierarchical mixture models in microarray studies.

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    Noma, Hisashi; Matsui, Shigeyuki

    2013-05-20

    The main purpose of microarray studies is screening of differentially expressed genes as candidates for further investigation. Because of limited resources in this stage, prioritizing genes are relevant statistical tasks in microarray studies. For effective gene selections, parametric empirical Bayes methods for ranking and selection of genes with largest effect sizes have been proposed (Noma et al., 2010; Biostatistics 11: 281-289). The hierarchical mixture model incorporates the differential and non-differential components and allows information borrowing across differential genes with separation from nuisance, non-differential genes. In this article, we develop empirical Bayes ranking methods via a semiparametric hierarchical mixture model. A nonparametric prior distribution, rather than parametric prior distributions, for effect sizes is specified and estimated using the "smoothing by roughening" approach of Laird and Louis (1991; Computational statistics and data analysis 12: 27-37). We present applications to childhood and infant leukemia clinical studies with microarrays for exploring genes related to prognosis or disease progression. Copyright © 2012 John Wiley & Sons, Ltd.

  18. Hybrid Feature Selection Approach Based on GRASP for Cancer Microarray Data

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    Arpita Nagpal

    2017-01-01

    Full Text Available Microarray data usually contain a large number of genes, but a small number of samples. Feature subset selection for microarray data aims at reducing the number of genes so that useful information can be extracted from the samples. Reducing the dimension of data sets further helps in improving the computational efficiency of the learning model. In this paper, we propose a modified algorithm based on the tabu search as local search procedures to a Greedy Randomized Adaptive Search Procedure (GRASP for high dimensional microarray data sets. The proposed Tabu based Greedy Randomized Adaptive Search Procedure algorithm is named as TGRASP. In TGRASP, a new parameter has been introduced named as Tabu Tenure and the existing parameters, NumIter and size have been modified. We observed that different parameter settings affect the quality of the optimum. The second proposed algorithm known as FFGRASP (Firefly Greedy Randomized Adaptive Search Procedure uses a firefly optimization algorithm in the local search optimzation phase of the greedy randomized adaptive search procedure (GRASP. Firefly algorithm is one of the powerful algorithms for optimization of multimodal applications. Experimental results show that the proposed TGRASP and FFGRASP algorithms are much better than existing algorithm with respect to three performance parameters viz. accuracy, run time, number of a selected subset of features. We have also compared both the approaches with a unified metric (Extended Adjusted Ratio of Ratios which has shown that TGRASP approach outperforms existing approach for six out of nine cancer microarray datasets and FFGRASP performs better on seven out of nine datasets.

  19. Genetic Bee Colony (GBC) algorithm: A new gene selection method for microarray cancer classification.

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    Alshamlan, Hala M; Badr, Ghada H; Alohali, Yousef A

    2015-06-01

    Naturally inspired evolutionary algorithms prove effectiveness when used for solving feature selection and classification problems. Artificial Bee Colony (ABC) is a relatively new swarm intelligence method. In this paper, we propose a new hybrid gene selection method, namely Genetic Bee Colony (GBC) algorithm. The proposed algorithm combines the used of a Genetic Algorithm (GA) along with Artificial Bee Colony (ABC) algorithm. The goal is to integrate the advantages of both algorithms. The proposed algorithm is applied to a microarray gene expression profile in order to select the most predictive and informative genes for cancer classification. In order to test the accuracy performance of the proposed algorithm, extensive experiments were conducted. Three binary microarray datasets are use, which include: colon, leukemia, and lung. In addition, another three multi-class microarray datasets are used, which are: SRBCT, lymphoma, and leukemia. Results of the GBC algorithm are compared with our recently proposed technique: mRMR when combined with the Artificial Bee Colony algorithm (mRMR-ABC). We also compared the combination of mRMR with GA (mRMR-GA) and Particle Swarm Optimization (mRMR-PSO) algorithms. In addition, we compared the GBC algorithm with other related algorithms that have been recently published in the literature, using all benchmark datasets. The GBC algorithm shows superior performance as it achieved the highest classification accuracy along with the lowest average number of selected genes. This proves that the GBC algorithm is a promising approach for solving the gene selection problem in both binary and multi-class cancer classification. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. PERBANDINGAN ANALISIS LEAST ABSOLUTE SHRINKAGE AND SELECTION OPERATOR DAN PARTIAL LEAST SQUARES (Studi Kasus: Data Microarray

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    KADEK DWI FARMANI

    2012-09-01

    Full Text Available Linear regression analysis is one of the parametric statistical methods which utilize the relationship between two or more quantitative variables. In linear regression analysis, there are several assumptions that must be met that is normal distribution of errors, there is no correlation between the error and error variance is constant and homogent. There are some constraints that caused the assumption can not be met, for example, the correlation between independent variables (multicollinearity, constraints on the number of data and independent variables are obtained. When the number of samples obtained less than the number of independent variables, then the data is called the microarray data. Least Absolute shrinkage and Selection Operator (LASSO and Partial Least Squares (PLS is a statistical method that can be used to overcome the microarray, overfitting, and multicollinearity. From the above description, it is necessary to study with the intention of comparing LASSO and PLS method. This study uses coronary heart and stroke patients data which is a microarray data and contain multicollinearity. With these two characteristics of the data that most have a weak correlation between independent variables, LASSO method produces a better model than PLS seen from the large RMSEP.

  1. Cancer microarray data feature selection using multi-objective binary particle swarm optimization algorithm

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    Annavarapu, Chandra Sekhara Rao; Dara, Suresh; Banka, Haider

    2016-01-01

    Cancer investigations in microarray data play a major role in cancer analysis and the treatment. Cancer microarray data consists of complex gene expressed patterns of cancer. In this article, a Multi-Objective Binary Particle Swarm Optimization (MOBPSO) algorithm is proposed for analyzing cancer gene expression data. Due to its high dimensionality, a fast heuristic based pre-processing technique is employed to reduce some of the crude domain features from the initial feature set. Since these pre-processed and reduced features are still high dimensional, the proposed MOBPSO algorithm is used for finding further feature subsets. The objective functions are suitably modeled by optimizing two conflicting objectives i.e., cardinality of feature subsets and distinctive capability of those selected subsets. As these two objective functions are conflicting in nature, they are more suitable for multi-objective modeling. The experiments are carried out on benchmark gene expression datasets, i.e., Colon, Lymphoma and Leukaemia available in literature. The performance of the selected feature subsets with their classification accuracy and validated using 10 fold cross validation techniques. A detailed comparative study is also made to show the betterment or competitiveness of the proposed algorithm. PMID:27822174

  2. Feature Genes Selection Using Supervised Locally Linear Embedding and Correlation Coefficient for Microarray Classification.

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    Xu, Jiucheng; Mu, Huiyu; Wang, Yun; Huang, Fangzhou

    2018-01-01

    The selection of feature genes with high recognition ability from the gene expression profiles has gained great significance in biology. However, most of the existing methods have a high time complexity and poor classification performance. Motivated by this, an effective feature selection method, called supervised locally linear embedding and Spearman's rank correlation coefficient (SLLE-SC 2 ), is proposed which is based on the concept of locally linear embedding and correlation coefficient algorithms. Supervised locally linear embedding takes into account class label information and improves the classification performance. Furthermore, Spearman's rank correlation coefficient is used to remove the coexpression genes. The experiment results obtained on four public tumor microarray datasets illustrate that our method is valid and feasible.

  3. Feature selection model based on clustering and ranking in pipeline for microarray data

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    Barnali Sahu

    2017-01-01

    Full Text Available Most of the available feature selection techniques in the literature are classifier bound. It means a group of features tied to the performance of a specific classifier as applied in wrapper and hybrid approach. Our objective in this study is to select a set of generic features not tied to any classifier based on the proposed framework. This framework uses attribute clustering and feature ranking techniques in pipeline in order to remove redundant features. On each uncovered cluster, signal-to-noise ratio, t-statistics and significance analysis of microarray are independently applied to select the top ranked features. Both filter and evolutionary wrapper approaches have been considered for feature selection and the data set with selected features are given to ensemble of predefined statistically different classifiers. The class labels of the test data are determined using majority voting technique. Moreover, with the aforesaid objectives, this paper focuses on obtaining a stable result out of various classification models. Further, a comparative analysis has been performed to study the classification accuracy and computational time of the current approach and evolutionary wrapper techniques. It gives a better insight into the features and further enhancing the classification accuracy with less computational time.

  4. An Entropy-based gene selection method for cancer classification using microarray data

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    Krishnan Arun

    2005-03-01

    Full Text Available Abstract Background Accurate diagnosis of cancer subtypes remains a challenging problem. Building classifiers based on gene expression data is a promising approach; yet the selection of non-redundant but relevant genes is difficult. The selected gene set should be small enough to allow diagnosis even in regular clinical laboratories and ideally identify genes involved in cancer-specific regulatory pathways. Here an entropy-based method is proposed that selects genes related to the different cancer classes while at the same time reducing the redundancy among the genes. Results The present study identifies a subset of features by maximizing the relevance and minimizing the redundancy of the selected genes. A merit called normalized mutual information is employed to measure the relevance and the redundancy of the genes. In order to find a more representative subset of features, an iterative procedure is adopted that incorporates an initial clustering followed by data partitioning and the application of the algorithm to each of the partitions. A leave-one-out approach then selects the most commonly selected genes across all the different runs and the gene selection algorithm is applied again to pare down the list of selected genes until a minimal subset is obtained that gives a satisfactory accuracy of classification. The algorithm was applied to three different data sets and the results obtained were compared to work done by others using the same data sets Conclusion This study presents an entropy-based iterative algorithm for selecting genes from microarray data that are able to classify various cancer sub-types with high accuracy. In addition, the feature set obtained is very compact, that is, the redundancy between genes is reduced to a large extent. This implies that classifiers can be built with a smaller subset of genes.

  5. Dynamic variable selection in SNP genotype autocalling from APEX microarray data

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    Zamar Ruben H

    2006-11-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are DNA sequence variations, occurring when a single nucleotide – adenine (A, thymine (T, cytosine (C or guanine (G – is altered. Arguably, SNPs account for more than 90% of human genetic variation. Our laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension (APEX. This mini-sequencing method is a powerful combination of a highly parallel microarray with distinctive Sanger-based dideoxy terminator sequencing chemistry. Using this microarray platform, our current genotype calling system (known as SNP Chart is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias. Results Using a set of 32 Coriell DNA samples plus three negative PCR controls as a training data set, we have developed a fully-automated genotyping algorithm based on simple linear discriminant analysis (LDA using dynamic variable selection. The algorithm combines separate analyses based on the multiple probe sets to give a final posterior probability for each candidate genotype. We have tested our algorithm on a completely independent data set of 270 DNA samples, with validated genotypes, from patients admitted to the intensive care unit (ICU of St. Paul's Hospital (plus one negative PCR control sample. Our method achieves a concordance rate of 98.9% with a 99.6% call rate for a set of 96 SNPs. By adjusting the threshold value for the final posterior probability of the called genotype, the call rate reduces to 94.9% with a higher concordance rate of 99.6%. We also reversed the two independent data sets in their training and testing roles, achieving a concordance rate up to 99.8%. Conclusion The strength of this APEX chemistry-based platform is its unique redundancy having multiple probes for a single SNP. Our

  6. Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data

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    Harris Lyndsay N

    2006-04-01

    Full Text Available Abstract Background Like microarray-based investigations, high-throughput proteomics techniques require machine learning algorithms to identify biomarkers that are informative for biological classification problems. Feature selection and classification algorithms need to be robust to noise and outliers in the data. Results We developed a recursive support vector machine (R-SVM algorithm to select important genes/biomarkers for the classification of noisy data. We compared its performance to a similar, state-of-the-art method (SVM recursive feature elimination or SVM-RFE, paying special attention to the ability of recovering the true informative genes/biomarkers and the robustness to outliers in the data. Simulation experiments show that a 5 %-~20 % improvement over SVM-RFE can be achieved regard to these properties. The SVM-based methods are also compared with a conventional univariate method and their respective strengths and weaknesses are discussed. R-SVM was applied to two sets of SELDI-TOF-MS proteomics data, one from a human breast cancer study and the other from a study on rat liver cirrhosis. Important biomarkers found by the algorithm were validated by follow-up biological experiments. Conclusion The proposed R-SVM method is suitable for analyzing noisy high-throughput proteomics and microarray data and it outperforms SVM-RFE in the robustness to noise and in the ability to recover informative features. The multivariate SVM-based method outperforms the univariate method in the classification performance, but univariate methods can reveal more of the differentially expressed features especially when there are correlations between the features.

  7. Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data.

    Directory of Open Access Journals (Sweden)

    Qingzhong Liu

    Full Text Available Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort out the datasets. In this paper, we propose a gene selection method called Recursive Feature Addition (RFA, which combines supervised learning and statistical similarity measures. We compare our method with the following gene selection methods: Support Vector Machine Recursive Feature Elimination (SVMRFE, Leave-One-Out Calculation Sequential Forward Selection (LOOCSFS, Gradient based Leave-one-out Gene Selection (GLGS. To evaluate the performance of these gene selection methods, we employ several popular learning classifiers on the MicroArray Quality Control phase II on predictive modeling (MAQC-II breast cancer dataset and the MAQC-II multiple myeloma dataset. Experimental results show that gene selection is strictly paired with learning classifier. Overall, our approach outperforms other compared methods. The biological functional analysis based on the MAQC-II breast cancer dataset convinced us to apply our method for phenotype prediction. Additionally, learning classifiers also play important roles in the classification of microarray data and our experimental results indicate that the Nearest Mean Scale Classifier (NMSC is a good choice due to its prediction reliability and its stability across the three performance measurements: Testing accuracy, MCC values, and

  8. Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data

    Directory of Open Access Journals (Sweden)

    Teng Shaolei

    2013-01-01

    Full Text Available Abstract Background Understanding how genes are expressed specifically in particular tissues is a fundamental question in developmental biology. Many tissue-specific genes are involved in the pathogenesis of complex human diseases. However, experimental identification of tissue-specific genes is time consuming and difficult. The accurate predictions of tissue-specific gene targets could provide useful information for biomarker development and drug target identification. Results In this study, we have developed a machine learning approach for predicting the human tissue-specific genes using microarray expression data. The lists of known tissue-specific genes for different tissues were collected from UniProt database, and the expression data retrieved from the previously compiled dataset according to the lists were used for input vector encoding. Random Forests (RFs and Support Vector Machines (SVMs were used to construct accurate classifiers. The RF classifiers were found to outperform SVM models for tissue-specific gene prediction. The results suggest that the candidate genes for brain or liver specific expression can provide valuable information for further experimental studies. Our approach was also applied for identifying tissue-selective gene targets for different types of tissues. Conclusions A machine learning approach has been developed for accurately identifying the candidate genes for tissue specific/selective expression. The approach provides an efficient way to select some interesting genes for developing new biomedical markers and improve our knowledge of tissue-specific expression.

  9. Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering

    Directory of Open Access Journals (Sweden)

    Landfors Mattias

    2010-10-01

    Full Text Available Abstract Background Cluster analysis, and in particular hierarchical clustering, is widely used to extract information from gene expression data. The aim is to discover new classes, or sub-classes, of either individuals or genes. Performing a cluster analysis commonly involve decisions on how to; handle missing values, standardize the data and select genes. In addition, pre-processing, involving various types of filtration and normalization procedures, can have an effect on the ability to discover biologically relevant classes. Here we consider cluster analysis in a broad sense and perform a comprehensive evaluation that covers several aspects of cluster analyses, including normalization. Result We evaluated 2780 cluster analysis methods on seven publicly available 2-channel microarray data sets with common reference designs. Each cluster analysis method differed in data normalization (5 normalizations were considered, missing value imputation (2, standardization of data (2, gene selection (19 or clustering method (11. The cluster analyses are evaluated using known classes, such as cancer types, and the adjusted Rand index. The performances of the different analyses vary between the data sets and it is difficult to give general recommendations. However, normalization, gene selection and clustering method are all variables that have a significant impact on the performance. In particular, gene selection is important and it is generally necessary to include a relatively large number of genes in order to get good performance. Selecting genes with high standard deviation or using principal component analysis are shown to be the preferred gene selection methods. Hierarchical clustering using Ward's method, k-means clustering and Mclust are the clustering methods considered in this paper that achieves the highest adjusted Rand. Normalization can have a significant positive impact on the ability to cluster individuals, and there are indications that

  10. Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering

    Science.gov (United States)

    2010-01-01

    Background Cluster analysis, and in particular hierarchical clustering, is widely used to extract information from gene expression data. The aim is to discover new classes, or sub-classes, of either individuals or genes. Performing a cluster analysis commonly involve decisions on how to; handle missing values, standardize the data and select genes. In addition, pre-processing, involving various types of filtration and normalization procedures, can have an effect on the ability to discover biologically relevant classes. Here we consider cluster analysis in a broad sense and perform a comprehensive evaluation that covers several aspects of cluster analyses, including normalization. Result We evaluated 2780 cluster analysis methods on seven publicly available 2-channel microarray data sets with common reference designs. Each cluster analysis method differed in data normalization (5 normalizations were considered), missing value imputation (2), standardization of data (2), gene selection (19) or clustering method (11). The cluster analyses are evaluated using known classes, such as cancer types, and the adjusted Rand index. The performances of the different analyses vary between the data sets and it is difficult to give general recommendations. However, normalization, gene selection and clustering method are all variables that have a significant impact on the performance. In particular, gene selection is important and it is generally necessary to include a relatively large number of genes in order to get good performance. Selecting genes with high standard deviation or using principal component analysis are shown to be the preferred gene selection methods. Hierarchical clustering using Ward's method, k-means clustering and Mclust are the clustering methods considered in this paper that achieves the highest adjusted Rand. Normalization can have a significant positive impact on the ability to cluster individuals, and there are indications that background correction is

  11. Small Molecule Microarrays Enable the Identification of a Selective, Quadruplex-Binding Inhibitor of MYC Expression.

    Science.gov (United States)

    Felsenstein, Kenneth M; Saunders, Lindsey B; Simmons, John K; Leon, Elena; Calabrese, David R; Zhang, Shuling; Michalowski, Aleksandra; Gareiss, Peter; Mock, Beverly A; Schneekloth, John S

    2016-01-15

    The transcription factor MYC plays a pivotal role in cancer initiation, progression, and maintenance. However, it has proven difficult to develop small molecule inhibitors of MYC. One attractive route to pharmacological inhibition of MYC has been the prevention of its expression through small molecule-mediated stabilization of the G-quadruplex (G4) present in its promoter. Although molecules that bind globally to quadruplex DNA and influence gene expression are well-known, the identification of new chemical scaffolds that selectively modulate G4-driven genes remains a challenge. Here, we report an approach for the identification of G4-binding small molecules using small molecule microarrays (SMMs). We use the SMM screening platform to identify a novel G4-binding small molecule that inhibits MYC expression in cell models, with minimal impact on the expression of other G4-associated genes. Surface plasmon resonance (SPR) and thermal melt assays demonstrated that this molecule binds reversibly to the MYC G4 with single digit micromolar affinity, and with weaker or no measurable binding to other G4s. Biochemical and cell-based assays demonstrated that the compound effectively silenced MYC transcription and translation via a G4-dependent mechanism of action. The compound induced G1 arrest and was selectively toxic to MYC-driven cancer cell lines containing the G4 in the promoter but had minimal effects in peripheral blood mononucleocytes or a cell line lacking the G4 in its MYC promoter. As a measure of selectivity, gene expression analysis and qPCR experiments demonstrated that MYC and several MYC target genes were downregulated upon treatment with this compound, while the expression of several other G4-driven genes was not affected. In addition to providing a novel chemical scaffold that modulates MYC expression through G4 binding, this work suggests that the SMM screening approach may be broadly useful as an approach for the identification of new G4-binding small

  12. Feature Selection with Conjunctions of Decision Stumps and Learning from Microarray Data.

    Science.gov (United States)

    Shah, M; Marchand, M; Corbeil, J

    2012-01-01

    One of the objectives of designing feature selection learning algorithms is to obtain classifiers that depend on a small number of attributes and have verifiable future performance guarantees. There are few, if any, approaches that successfully address the two goals simultaneously. To the best of our knowledge, such algorithms that give theoretical bounds on the future performance have not been proposed so far in the context of the classification of gene expression data. In this work, we investigate the premise of learning a conjunction (or disjunction) of decision stumps in Occam's Razor, Sample Compression, and PAC-Bayes learning settings for identifying a small subset of attributes that can be used to perform reliable classification tasks. We apply the proposed approaches for gene identification from DNA microarray data and compare our results to those of the well-known successful approaches proposed for the task. We show that our algorithm not only finds hypotheses with a much smaller number of genes while giving competitive classification accuracy but also having tight risk guarantees on future performance, unlike other approaches. The proposed approaches are general and extensible in terms of both designing novel algorithms and application to other domains.

  13. A kernel-based multivariate feature selection method for microarray data classification.

    Directory of Open Access Journals (Sweden)

    Shiquan Sun

    Full Text Available High dimensionality and small sample sizes, and their inherent risk of overfitting, pose great challenges for constructing efficient classifiers in microarray data classification. Therefore a feature selection technique should be conducted prior to data classification to enhance prediction performance. In general, filter methods can be considered as principal or auxiliary selection mechanism because of their simplicity, scalability, and low computational complexity. However, a series of trivial examples show that filter methods result in less accurate performance because they ignore the dependencies of features. Although few publications have devoted their attention to reveal the relationship of features by multivariate-based methods, these methods describe relationships among features only by linear methods. While simple linear combination relationship restrict the improvement in performance. In this paper, we used kernel method to discover inherent nonlinear correlations among features as well as between feature and target. Moreover, the number of orthogonal components was determined by kernel Fishers linear discriminant analysis (FLDA in a self-adaptive manner rather than by manual parameter settings. In order to reveal the effectiveness of our method we performed several experiments and compared the results between our method and other competitive multivariate-based features selectors. In our comparison, we used two classifiers (support vector machine, [Formula: see text]-nearest neighbor on two group datasets, namely two-class and multi-class datasets. Experimental results demonstrate that the performance of our method is better than others, especially on three hard-classify datasets, namely Wang's Breast Cancer, Gordon's Lung Adenocarcinoma and Pomeroy's Medulloblastoma.

  14. mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using Microarray Gene Expression Profiling

    Directory of Open Access Journals (Sweden)

    Hala Alshamlan

    2015-01-01

    Full Text Available An artificial bee colony (ABC is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR, and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO. The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems.

  15. mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using Microarray Gene Expression Profiling.

    Science.gov (United States)

    Alshamlan, Hala; Badr, Ghada; Alohali, Yousef

    2015-01-01

    An artificial bee colony (ABC) is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR), and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM) algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA) and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO). The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems.

  16. A hybrid gene selection approach for microarray data classification using cellular learning automata and ant colony optimization.

    Science.gov (United States)

    Vafaee Sharbaf, Fatemeh; Mosafer, Sara; Moattar, Mohammad Hossein

    2016-06-01

    This paper proposes an approach for gene selection in microarray data. The proposed approach consists of a primary filter approach using Fisher criterion which reduces the initial genes and hence the search space and time complexity. Then, a wrapper approach which is based on cellular learning automata (CLA) optimized with ant colony method (ACO) is used to find the set of features which improve the classification accuracy. CLA is applied due to its capability to learn and model complicated relationships. The selected features from the last phase are evaluated using ROC curve and the most effective while smallest feature subset is determined. The classifiers which are evaluated in the proposed framework are K-nearest neighbor; support vector machine and naïve Bayes. The proposed approach is evaluated on 4 microarray datasets. The evaluations confirm that the proposed approach can find the smallest subset of genes while approaching the maximum accuracy. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. 20 CFR 638.303 - Site selection and facilities management.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Site selection and facilities management. 638... Facilities Management § 638.303 Site selection and facilities management. (a) The Job Corps Director shall... center, facilities engineering and real estate management will be conducted by the Job Corps Director or...

  18. Replacement Power Facility site selection report

    Energy Technology Data Exchange (ETDEWEB)

    Wike, L.D.; Toole, G.L.; Specht, W.L.

    1992-06-01

    The Department of Energy (DOE) has proposed the construction and operation of a Replacement Power Facility (RPF) for supplementing and replacing existing sources of steam and possibly electricity at the Savannah River Site (SRS). DOE is preparing an Environmental Impact Statement (EIS) for this project As part of the impact analysis of the proposed action, the EIS will include a detailed description of the environment where the RPF will be constructed. This description must be specific to the recommended site at SRS, which contains more than 300 square miles of land including streams, lakes, impoundments, wetlands, and upland areas. A formal site-selection process was designed and implemented to identify the preferred RPF site.

  19. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola

    2012-01-01

    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray...... of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research....

  20. Facility overview for commercial application of selected Rocky Flats facilities

    International Nuclear Information System (INIS)

    1996-11-01

    The purpose of this Facility Overview is to support the Rocky Flats Local Impacts Initiative's Request for Interest, to solicit interest from commercial corporations for utilizing buildings 865 and 883, and the equipment contained within each building, for a commercial venture. In the following sections, this document describes the Rocky Flats Site, the buildings available for lease, the equipment within these buildings, the site services available to a tenant, the human resources available to support operations in buildings 865 and 883, and the environmental condition of the buildings and property. In addition, a brief description is provided of the work performed to date to explore the potential products that might be manufactured in Buildings 865 and 883, and the markets for these products

  1. Analysis on working pressure selection of ACME integral test facility

    International Nuclear Information System (INIS)

    Chen Lian; Chang Huajian; Li Yuquan; Ye Zishen; Qin Benke

    2011-01-01

    An integral effects test facility, advanced core cooling mechanism experiment facility (ACME) was designed to verify the performance of the passive safety system and validate its safety analysis codes of a pressurized water reactor power plant. Three test facilities for AP1000 design were introduced and review was given. The problems resulted from the different working pressures of its test facilities were analyzed. Then a detailed description was presented on the working pressure selection of ACME facility as well as its characteristics. And the approach of establishing desired testing initial condition was discussed. The selected 9.3 MPa working pressure covered almost all important passive safety system enables the ACME to simulate the LOCAs with the same pressure and property similitude as the prototype. It's expected that the ACME design would be an advanced core cooling integral test facility design. (authors)

  2. Entropy-based gene ranking without selection bias for the predictive classification of microarray data

    Directory of Open Access Journals (Sweden)

    Serafini Maria

    2003-11-01

    Full Text Available Abstract Background We describe the E-RFE method for gene ranking, which is useful for the identification of markers in the predictive classification of array data. The method supports a practical modeling scheme designed to avoid the construction of classification rules based on the selection of too small gene subsets (an effect known as the selection bias, in which the estimated predictive errors are too optimistic due to testing on samples already considered in the feature selection process. Results With E-RFE, we speed up the recursive feature elimination (RFE with SVM classifiers by eliminating chunks of uninteresting genes using an entropy measure of the SVM weights distribution. An optimal subset of genes is selected according to a two-strata model evaluation procedure: modeling is replicated by an external stratified-partition resampling scheme, and, within each run, an internal K-fold cross-validation is used for E-RFE ranking. Also, the optimal number of genes can be estimated according to the saturation of Zipf's law profiles. Conclusions Without a decrease of classification accuracy, E-RFE allows a speed-up factor of 100 with respect to standard RFE, while improving on alternative parametric RFE reduction strategies. Thus, a process for gene selection and error estimation is made practical, ensuring control of the selection bias, and providing additional diagnostic indicators of gene importance.

  3. Differential gene expression from genome-wide microarray analyses distinguishes Lohmann Selected Leghorn and Lohmann Brown layers.

    Directory of Open Access Journals (Sweden)

    Christin Habig

    Full Text Available The Lohmann Selected Leghorn (LSL and Lohmann Brown (LB layer lines have been selected for high egg production since more than 50 years and belong to the worldwide leading commercial layer lines. The objectives of the present study were to characterize the molecular processes that are different among these two layer lines using whole genome RNA expression profiles. The hens were kept in the newly developed small group housing system Eurovent German with two different group sizes. Differential expression was observed for 6,276 microarray probes (FDR adjusted P-value <0.05 among the two layer lines LSL and LB. A 2-fold or greater change in gene expression was identified on 151 probe sets. In LSL, 72 of the 151 probe sets were up- and 79 of them were down-regulated. Gene ontology (GO enrichment analysis accounting for biological processes evinced 18 GO-terms for the 72 probe sets with higher expression in LSL, especially those taking part in immune system processes and membrane organization. A total of 32 enriched GO-terms were determined among the 79 down-regulated probe sets of LSL. Particularly, these terms included phosphorus metabolic processes and signaling pathways. In conclusion, the phenotypic differences among the two layer lines LSL and LB are clearly reflected in their gene expression profiles of the cerebrum. These novel findings provide clues for genes involved in economically important line characteristics of commercial laying hens.

  4. New theory of discriminant analysis after R. Fisher advanced research by the feature selection method for microarray data

    CERN Document Server

    Shinmura, Shuichi

    2016-01-01

    This is the first book to compare eight LDFs by different types of datasets, such as Fisher’s iris data, medical data with collinearities, Swiss banknote data that is a linearly separable data (LSD), student pass/fail determination using student attributes, 18 pass/fail determinations using exam scores, Japanese automobile data, and six microarray datasets (the datasets) that are LSD. We developed the 100-fold cross-validation for the small sample method (Method 1) instead of the LOO method. We proposed a simple model selection procedure to choose the best model having minimum M2 and Revised IP-OLDF based on MNM criterion was found to be better than other M2s in the above datasets. We compared two statistical LDFs and six MP-based LDFs. Those were Fisher’s LDF, logistic regression, three SVMs, Revised IP-OLDF, and another two OLDFs. Only a hard-margin SVM (H-SVM) and Revised IP-OLDF could discriminate LSD theoretically (Problem 2). We solved the defect of the generalized inverse matrices (Problem 3). For ...

  5. Microarray study of temperature-dependent sensitivity and selectivity of metal/oxide sensing interfaces

    Science.gov (United States)

    Tiffany, Jason; Cavicchi, Richard E.; Semancik, Stephen

    2001-02-01

    Conductometric gas microsensors offer the benefits of ppm-level sensitivity, real-time data, simple interfacing to electronics hardware, and low power consumption. The type of device we have been exploring consists of a sensor film deposited on a "microhotplate"- a 100 micron platform with built-in heating (to activate reactions on the sensing surface) and thermometry. We have been using combinatorial studies of 36-element arrays to characterize the relationship between sensor film composition, operating temperature, and response, as measured by the device's sensitivity and selectivity. Gases that have been tested on these arrays include methanol, ethanol, dichloromethane, propane, methane, acetone, benzene, hydrogen, and carbon monoxide, and are of interest in the management of environmental waste sites. These experiments compare tin oxide films modified by catalyst overlayers, and ultrathin metal seed layers. The seed layers are used as part of a chemical vapor deposition process that uses each array element's microheater to activate the deposition of SnO2, and control its microstructure. Low coverage (20 Ê) catalytic metals (Pd, Cu, Cr, In, Au) are deposited on the oxides by masked evaporation or sputtering. This presentation demonstrates the value of an array-based approach for developing film processing methods, measuring performance characteristics, and establishing reproducibility. It also illustrates how temperature-dependent response data for varied metal/oxide compositions can be used to tailor a microsensor array for a given application.

  6. Novel approach to select genes from RMA normalized microarray data using functional hearing tests in aging mice

    Science.gov (United States)

    D'Souza, Mary; Zhu, Xiaoxia; Frisina, Robert D.

    2008-01-01

    Presbycusis – age-related hearing loss – is the number one communicative disorder and one of the top three chronic medical condition of our aged population. High-throughput technologies potentially can be used to identify differentially expressed genes that may be better diagnostic and therapeutic targets for sensory and neural disorders. Here we analyzed gene expression for a set of GABA receptors in the cochlea of aging CBA mice using the Affymetrix GeneChip MOE430A. Functional phenotypic hearing measures were made, including auditory brainstem response (ABR) thresholds and distortion-product otoacoustic emission (DPOAE) amplitudes (four age groups). Four specific criteria were used to assess gene expression changes from RMA normalized microarray data (40 replicates). Linear regression models were used to fit the neurophysiological hearing measurements to probe-set expression profiles. These data were first subjected to one-way ANOVA, and then linear regression was performed. In addition, the log signal ratio was converted to fold change, and selected gene expression changes were confirmed by relative real-time PCR. Major findings: expression of GABA-A receptor subunit α6 was upregulated with age and hearing loss, whereas subunit α1 was repressed. In addition, GABA-A receptor associated protein like-1 and GABA-A receptor associated protein like-2 were strongly downregulated with age and hearing impairment. Lastly, gene expression measures were correlated with pathway/network relationships relevant to the inner ear using Pathway Architect, to identify key pathways consistent with the gene expression changes observed. PMID:18455804

  7. Strategy selection for the decommissioning of nuclear facilities

    International Nuclear Information System (INIS)

    2004-01-01

    As modern nuclear power programmes mature and large, commercial nuclear power plants and fuel cycle facilities approach the end of their useful life by reason of age, economics or change of policy on the use of nuclear power, new challenges associated with decommissioning and dismantling come to the fore. Politicians and the public may expect there to be a 'right answer' to the choice of strategy for a particular type of facility, or even all facilities. Both this seminar and wider experience show that this is not the case. Local factors and national political positions have a significant input and often result in widely differing strategy approaches to broadly similar decommissioning projects. All facility owners represented at the seminar were able to demonstrate a rational process for strategy selection and compelling arguments for the choices made. In addition to the papers that were presented, these proceedings include a summary of the discussions that took place. (author)

  8. Selective recognition of DNA from olive leaves and olive oil by PNA and modified-PNA microarrays

    Science.gov (United States)

    Rossi, Stefano; Calabretta, Alessandro; Tedeschi, Tullia; Sforza, Stefano; Arcioni, Sergio; Baldoni, Luciana; Corradini, Roberto; Marchelli, Rosangela

    2012-01-01

    PNA probes for the specific detection of DNA from olive oil samples by microarray technology were developed. The presence of as low as 5% refined hazelnut (Corylus avellana) oil in extra-virgin olive oil (Olea europaea L.) could be detected by using a PNA microarray. A set of two single nucleotide polymorphisms (SNPs) from the Actin gene of Olive was chosen as a model for evaluating the ability of PNA probes for discriminating olive cultivars. Both unmodified and C2-modified PNAs bearing an arginine side-chain were used, the latter showing higher sequence specificity. DNA extracted from leaves of three different cultivars (Ogliarola leccese, Canino and Frantoio) could be easily discriminated using a microarray with unmodified PNA probes, whereas discrimination of DNA from oil samples was more challenging, and could be obtained only by using chiral PNA probes. PMID:22772038

  9. Gene features selection for three-class disease classification via multiple orthogonal partial least square discriminant analysis and S-plot using microarray data.

    Science.gov (United States)

    Yang, Mingxing; Li, Xiumin; Li, Zhibin; Ou, Zhimin; Liu, Ming; Liu, Suhuan; Li, Xuejun; Yang, Shuyu

    2013-01-01

    DNA microarray analysis is characterized by obtaining a large number of gene variables from a small number of observations. Cluster analysis is widely used to analyze DNA microarray data to make classification and diagnosis of disease. Because there are so many irrelevant and insignificant genes in a dataset, a feature selection approach must be employed in data analysis. The performance of cluster analysis of this high-throughput data depends on whether the feature selection approach chooses the most relevant genes associated with disease classes. Here we proposed a new method using multiple Orthogonal Partial Least Squares-Discriminant Analysis (mOPLS-DA) models and S-plots to select the most relevant genes to conduct three-class disease classification and prediction. We tested our method using Golub's leukemia microarray data. For three classes with subtypes, we proposed hierarchical orthogonal partial least squares-discriminant analysis (OPLS-DA) models and S-plots to select features for two main classes and their subtypes. For three classes in parallel, we employed three OPLS-DA models and S-plots to choose marker genes for each class. The power of feature selection to classify and predict three-class disease was evaluated using cluster analysis. Further, the general performance of our method was tested using four public datasets and compared with those of four other feature selection methods. The results revealed that our method effectively selected the most relevant features for disease classification and prediction, and its performance was better than that of the other methods.

  10. Requirements for facilities transferring or receiving select agents. Final rule.

    Science.gov (United States)

    2001-08-31

    CDC administers regulations that govern the transfer of certain biological agents and toxins ("select agents"). These regulations require entities that transfer or receive select agents to register with CDC and comply with biosafety standards contained in the Third Edition of the CDC/NIH publication "Biosafety in Microbiological and Biomedical Laboratories ("BMBL")." On October 28,1999, CDC published a Notice of Proposed Rulemaking ("NPRM") seeking both to revise the biosafety standards facilities must follow when handling select agents and to provide new biosecurity standards for such facilities. These new standards are contained in the Fourth Edition of BMBL, which the NPRM proposed to incorporate by reference, thereby replacing the Third Edition. No comments were received in response to this proposal. CDC is therefore amending its regulations to incorporate the Fourth Edition.

  11. Material selection for Multi-Function Waste Tank Facility tanks

    International Nuclear Information System (INIS)

    Carlos, W.C.

    1994-01-01

    This report briefly summarizes the history of the materials selection for the US Department of Energy's high-level waste carbon steel storage tanks. It also provide an evaluation of the materials for the construction of new tanks at the Multi-Function Waste Tank Facility. The evaluation included a materials matrix that summarized the critical design, fabrication, construction, and corrosion resistance requirements; assessed each requirement; and cataloged the advantages and disadvantages of each material. This evaluation is based on the mission of the Multi-Function Waste Tank Facility. On the basis of the compositions of the wastes stored in Hanford waste tanks, it is recommended that tanks for the Multi-Function Waste Tank Facility be constructed of normalized ASME SA 516, Grade 70, carbon steel

  12. Linguistic fuzzy selection of liquid levelmeters in nuclear facilities

    International Nuclear Information System (INIS)

    Ghyym, S. H.

    1999-01-01

    In this work, a selection methodology of liquid levelmeters, especially, level sensors in non-nuclear category, to be installed in nuclear facilities is developed using a linguistic fuzzy approach. Depending on defuzzification techniques, the linguistic fuzzy methodology leads to either linguistic (exactly, fully-linguistic) or cardinal (i.e., semi-linguistic) evaluation. In the case of the linguistic method, for each alternative, fuzzy preference index is converted to linguistic utility value by means of a similarity measure determining the degree of similarity between fuzzy index and linguistic ratings. For the cardinal method, the index is translated to cardinal overall utility value. According to these values, alternatives of interest are linguistically or numerically evaluated and a suitable alternative can be selected. Under given selection criteria, the suitable selections out of some liquid levelmeters for nuclear facilities are dealt with using the linguistic fuzzy methodology proposed. Then, linguistic fuzzy evaluation results are compared with numerical results available in the literature. It is found that as to a suitable option the linguistic fuzzy selection is in agreement with the crisp numerical selection. In addition, this comparison shows that the fully-linguistic method facilitates linguistic interpretation regarding evaluation results

  13. Linguistic fuzzy selection of liquid levelmeters in nuclear facilities

    Energy Technology Data Exchange (ETDEWEB)

    Ghyym, S. H. [KEPRI, Taejon (Korea, Republic of)

    1999-10-01

    In this work, a selection methodology of liquid levelmeters, especially, level sensors in non-nuclear category, to be installed in nuclear facilities is developed using a linguistic fuzzy approach. Depending on defuzzification techniques, the linguistic fuzzy methodology leads to either linguistic (exactly, fully-linguistic) or cardinal (i.e., semi-linguistic) evaluation. In the case of the linguistic method, for each alternative, fuzzy preference index is converted to linguistic utility value by means of a similarity measure determining the degree of similarity between fuzzy index and linguistic ratings. For the cardinal method, the index is translated to cardinal overall utility value. According to these values, alternatives of interest are linguistically or numerically evaluated and a suitable alternative can be selected. Under given selection criteria, the suitable selections out of some liquid levelmeters for nuclear facilities are dealt with using the linguistic fuzzy methodology proposed. Then, linguistic fuzzy evaluation results are compared with numerical results available in the literature. It is found that as to a suitable option the linguistic fuzzy selection is in agreement with the crisp numerical selection. In addition, this comparison shows that the fully-linguistic method facilitates linguistic interpretation regarding evaluation results.

  14. Identification and selection of initiating events for experimental fusion facilities

    International Nuclear Information System (INIS)

    Cadwallader, L.C.

    1989-01-01

    This paper describes the current approaches used in probabilistic risk assessment (PRA) to identify and select accident initiating events for study in either probabilistic safety analysis or PRA. Current methods directly apply to fusion facilities as well as other types of industries, such as chemical processing and nuclear fission. These identification and selection methods include the Master Logic Diagram, historical document review, system level Failure Modes and Effects Analysis, and others. A combination of the historical document review, such as Safety Analysis Reports and fusion safety studies, and the Master Logic Diagram with appropriate quality assurance reviews, is suggested for standardizing US fusion PRA effects. A preliminary set of generalized initiating events applicable to fusion facilities derived from safety document review is presented as a framework to start from for the historical document review and Master Logic Diagram approach. Fusion designers should find this list useful for their design reviews. 29 refs., 2 tabs

  15. Identification and selection of initiating events for experimental fusion facilities

    International Nuclear Information System (INIS)

    Cadwallader, L.C.

    1989-01-01

    This paper describes the current approaches used in probabilistic risk assessment (PRA) to identify and select accident initiating events for study in either probabilistic safety analysis or PRA. Current methods directly apply to fusion facilities as well as other types of industries, such as chemical processing and nuclear fission. These identification and selection methods include the Master Logic Diagram, historical document review, system level Failure Modes and Effects Analysis, and others. A combination of the historical document review, such as Safety Analysis Reports and fusion safety studies, and the Master Logic Diagram with appropriate quality assurance reviews, is suggested for standardizing U.S. fusion PRA efforts. A preliminary set of generalized initiating events applicable to fusion facilities derived from safety document review is presented as a framework to start from for the historical document review and Master Logic Diagram approach. Fusion designers should find this list useful for their design reviews. 29 refs., 1 tab

  16. Selecting strategies for the decommissioning of nuclear facilities

    International Nuclear Information System (INIS)

    2006-01-01

    This status report on Selecting Strategies for the Decommissioning of Nuclear Facilities is based on the viewpoints and materials presented at the Tarragona seminar as well as the experience of the WPDD. It identifies, reviews and analyses factors influencing decommissioning strategies and addresses the challenges associated with balancing these factors in the process of strategy selection. It gives recognition to the fact that, in addition to technical characteristics, there are many other factors that influence the selection of a decommissioning strategy and that cannot be quantified, such as policy, regulatory and socio-economic factors and aspects that reach far into the future. Uncertainties associated with such factors are a challenge to those who have to take decisions on a decommissioning strategy. (author)

  17. Design of a new therapy for patients with chronic kidney disease: use of microarrays for selective hemoadsorption of uremic wastes and toxins to improve homeostasis

    Directory of Open Access Journals (Sweden)

    Shahidi Bonjar MR

    2015-01-01

    Full Text Available Mohammad Rashid Shahidi Bonjar,1 Leyla Shahidi Bonjar2 1School of Dentistry, Kerman University of Medical Sciences, Kerman, Iran; 2Department of Pharmacology, College of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran Abstract: The hypothesis proposed here would provide near to optimum homeostasis for patients with chronic kidney disease (CKD without the need for hemodialysis. This strategy has not been described previously in the scientific literature. It involves a targeted therapy that may prevent progression of the disease and help to improve the well-being of CKD patients. It proposes a nanotechnological device, ie, a microarray-oriented homeostasis provider (MOHP, to improve homeostasis in CKD patients. MOHP would be an auxiliary kidney aid, and would improve the filtration functions that impaired kidneys cannot perform by their own. MOHP is composed of two main computer-oriented components, ie, a quantitative microarray detector (QMD and a homeostasis-oriented microarray column (HOMC. QMD detects and HOMC selectively removes defined quantities of uremic wastes, toxins and any other metabolites which is programmed for. The QMD and HOMC would accomplish this with the help of a peristaltic blood pump that would circulate blood aseptically in an extracorporeal closed circuit. During the passage of blood through the QMD, this microarray detector would quantitatively monitor all of the blood compounds that accumulate in the blood of a patient with impaired glomerular filtration, including small-sized, middle-sized and large-sized molecules. The electronic information collected by QMD would be electronically transmitted to the HOMC, which would adjust the molecules to the concentrations they are electronically programmed for and/or receive from QMD. This process of monitoring and removal of waste continues until the programmed homeostasis criteria are reached. Like a conventional kidney machine, MOHP can be used in hospitals and

  18. An Evaluation of Facility Maintenance and Repair Strategies of Select Companies

    National Research Council Canada - National Science Library

    Sharp, Christopher

    2002-01-01

    ...) with the benefits derived from those facilities. This thesis documents how a selection of companies implemented that balance by determining their facilities requirements based on their chosen facility condition level and how they then allocated funds...

  19. Leukemia and colon tumor detection based on microarray data classification using momentum backpropagation and genetic algorithm as a feature selection method

    Science.gov (United States)

    Wisesty, Untari N.; Warastri, Riris S.; Puspitasari, Shinta Y.

    2018-03-01

    Cancer is one of the major causes of mordibility and mortality problems in the worldwide. Therefore, the need of a system that can analyze and identify a person suffering from a cancer by using microarray data derived from the patient’s Deoxyribonucleic Acid (DNA). But on microarray data has thousands of attributes, thus making the challenges in data processing. This is often referred to as the curse of dimensionality. Therefore, in this study built a system capable of detecting a patient whether contracted cancer or not. The algorithm used is Genetic Algorithm as feature selection and Momentum Backpropagation Neural Network as a classification method, with data used from the Kent Ridge Bio-medical Dataset. Based on system testing that has been done, the system can detect Leukemia and Colon Tumor with best accuracy equal to 98.33% for colon tumor data and 100% for leukimia data. Genetic Algorithm as feature selection algorithm can improve system accuracy, which is from 64.52% to 98.33% for colon tumor data and 65.28% to 100% for leukemia data, and the use of momentum parameters can accelerate the convergence of the system in the training process of Neural Network.

  20. Peptides and Anti-peptide Antibodies for Small and Medium Scale Peptide and Anti-peptide Affinity Microarrays: Antigenic Peptide Selection, Immobilization, and Processing.

    Science.gov (United States)

    Zhang, Fan; Briones, Andrea; Soloviev, Mikhail

    2016-01-01

    This chapter describes the principles of selection of antigenic peptides for the development of anti-peptide antibodies for use in microarray-based multiplex affinity assays and also with mass-spectrometry detection. The methods described here are mostly applicable to small to medium scale arrays. Although the same principles of peptide selection would be suitable for larger scale arrays (with 100+ features) the actual informatics software and printing methods may well be different. Because of the sheer number of proteins/peptides to be processed and analyzed dedicated software capable of processing all the proteins and an enterprise level array robotics may be necessary for larger scale efforts. This report aims to provide practical advice to those who develop or use arrays with up to ~100 different peptide or protein features.

  1. Design of a new therapy for patients with chronic kidney disease: use of microarrays for selective hemoadsorption of uremic wastes and toxins to improve homeostasis.

    Science.gov (United States)

    Shahidi Bonjar, Mohammad Rashid; Shahidi Bonjar, Leyla

    2015-01-01

    The hypothesis proposed here would provide near to optimum homeostasis for patients with chronic kidney disease (CKD) without the need for hemodialysis. This strategy has not been described previously in the scientific literature. It involves a targeted therapy that may prevent progression of the disease and help to improve the well-being of CKD patients. It proposes a nanotechnological device, ie, a microarray-oriented homeostasis provider (MOHP), to improve homeostasis in CKD patients. MOHP would be an auxiliary kidney aid, and would improve the filtration functions that impaired kidneys cannot perform by their own. MOHP is composed of two main computer-oriented components, ie, a quantitative microarray detector (QMD) and a homeostasis-oriented microarray column (HOMC). QMD detects and HOMC selectively removes defined quantities of uremic wastes, toxins and any other metabolites which is programmed for. The QMD and HOMC would accomplish this with the help of a peristaltic blood pump that would circulate blood aseptically in an extracorporeal closed circuit. During the passage of blood through the QMD, this microarray detector would quantitatively monitor all of the blood compounds that accumulate in the blood of a patient with impaired glomerular filtration, including small-sized, middle-sized and large-sized molecules. The electronic information collected by QMD would be electronically transmitted to the HOMC, which would adjust the molecules to the concentrations they are electronically programmed for and/or receive from QMD. This process of monitoring and removal of waste continues until the programmed homeostasis criteria are reached. Like a conventional kidney machine, MOHP can be used in hospitals and homes under the supervision of a trained technician. The main advantages of this treatment would include improved homeostasis, a reduced likelihood of side effects and of the morbidity resulting from CKD, slower progression of kidney impairment, prevention of

  2. BSL-3 laboratory practices in the United States: comparison of select agent and non-select agent facilities.

    Science.gov (United States)

    Richards, Stephanie L; Pompei, Victoria C; Anderson, Alice

    2014-01-01

    New construction of biosafety level 3 (BSL-3) laboratories in the United States has increased in the past decade to facilitate research on potential bioterrorism agents. The Centers for Disease Control and Prevention inspect BSL-3 facilities and review commissioning documentation, but no single agency has oversight over all BSL-3 facilities. This article explores the extent to which standard operating procedures in US BSL-3 facilities vary between laboratories with select agent or non-select agent status. Comparisons are made for the following variables: personnel training, decontamination, personal protective equipment (PPE), medical surveillance, security access, laboratory structure and maintenance, funding, and pest management. Facilities working with select agents had more complex training programs and decontamination procedures than non-select agent facilities. Personnel working in select agent laboratories were likely to use powered air purifying respirators, while non-select agent laboratories primarily used N95 respirators. More rigorous medical surveillance was carried out in select agent workers (although not required by the select agent program) and a higher level of restrictive access to laboratories was found. Most select agent and non-select agent laboratories reported adequate structural integrity in facilities; however, differences were observed in personnel perception of funding for repairs. Pest management was carried out by select agent personnel more frequently than non-select agent personnel. Our findings support the need to promote high quality biosafety training and standard operating procedures in both select agent and non-select agent laboratories to improve occupational health and safety.

  3. Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae

    Directory of Open Access Journals (Sweden)

    MacInnes Janet I

    2009-02-01

    Full Text Available Abstract Background Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is a highly contagious respiratory pathogen that causes severe losses to the swine industry worldwide. Current commercially-available vaccines are of limited value because they do not induce cross-serovar immunity and do not prevent development of the carrier state. Microarray-based comparative genomic hybridizations (M-CGH were used to estimate whole genomic diversity of representative Actinobacillus pleuropneumoniae strains. Our goal was to identify conserved genes, especially those predicted to encode outer membrane proteins and lipoproteins because of their potential for the development of more effective vaccines. Results Using hierarchical clustering, our M-CGH results showed that the majority of the genes in the genome of the serovar 5 A. pleuropneumoniae L20 strain were conserved in the reference strains of all 15 serovars and in representative field isolates. Fifty-eight conserved genes predicted to encode for outer membrane proteins or lipoproteins were identified. As well, there were several clusters of diverged or absent genes including those associated with capsule biosynthesis, toxin production as well as genes typically associated with mobile elements. Conclusion Although A. pleuropneumoniae strains are essentially clonal, M-CGH analysis of the reference strains of the fifteen serovars and representative field isolates revealed several classes of genes that were divergent or absent. Not surprisingly, these included genes associated with capsule biosynthesis as the capsule is associated with sero-specificity. Several of the conserved genes were identified as candidates for vaccine development, and we conclude that M-CGH is a valuable tool for reverse vaccinology.

  4. The status of school sanitation facilities in some selected primary ...

    African Journals Online (AJOL)

    admin

    The access to drinking water facilities. (water taps) ... in access by male and female pupils (latrine to students' ratio) is very .... utilization of WASH facilities and attaining clean school ... productive cooperation in rendering valuable information.

  5. Decommissioning Strategies Selection for Facilities Using Radioactive Material

    International Nuclear Information System (INIS)

    Husen Zamroni; Jaka Rachmadetin

    2008-01-01

    The facilities using radioactive material that have been stopped operation will require some form of the decommissioning for public and environment safety. The approaches are identified by three decommissioning strategies: immediate dismantling, deferred dismantling and entombment. If a facility undergoes immediate dismantling, most radio nuclides will have no such sufficient time to decay and therefore this strategy may not provide reduction in the worker exposure. A facility that undergoes deferred dismantling may advantage from the radioactive decay of residual radio nuclides during the long term storage period and entombment could be a viable option for other nuclear facilities containing only short lived or limited concentrations of long lived radionuclides. Mostly, only two types of the decommissioning used to be done in the world, immediate and deferred dismantling. (author)

  6. A Methodology for Base Camp Site Selection and Facility Layout

    National Research Council Canada - National Science Library

    Snyder, Frank

    2002-01-01

    ..., and disaster relief missions throughout the world. To maintain a deployed force conducting such potentially lengthy operations, semi-permanent basecamps are required to provide the needed unit and soldier support facilities...

  7. Healthcare waste management: current practices in selected healthcare facilities, Botswana.

    Science.gov (United States)

    Mbongwe, Bontle; Mmereki, Baagi T; Magashula, Andrew

    2008-01-01

    Healthcare waste management continues to present an array of challenges for developing countries, and Botswana is no exception. The possible impact of healthcare waste on public health and the environment has received a lot of attention such that Waste Management dedicated a special issue to the management of healthcare waste (Healthcare Wastes Management, 2005. Waste Management 25(6) 567-665). As the demand for more healthcare facilities increases, there is also an increase on waste generation from these facilities. This situation requires an organised system of healthcare waste management to curb public health risks as well as occupational hazards among healthcare workers as a result of poor waste management. This paper reviews current waste management practices at the healthcare facility level and proposes possible options for improvement in Botswana.

  8. Information on award fees paid at selected DOE facilities

    International Nuclear Information System (INIS)

    1989-10-01

    This report states that the Department of Energy uses award fees to encourage effective work and to improve the quality of performance by its contractors. These fees are in addition to reimbursing the contractor for its cost and any possible base fees. Such fees are determined through DOE's evaluations of a contractor's performance. This report's review of award fees paid by DOE at six facilities during fiscal years 1987 and 1988 found that contractors at five of the six facilities were rated by DOE as very good to excellent for their overall performance and received award fees ranging from $1.4 million to nearly $10 million

  9. Site Selection for Surplus Plutonium Disposition Facilities at the Savannah River Site

    International Nuclear Information System (INIS)

    Wike, L.D.

    2000-01-01

    A site selection study was conducted to evaluate locations for the proposed Surplus Plutonium Disposition Facilities. Facilities to be located include the Mixed Oxide (MOX) Fuel Fabrication Facility, the Pit Disassembly and Conversion Facility (PDCF), and the Plutonium Immobilization Project (PIP) facility. Objectives of the study include: (1) Confirm that the Department of Energy (DOE) selected locations for the MOX and PDCF were suitable based on selected siting criteria, (2) Recommend a site in the vicinity of F Area that is suitable for the PIP, and (3) Identify alternative suitable sites for one or more of these facilities in the event that further geotechnical characterization or other considerations result in disqualification of a currently proposed site

  10. The status of school sanitation facilities in some selected primary ...

    African Journals Online (AJOL)

    Background: There is a growing demand on school hygiene and sanitation facilities given the growing number of school enrolment in Ethiopia. A safe school environment plays a key role in facilitating education and enduring pupils with improved life skills. Although there is much attention given for the expansion of schools ...

  11. Metric learning for DNA microarray data analysis

    International Nuclear Information System (INIS)

    Takeuchi, Ichiro; Nakagawa, Masao; Seto, Masao

    2009-01-01

    In many microarray studies, gene set selection is an important preliminary step for subsequent main task such as tumor classification, cancer subtype identification, etc. In this paper, we investigate the possibility of using metric learning as an alternative to gene set selection. We develop a simple metric learning algorithm aiming to use it for microarray data analysis. Exploiting a property of the algorithm, we introduce a novel approach for extending the metric learning to be adaptive. We apply the algorithm to previously studied microarray data on malignant lymphoma subtype identification.

  12. Study for the selection of a supplementary spent fuel storage facility for KANUPP

    International Nuclear Information System (INIS)

    Ahmed, W.; Iqbal, M.J.; Arshad, M.

    1999-01-01

    Steps taken for construction of the spent fuel facility of Karachi Nuclear Power Plant (KANUPP) are the following: choice of conceptual design and site selection; preliminary design and preparation of Preliminary Safety Analysis Report (PSAR); Construction of the facility and preparation of PSAR; testing/commissioning and loading of the storage facility. Characterisation of the spent fuel is essential for design of the storage facility. After comparison of various storage types, it seems that construction of dry storage facility based on concrete canisters at KANUPP site is a suitable option to enhance the storage capacity

  13. The selection of probabilistic safety assessment techniques for non-reactor nuclear facilities

    International Nuclear Information System (INIS)

    Vail, J.

    1992-01-01

    Historically, the probabilistic safety assessment (PSA) methodology of choice is the well known event tree/fault tree inductive technique. For reactor facilities is has stood the test of time. Some non-reactor nuclear facilities have found inductive methodologies difficult to apply. The stand-alone fault tree deductive technique has been used effectively to analyze risk in nuclear chemical processing facilities and waste handling facilities. The selection between the two choices suggest benefits from use of the deductive method for non-reactor facilities

  14. Hanford tank initiative test facility site selection study

    International Nuclear Information System (INIS)

    Staehr, T.W.

    1997-01-01

    The Hanford Tanks Initiative (HTI) project is developing equipment for the removal of hard heel waste from the Hanford Site underground single-shell waste storage tanks. The HTI equipment will initially be installed in the 241-C-106 tank where its operation will be demonstrated. This study evaluates existing Hanford Site facilities and other sites for functional testing of the HTI equipment before it is installed into the 241-C-106 tank

  15. Nuclear facility decommissioning and site remedial actions: a selected bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Owen, P.T.; Knox, N.P.; Fielden, J.M.; Johnson, C.A.

    1982-09-01

    This bibliography contains 693 references with abstracts on the subject of nuclear facility decommissioning, uranium mill tailings management, and site remedial actions. Foreign, as well as domestic, literature of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - has been included in this publication. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's Remedial Action Program. Major chapters are Surplus Facilities Management Program, Nuclear Facilities Decommissioning, Formerly Utilized Sites Remedial Action Program, Uranium Mill Tailings Remedial Action Program, Grand Junction Remedial Action Program, and Uranium Mill Tailings Management. Chapter sections for chapters 1 and 2 include: Design, Planning, and Regulations; Site Surveys; Decontamination Studies; Dismantlement and Demolition; Land Decontamination and Reclamation; Waste Disposal; and General Studies. The references within each chapter are arranged alphabetically by leading author. References having no individual author are arranged by corporate author or by title. Indexes are provided for (1) author; (2) corporate affiliation; (3) title; (4) publication description; (5) geographic location; and (6) keywords. An appendix of 202 bibliographic references without abstracts or indexes has been included in this bibliography. This appendix represents literature identified but not abstracted due to time constraints.

  16. Nuclear facility decommissioning and site remedial actions: a selected bibliography

    International Nuclear Information System (INIS)

    Owen, P.T.; Knox, N.P.; Fielden, J.M.; Johnson, C.A.

    1982-09-01

    This bibliography contains 693 references with abstracts on the subject of nuclear facility decommissioning, uranium mill tailings management, and site remedial actions. Foreign, as well as domestic, literature of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - has been included in this publication. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's Remedial Action Program. Major chapters are Surplus Facilities Management Program, Nuclear Facilities Decommissioning, Formerly Utilized Sites Remedial Action Program, Uranium Mill Tailings Remedial Action Program, Grand Junction Remedial Action Program, and Uranium Mill Tailings Management. Chapter sections for chapters 1 and 2 include: Design, Planning, and Regulations; Site Surveys; Decontamination Studies; Dismantlement and Demolition; Land Decontamination and Reclamation; Waste Disposal; and General Studies. The references within each chapter are arranged alphabetically by leading author. References having no individual author are arranged by corporate author or by title. Indexes are provided for (1) author; (2) corporate affiliation; (3) title; (4) publication description; (5) geographic location; and (6) keywords. An appendix of 202 bibliographic references without abstracts or indexes has been included in this bibliography. This appendix represents literature identified but not abstracted due to time constraints

  17. Energy use in selected metal casting facilities - 2003

    Energy Technology Data Exchange (ETDEWEB)

    Eppich, Robert E. [Eppich Technologies, Syracuse, IN (United States)

    2004-05-01

    This report represents an energy benchmark for various metal casting processes. It describes process flows and energy use by fuel type and processes for selected casting operations. It also provides recommendations for improving energy efficiency in casting.

  18. Site selection and design basis of the National Disposal Facility for LILW. Geological and engineering barriers

    International Nuclear Information System (INIS)

    Boyanov, S.

    2010-01-01

    Content of the presentation: Site selection; Characteristics of the “Radiana” site (location, geological structure, physical and mechanical properties, hydro-geological conditions); Design basis of the Disposal Facility; Migration analysis; Safety assessment approach

  19. Selection of portable tools for use in a size reduction facility

    International Nuclear Information System (INIS)

    Hawley, L.N.

    1986-07-01

    A range of portable tools are identified for development and eventual use within a remote operations facility for the size reduction of plutonium contaminated materials. The process of selection defines the work to be performed within the facility and matches this to the general categories of suitable tools. Specific commercial tools are then selected or, where none exists, proposals are made for the development of special tools. (author)

  20. Selection criteria and requirements for floors in nuclear facilities

    International Nuclear Information System (INIS)

    Kunze, S.

    1988-01-01

    As a surface protection of floors in nuclear facilities coatings, rubber and PVC coverings, respectively, are normally used, whereas stoneware tiles are still provided in rare cases only. All floor materials must be well decontaminable according to the German standard DIN 25415, Part 1. The general requirement is that low-porous, smooth products with little filler content, made of chemically resistant material, are very well decontaminable. Further investigations will be necessary for heavily loaded floor coatings. They include above all examinations for decontaminability after radiation and for wear and resistance to chemicals. These requirements have been compiled in DIN 55991. The examination of about 212 industrial products has revealed that the decontaminability of covering materials is frequently poor. Investigations have shown that the decontaminability is always deteriorated by additions of hygroscopic fillers. Additions of non-hygroscopic fillers and pigments may result in an excellent to poor decontaminability. The pore-free bonding of the covering materials by welding or jointing is of great importance with respect to the decontaminability of these floors. Care should be taken that the jointing compounds are as well decontaminable as the rubber coverings and stonewares. (orig.) [de

  1. Differential effects of selective frankincense (Ru Xiang) essential oil versus non-selective sandalwood (Tan Xiang) essential oil on cultured bladder cancer cells: a microarray and bioinformatics study

    Science.gov (United States)

    2014-01-01

    cancer cell death. While frankincense essential oil elicited selective cancer cell death via NRF-2-mediated oxidative stress, sandalwood essential oil induced non-selective cell death via DNA damage and cell cycle arrest. PMID:25006348

  2. Fibre optic microarrays.

    Science.gov (United States)

    Walt, David R

    2010-01-01

    This tutorial review describes how fibre optic microarrays can be used to create a variety of sensing and measurement systems. This review covers the basics of optical fibres and arrays, the different microarray architectures, and describes a multitude of applications. Such arrays enable multiplexed sensing for a variety of analytes including nucleic acids, vapours, and biomolecules. Polymer-coated fibre arrays can be used for measuring microscopic chemical phenomena, such as corrosion and localized release of biochemicals from cells. In addition, these microarrays can serve as a substrate for fundamental studies of single molecules and single cells. The review covers topics of interest to chemists, biologists, materials scientists, and engineers.

  3. A game-theoretical model for selecting a site of non-preferred waste facilities

    International Nuclear Information System (INIS)

    Kim, Seong Ho; Kim, Tae Woon

    2006-01-01

    In the present work, a game-theoretic model (GTM) as a tool of conflict analysis is proposed for multiplayer multicriteria decision-making problems in a conflict situation. The developed GTM is used for obtaining the most possible resolutions in the conflict among multiple decision makers. The GTM is based on directed graph structure and solution concepts. To demonstrate the performance of the GTM, using a numerical example, the GTM is applied to an environmental conflict problem, especially a non-preferred waste disposal siting conflict available in the literature. It is found that with GTM the states in equilibrium can be recognized. The conflict under consideration is to select a site of non-preferred waste facilities. The government is to choose a site of installation for users of a toxic waste disposal facility. A certain time-point of interest is a period of time to select one of candidate sites that completely meet regular criteria of governmental body in charge of permitting a facility site. The facility siting conflict among multiple players (i.e., decision-makers, DMs) of concern is viewed as a multiple player-multiple criteria (MPMC) domain. For instance, three possible sites (i.e., site A, site B, and site C) to be selected by multiple players are characterized by the building cost, accessibility, and proximity to the residential area. Concerning the site A, the installation of a facility is not expensive, the accessible to a facility is easy, and the site A is located very near a residential area. Concerning site B, the facility is expensive to build, the facility is easily accessible, and the site is located near the residential area. Concerning site C, the installation cost is expensive, the accessibility is difficult, and the location of site is far from the residential area. In simple models, three main groups of players could be considered to be the government, users, and local residents. The government is to play a role as one of proponents or

  4. Present status of ESNIT (energy selective neutron irradiation test facility) program

    International Nuclear Information System (INIS)

    Noda, K.; Ohno, H.; Sugimoto, M.; Kato, Y.; Matsuo, H.; Watanabe, K.; Kikuchi, T.; Sawai, T.; Usui, T.; Oyama, Y.; Kondo, T.

    1994-01-01

    The present status of technical studies of a high energy neutron irradiation facility, ESNIT (energy selective neutron irradiation test facility), is summarized. Technological survey and feasibility studies of ESNIT have continued since 1988. The results of technical studies of the accelerator, the target and the experimental systems in ESNIT program were reviewed by an International Advisory Committee in February 1993. Recommendations for future R and D on ESNIT program are also summarized in this paper. ((orig.))

  5. Site Selection for the Salt Disposition Facility at the Savannah River Site

    International Nuclear Information System (INIS)

    Gladden, J.B.; Rueter, K.J.; Morin, J.P.

    2000-01-01

    A site selection study was conducted to identify a suitable location for the construction and operation of a new Salt Disposition Facility (SDF) at the Savannah River Site (SRS). The facility to be sited is a single processing facility and support buildings that could house either of three technology alternatives being developed by the High Level Waste Systems Engineering Team: Small Tank Tetraphenylborate Precipitation, Crystalline Silicotitanate Non-Elutable Ion Exchange or Caustic Side Solvent Extraction. A fourth alternative, Direct Disposal in grout, is not part of the site selection study because a location has been identified that is unique to this technology (i.e., Z-Area). Facility site selection at SRS is a formal, documented process that seeks to optimize siting of new facilities with respect to facility-specific engineering requirements, sensitive environmental resources, and applicable regulatory requirements. In this manner, the prime objectives of cost minimization, environmental protection, and regulatory compliance are achieved. The results from this geotechnical characterization indicated that continued consideration be given to Site B for the proposed SDF. Suitable topography, the lack of surface hydrology and floodplain issues, no significant groundwater contamination, the presence of minor soft zones along the northeast portion of footprint, and no apparent geological structure in the Gordon Aquitard support this recommendation

  6. DNA Microarray Technology

    Science.gov (United States)

    Skip to main content DNA Microarray Technology Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions Funding ...

  7. Site selection handbook: Workshop on site selection for low-level radioactive waste disposal facilities

    International Nuclear Information System (INIS)

    1987-10-01

    The Low-Level Radioactive Waste Policy Amendments Act of 1985 (LLRWPAA) requires the Department of Energy (DOE) to provide technical assistance to ''...those compact regions, host States and nonmember States determined by the Secretary to require assistance.'' Technical assistance has been defined to include, but not be limited to, ''technical guidelines for site selection.'' This site selection workshop was developed to assist States and Compacts in developing new low-level radioactive waste (LLW) disposal sites in accordance with the requirements of the LLRWPAA. The workshop comprises a series of lectures, discussion topics, and exercises, supported by this Site Selection Workshop Handbook, designed to examine various aspects of a comprehensive site selection program. It is not an exhaustive treatment of all aspects of site selection, nor is it prescriptive. The workshop focuses on the major elements of site selection and the tools that can be used to implement the site selection program

  8. The Mixed Waste Management Facility: Technology selection and implementation plan, Part 2, Support processes

    International Nuclear Information System (INIS)

    Streit, R.D.; Couture, S.A.

    1995-03-01

    The purpose of this document is to establish the foundation for the selection and implementation of technologies to be demonstrated in the Mixed Waste Management Facility, and to select the technologies for initial pilot-scale demonstration. Criteria are defined for judging demonstration technologies, and the framework for future technology selection is established. On the basis of these criteria, an initial suite of technologies was chosen, and the demonstration implementation scheme was developed. Part 1, previously released, addresses the selection of the primary processes. Part II addresses process support systems that are considered ''demonstration technologies.'' Other support technologies, e.g., facility off-gas, receiving and shipping, and water treatment, while part of the integrated demonstration, use best available commercial equipment and are not selected against the demonstration technology criteria

  9. DNA Microarray Technology; TOPICAL

    International Nuclear Information System (INIS)

    WERNER-WASHBURNE, MARGARET; DAVIDSON, GEORGE S.

    2002-01-01

    Collaboration between Sandia National Laboratories and the University of New Mexico Biology Department resulted in the capability to train students in microarray techniques and the interpretation of data from microarray experiments. These studies provide for a better understanding of the role of stationary phase and the gene regulation involved in exit from stationary phase, which may eventually have important clinical implications. Importantly, this research trained numerous students and is the basis for three new Ph.D. projects

  10. Site selection process for radioactive waste repository (radioactive facility) in Cuba as a fundamental safety criteria

    International Nuclear Information System (INIS)

    Vital, Jose Luis Peralta; Castillo, Reinaldo Gil; Chales Suarez, Gustavo; Rodriguez Reyes, Aymee

    1999-01-01

    The paper show the process of search carried out for the selection of the safest site in the National territory, in order to sitting the Facility (Repository) that will disposal the low and intermediate level radioactive wastes, as well as the possible Storage Facility for nuclear spent Fuel (radioactive wastes of high activity). We summarize the obtained Methodology and the Criterions of exclusion adopted for the development of the Process of site selection, as well as the current condition of the researches that will permit the obtaining of the nominative objectives. (author)

  11. Site selection report basalt waste isolation program near-surface test facility

    International Nuclear Information System (INIS)

    Sharpe, S.D.

    1978-01-01

    A site selection committee was established to review the information gathered on potential sites and to select a site for the Near-Surface Test Facility Phase I. A decision was made to use a site on the north face of Gable Mountain located on the Hanford Site. This site provided convenient access to the Pomona Basalt Flow. This flow was selected for use at this site because it exhibited the characteristics established in the primary criteria. These criteria were: the flows thickness; its dryness; its nearness to the surface; and, its similarities to basalt units which are candidates for the repository. After the selection of the Near-Surface Test Facility Phase I Site, the need arose for an additional facility to demonstrate safe handling, storage techniques, and the physical effects of radioactive materials on an in situ basalt formation. The committee reviewed the sites selected for Phase I and chose the same site for locating Phase II of the Near-Surface Test Facility

  12. PATMA: parser of archival tissue microarray

    Directory of Open Access Journals (Sweden)

    Lukasz Roszkowiak

    2016-12-01

    Full Text Available Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

  13. Study of a Country Level Facility LocationSelection for a Small Company

    OpenAIRE

    Eterovic, Mirko; Özgül, Simge

    2012-01-01

    Selection of an optimal facility location is a challenging decision for companies, since it would be costly and dicult to change the location after an installation has been already made. Existing numerical methods in the decision-making process help companies to perform their operations with minimum cost and maximum value based on their strategic objectives. Decision making process requires the selection of relative processes among several alternatives corresponding to a set of location facto...

  14. The December 7, 1988 Armenia earthquake effects on selected power, industrial and commercial facilities

    International Nuclear Information System (INIS)

    Campbell, R.D.; Griffin, M.J.; Bragagnolo, L.J.; Yanev, P.I.

    1996-01-01

    A detailed overview of the Armenia earthquake (occurred on December 7, 1988) effects on selected power, industrial and commercial facilities is presented in this paper. It involves geologic and seismology study of the region; description of the design building standards; detailed description of the damaged nuclear and other power plants as well as other industrial facilities. Extensive damage was sustained by the industrial facilities in the epicentral area, the majority due to poor design and construction. The effects on power facilities were much less severe. response time to restore power to the transmission was 2 to 3 days following the earthquake. Power plant equipment without rigorous seismic design performed well. Mechanical equipment, pumps, valves, compressors, and piping all performed with minimal damage, Electrical control equipment if properly anchored performed well without exception

  15. Treatment compliance and challenges among tuberculosis patients across selected health facilities in Osun State Nigeria.

    Science.gov (United States)

    Ajao, K O; Ogundun, O A; Afolabi, O T; Ojo, T O; Atiba, B P; Oguntunase, D O

    2014-12-01

    Tuberculosis (TB) is a major public health problem in the world and Africa has approximately one quarter of the world's cases. One of the greatest challenges facing most TB programmes is the non-compliance to TB treatment among TB patients. This study aimed at determining the challenges of management of tuberculosis (TB) across selected Osun State health facilities. The study employed a descriptive cross-sectional design. A semi-structured questionnaire was used to collect data from 102 TB patients in the health facilities. The instrument measured socio-demographic variables, patient related factors, socio-economic variables, health care system related factors to TB disease and treatment. Data were analysed and summarized using descriptive and inferential statistics. Statistical significance was placed at p facilities (χ2 = 21.761, p facility and patient-related factors were largely responsible.

  16. Review Article : Utilization of Environmental Radiochemistry Techniques for Selection and Evaluation of Nuclear Facility Sites

    International Nuclear Information System (INIS)

    Atta, E.R.; Madbouly, A.M.; Zakaria, Kh.M.

    2016-01-01

    This research review puts necessary considerations on the available environmental radiochemistry techniques for selection and evaluation of a nuclear facility sites.The main bjective in site evaluation for nuclear facilities in terms of nuclear safety is to protect the site workers, the public and the environment from the effects of ionizing radiation release from nuclear facilities due to accidents. The extreme sensitivity and speed of radiochemical methods make their applications of considerable importance in several fields and they have found many uses. Information about the existed radioactivity in the different nuclear facilities is an essential requirement for their environmental assessment. It is necessary to estimate the various radioactivity levels in the environment through qualitative and quantitative analytical techniques and to assess the potential effects of the nuclear facility in the region by considering the characteristics of sites.The siting and site evaluation requirements are discussed. Emphasis was given to types of radiochemical techniques used for characterization of the site parameters which determine the potential hazards of the site on the facility and the facility on the site. Emphasis has been also given to the quantitative and qualitative analysis of naturally occurring radionuclides for monitoring and control .There are some techniques employed such as radioactive tracer technique, liquid scintillation technique, gamma spectrometry technique, neutron activation analysis technique, fluorimetric technique and isotope hydrology technique.

  17. Design and selection criteria of a commercial irradiation facility for spices and dry products

    International Nuclear Information System (INIS)

    Aggarwal, K.S.

    1990-01-01

    Apart from cost considerations, various factors which should be taken into consideration in design of a commercial irradiation facility for spices and dry products and the factors which a user should consider for selecting a food irradiator are discussed in brief. (author)

  18. An Evaluation of Industrial Facilities Defects in Selected Industrial Estates in Lagos State, Nigeria

    Directory of Open Access Journals (Sweden)

    Oseghale, G.E.

    2014-01-01

    Full Text Available The study appraised the state of industrial facilities in selected industrial estates established between 1957 and 1981 in Lagos State by examining the nature and causes of facilities’ defects in the selected industrial estates. The buildings sampled were load bearing sandcrete block wall (1%, concrete framed structure (83% and steel framed structure (16%. Data were sourced using structured questionnaire administered on the staff of maintenance department of 35 building materials and plastic manufacturing industries purposively selected and located in 18 industrial estates. Data obtained were analyzed using descriptive statistic. The study found the structural elements of the buildings, i.e. foundations, beams, walls, and floors satisfactory. Using the mean response analysis, the result showed that the most severe factors responsible for industrial facilities’ defects were combined effects of geo-climatic factors (2.35, combined effects of biological agencies (2.15, corrosion (1.98, and physical aggression on the facilities (1.71.

  19. Evaluation and Selection of Renewable Energy Technologies for Highway Maintenance Facilities

    Science.gov (United States)

    Andrews, Taylor

    The interest in renewable energy has been increasing in recent years as attempts to reduce energy costs as well the consumption of fossil fuels are becoming more common. Companies and organizations are recognizing the increasing reliance on limited fossil fuels' resources, and as competition and costs for these resources grow, alternative solutions are becoming more appealing. Many federally run buildings and associations also have the added pressure of meeting the mandates of federal energy policies that dictate specific savings or reductions. Federal highway maintenance facilities run by the Department of Transportation fall into this category. To help meet energy saving goals, an investigation into potential renewable energy technologies was completed for the Ohio Department of Transportation. This research examined several types of renewable energy technologies and the major factors that affect their performance and evaluated their potential for implementation at highway maintenance facilities. Facilities energy usage data were provided, and a facility survey and site visits were completed to enhance the evaluation of technologies and the suitability for specific projects. Findings and technology recommendations were presented in the form of selection matrices, which were designed to help make selections in future projects. The benefits of utilization of other tools such as analysis software and life cycle assessments were also highlighted. These selection tools were designed to be helpful guides when beginning the pursuit of a renewable energy technology for highway maintenance facilities, and can be applied to other similar building types and projects. This document further discusses the research strategies and findings as well as the recommendations that were made to the personnel overseeing Ohio's highway maintenance facilities.

  20. Process cost and facility considerations in the selection of primary cell culture clarification technology.

    Science.gov (United States)

    Felo, Michael; Christensen, Brandon; Higgins, John

    2013-01-01

    The bioreactor volume delineating the selection of primary clarification technology is not always easily defined. Development of a commercial scale process for the manufacture of therapeutic proteins requires scale-up from a few liters to thousands of liters. While the separation techniques used for protein purification are largely conserved across scales, the separation techniques for primary cell culture clarification vary with scale. Process models were developed to compare monoclonal antibody production costs using two cell culture clarification technologies. One process model was created for cell culture clarification by disc stack centrifugation with depth filtration. A second process model was created for clarification by multi-stage depth filtration. Analyses were performed to examine the influence of bioreactor volume, product titer, depth filter capacity, and facility utilization on overall operating costs. At bioreactor volumes 5,000 L, clarification using centrifugation followed by depth filtration offers significant cost savings. For bioreactor volumes of ∼ 2,000 L, clarification costs are similar between depth filtration and centrifugation. At this scale, factors including facility utilization, available capital, ease of process development, implementation timelines, and process performance characterization play an important role in clarification technology selection. In the case study presented, a multi-product facility selected multi-stage depth filtration for cell culture clarification at the 500 and 2,000 L scales of operation. Facility implementation timelines, process development activities, equipment commissioning and validation, scale-up effects, and process robustness are examined. © 2013 American Institute of Chemical Engineers.

  1. Concept Of Revitalization Of Selected Military Facilities Of Dragoons Barracks In Olsztyn

    Science.gov (United States)

    Zagroba, Marek

    2015-12-01

    Revitalization is a complex program to restore the functioning of the neglected urban areas in terms of spatial, economic and social. Revitalization activities on post-military facilities are stopping negative phenomena, such as degradation of space, social pathology or lack of proper functioning of the area, adapted to modern needs. The object of the work is to present some aspects with the revitalization of former military facilities in the area of the Artyleryjska Street in Olsztyn. The presented design concept aims to revitalize a neglected area of the barracks, which will enable the activation site and include it in the city urban space. The method adopted in this work is the architectural project of adapting selected post-military facilities for new functions, affecting the economic development and social integration of people.

  2. Principles of geological substantiation for toxic waste disposal facilities sites selection

    International Nuclear Information System (INIS)

    Khrushchov, D. P.; Matorin, Eu. M.; Shekhunova, S. B.

    2002-01-01

    Industrial, domestic and military activities result in accumulation of toxic and hazardous waste. Disposal of these waste comprises two main approaches: technological processing (utilization and destruction) and landfill. According to concepts and programs of advanced countries technological solutions are preferable, but in fact over 70 % of waste are buried in storages, prevailingly of near surface type. The target of this paper is to present principles of geological substantiation of sites selection for toxic and hazardous waste isolation facilities location. (author)

  3. Selection of away-from-reactor facilities for spent fuel storage. A guidebook

    International Nuclear Information System (INIS)

    2007-09-01

    This publication aims to provide information on the approaches and criteria that would have to be considered for the selection of away-from-reactor (AFR) type spent fuel storage facilities, needs for which have been growing in an increasing number of Member States producing nuclear power. The AFR facilities can be defined as a storage system functionally independent of the reactor operation providing the role of storage until a further destination such as a disposal) becomes available. Initially developed to provide additional storage space for spent fuel, some AFR storage options are now providing additional spaces for extended storage of spent fuel with a prospect for long term storage, which is becoming a progressive reality in an increasing number of Member States due to the continuing debate on issues associated with the endpoints for spent fuel management and consequent delays in the implementation of final steps, such as disposal. The importance of AFR facilities for storage of spent fuel has been recognized for several decades and addressed in various IAEA publications in the area of spent fuel management. The Guidebook on Spent Fuel Storage (Technical Reports Series No. 240 published in 1984 and revised in 1991) discusses factors to be considered in the evaluation of spent fuel storage options. A technical committee meeting (TCM) on Selection of Dry Spent Fuel Storage Technologies held in Tokyo in 1995 also deliberated on this issue. However, there has not been any stand-alone publication focusing on the topic of selection of AFR storage facilities. The selection of AFR storage facilities is in fact a critical step for the successful implementation of spent fuel management programmes, due to the long operational periods required for storage and fuel handling involved with the additional implication of subsequent penalties in reversing decisions or changing the option mid-stream especially after the construction of the facility. In such a context, the long

  4. Selection of targets and ion sources for RIB generation at the Holifield Radioactive Ion Beam Facility

    International Nuclear Information System (INIS)

    Alton, G.D.

    1995-01-01

    In this report, the authors describe the performance characteristics for a selected number of target ion sources that will be employed for initial use at the Holifield Radioactive Ion Beam Facility (HRIBF) as well as prototype ion sources that show promise for future use for RIB applications. A brief review of present efforts to select target materials and to design composite target matrix/heat-sink systems that simultaneously incorporate the short diffusion lengths, high permeabilities, and controllable temperatures required to effect fast and efficient diffusion release of the short-lived species is also given

  5. Selection of possible candidate area for nuclear energy facility in Johor, Malaysia

    International Nuclear Information System (INIS)

    Nor Afifah Basri; Ahmad Termizi Ramli

    2012-01-01

    Nuclear power is considered as one of the best option for future energy development in Malaysia. Since Malaysia has no experience in nuclear energy generation, commissioning the first nuclear power plant needs tremendous effort in various aspects. Site selection is one of important step in nuclear power plant commissioning process. This paper proposes candidate sites for nuclear power plant in Mersing, Kota Tinggi, Muar and Batu Pahat district in Johor, Malaysia. The candidate selection process uses the IAEA document and AELB guideline as main reference, supported by site selection procedure by various countries. MapInfo Professional software was used to stimulate the selection process for candidate areas for the nuclear power plant. This paper concluded that Tenggaroh and Jemaluang area are the most suitable area for nuclear power plant facilities in Johor, Malaysia. (Author)

  6. External quality assessment of malaria microscopy diagnosis in selected health facilities in Western Oromia, Ethiopia.

    Science.gov (United States)

    Sori, Getachew; Zewdie, Olifan; Tadele, Geletta; Samuel, Abdi

    2018-06-18

    Accurate early diagnosis and prompt treatment are one of the key strategies to control and prevent malaria disease. External quality assessment is the most effective method for evaluation of the quality of malaria microscopy diagnosis. The aim of this study was to assess the quality of malaria microscopy diagnosis and its associated factors in selected public health facility laboratories in East Wollega Zone, Western Ethiopia. Facility-based cross-sectional study design was conducted in 30 randomly selected public health facility laboratories from November 2014 to January 2015 in East Wollega Zone, Western Ethiopia. Ten validated stained malaria panel slides with known Plasmodium species, developmental stage and parasite density were distributed. Data were captured; cleaned and analyzed using SPSS version 20 statistical software-multivariate logistic regressions and the agreement in reading between the peripheral diagnostic centers and the reference laboratory were done using kappa statistics. A total of 30 health facility laboratories were involved in the study and the overall quality of malaria microscopy diagnosis was poor (62.3%). The associated predictors of quality in this diagnosis were in-service training [(AOR = 16, 95% CI (1.3, 1.96)], smearing quality [(AOR = 24, 95% CI (1.8, 3.13)], staining quality [(AOR = 15, 95% CI (2.35, 8.61), parasite detection [(AOR = 9, 95% CI (1.1, 8.52)] and identification skills [(AOR = 8.6, 95% CI (1.21, 1.63)]. Eighteen (60%) of health facility laboratories had in-service trained laboratory professionals on malaria microscopy diagnosis. Overall quality of malaria microscopy diagnosis was poor and a significant gap in this service was observed that could impact on its diagnostic services.

  7. A note on “An alternative multiple attribute decision making methodology for solving optimal facility layout design selection problems”

    OpenAIRE

    R. Venkata Rao

    2012-01-01

    A paper published by Maniya and Bhatt (2011) (An alternative multiple attribute decision making methodology for solving optimal facility layout design selection problems, Computers & Industrial Engineering, 61, 542-549) proposed an alternative multiple attribute decision making method named as “Preference Selection Index (PSI) method” for selection of an optimal facility layout design. The authors had claimed that the method was logical and more appropriate and the method gives directly the o...

  8. Nuclear facility decommissioning and site remedial actions. Volume 1. A selected bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Faust, R.A.; Fore, C.S.; Knox, N.P.

    1980-09-01

    This bibliography of 633 references represents the first in a series to be produced by the Remedial Actions Program Information Center (RAPIC) containing scientific, technical, economic, and regulatory information concerning the decommissioning of nuclear facilities. Major chapters selected for this bibliography are Facility Decommissioning, Uranium Mill Tailings Cleanup, Contaminated Site Restoration, and Criteria and Standards. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. When the author is not given, the corporate affiliation appears first. If these two levels of authorship are not given, the title of the document is used as the identifying level. Indexes are provided for (1) author(s), (2) keywords, (3) title, (4) technology development, and (5) publication description. An appendix of 123 entries lists recently acquired references relevant to decommissioning of nuclear facilities. These references are also arranged according to one of the four subject categories and followed by author, title, and publication description indexes. The bibliography was compiled from a specialized data base established and maintained by RAPIC to provide information support for the Department of Energy's Remedial Actions Program, under the cosponsorship of its three major components: Surplus Facilities Management Program, Uranium Mill Tailings Remedial Actions Program, and Formerly Utilized Sites Remedial Actions Program. RAPIC is part of the Ecological Sciences Information Center within the Information Center Complex at Oak Ridge National Laboratory.

  9. Nuclear facility decommissioning and site remedial actions. Volume 1. A selected bibliography

    International Nuclear Information System (INIS)

    Faust, R.A.; Fore, C.S.; Knox, N.P.

    1980-09-01

    This bibliography of 633 references represents the first in a series to be produced by the Remedial Actions Program Information Center (RAPIC) containing scientific, technical, economic, and regulatory information concerning the decommissioning of nuclear facilities. Major chapters selected for this bibliography are Facility Decommissioning, Uranium Mill Tailings Cleanup, Contaminated Site Restoration, and Criteria and Standards. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. When the author is not given, the corporate affiliation appears first. If these two levels of authorship are not given, the title of the document is used as the identifying level. Indexes are provided for (1) author(s), (2) keywords, (3) title, (4) technology development, and (5) publication description. An appendix of 123 entries lists recently acquired references relevant to decommissioning of nuclear facilities. These references are also arranged according to one of the four subject categories and followed by author, title, and publication description indexes. The bibliography was compiled from a specialized data base established and maintained by RAPIC to provide information support for the Department of Energy's Remedial Actions Program, under the cosponsorship of its three major components: Surplus Facilities Management Program, Uranium Mill Tailings Remedial Actions Program, and Formerly Utilized Sites Remedial Actions Program. RAPIC is part of the Ecological Sciences Information Center within the Information Center Complex at Oak Ridge National Laboratory

  10. Facile Selective and Diverse Fabrication of Superhydrophobic, Superoleophobic-Superhydrophilic and Superamphiphobic Materials from Kaolin.

    Science.gov (United States)

    Qu, Mengnan; Ma, Xuerui; He, Jinmei; Feng, Juan; Liu, Shanshan; Yao, Yali; Hou, Lingang; Liu, Xiangrong

    2017-01-11

    As the starting material, kaolin is selectively and diversely fabricated to the superhydrophobic, superoleophobic-superhydrophilic, and superamphiphobic materials, respectively. The wettability of the kaolin surface can be selectively controlled and regulated to different superwetting states by choosing the corresponding modification reagent. The procedure is facile to operate, and no special technique or equipment is required. In addition, the procedure is cost-effective and time-saving and the obtained super-repellent properties are very stable. The X-ray photoelectron spectroscopy analysis demonstrates different changes of kaolin particles surfaces which are responsible for the different super-repellency. The scanning electron microscopy displays geometric micro- and nanometer structures of the obtained three kinds of super-repellent materials. The results show that kaolin has good applications in many kinds of superwetting materials. The method demonstrated in this paper provides a new strategy for regulating and controlling the wettability of solid surfaces selectively, diversely, and comprehensively.

  11. Materials selection of surface coatings in an advanced size reduction facility

    International Nuclear Information System (INIS)

    Briggs, J.L.; Younger, A.F.

    1980-01-01

    A materials selection test program was conducted to characterize optimum interior surface coatings for an advanced size reduction facility. The equipment to be processed by this facility consists of stainless steel apparatus (e.g., glove boxes, piping, and tanks) used for the chemical recovery of plutonium. Test results showed that a primary requirement for a satisfactory coating is ease of decontamination. A closely related concern is the resistance of paint films to nitric acid - plutonium environments. A vinyl copolymer base paint was the only coating, of eight paints tested, with properties that permitted satisfactory decontamination of plutonium and also performed equal to or better than the other paints in the chemical resistance, radiation stability, and impact tests

  12. Selection of candidate sites for a LLRW disposal facility in Connecticut

    International Nuclear Information System (INIS)

    Gingerich, Ronald E.; Holeman, George R.; Hileman, James A.

    1992-01-01

    Connecticut, one of the two members of the Northeast Interstate Low-Level Radioactive Waste Management Compact, has been directed by the Compact Commission to site a facility to manage the low-level radioactive waste (LLRW) generated in Connecticut. The Connecticut Hazardous Waste Management Service (CHWMS) has been given the responsibility to identify a site in the state for a LLRW disposal facility. The CHWMS has decided to plan for a site with an operating life of 50 years. A site of at least 160 acres will be needed to accommodate (he expected volume of LLRW and meet state and federal site requirements. A Site Selection Plan establishing the process and criteria to be used in siting a facility was adopted by the CHWMS in November 1990. The Plan calls for a stepwise screening of the state using published data to identify three candidate sites. A preferred site will be selected from among the candidate sites using onsite testing. The site selection criteria, which closely follow state and federal statutory and regulatory requirements, are divided into three types: exclusionary, avoidance and preference. Battelle Memorial Institute was selected as the contractor to assist the CHWMS in site screening. With guidance from the CHWMS, Battelle undertook screening of the state by applying the exclusionary, avoidance and preference criteria in three steps to identify from eight to twelve potential sites. The CHWMS Board of Directors bad decided that it wanted to be closely involved in the selection of the three candidate sites and to do so in a way that precluded the political and parochial pressures that are inevitably associated with a siting process. To meet these two goals a geographically neutral approach was devised for candidate site selection. In June, 1991 the CHWMS, with assistance from Battelle, conducted a three day workshop, open to the public, in which eight sites were presented to the Board. Data on the sites were presented in a way that did not disclose

  13. An independent safety assessment of Department of Energy nuclear reactor facilities: Training of operating personnel and personnel selection

    International Nuclear Information System (INIS)

    Drain, J.F.

    1981-02-01

    This study has been prepared for the Department of Energy's Nuclear Facilities Personnel Qualification and Training (NFPQT) Committee. Its purpose is to provide the Committee with background information on, and assessment of, the selection, training, and qualification of nuclear reactor operating personnel at DOE-owned facilities

  14. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 12

    International Nuclear Information System (INIS)

    1991-09-01

    The 664 abstracted references on environmental restoration, nuclear facility decommissioning, uranium mill tailings management, and site remedial actions constitute the twelfth in a series of reports prepared annually for the US Department of Energy Remedial Action Programs. Citations to foreign and domestic literature of all types -- technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions -- have been included. The bibliography contains scientific, technical, economic, regulatory, and legal information pertinent to the US Department of Energy Remedial Action Programs. Major sections are (1) Decontamination and Decommissioning Program, (2) Nuclear Facilities Decommissioning, (3) Formerly Utilized Sites Remedial Action Program, (4) Facilities Contaminated with Naturally Occurring Radionuclides, (5) Uranium Mill Tailings Remedial Action Program, (6) Uranium Mill Tailings Management, (7) Technical Measurements Center, and (8) Environmental Restoration Program. Within these categories, references are arranged alphabetically by first author. Those references having no individual author are listed by corporate affiliation or by publication title. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, subject category, and key word. This report is a product of the Remedial Action Program Information Center (RAPIC), which selects, analyzes, and disseminates information on environmental restoration and remedial actions. RAPIC staff and resources are available to meet a variety of information needs. Contact the center at FTS 624-7764 or (615) 574-7764

  15. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 12. Environmental Restoration Program

    Energy Technology Data Exchange (ETDEWEB)

    1991-09-01

    The 664 abstracted references on environmental restoration, nuclear facility decommissioning, uranium mill tailings management, and site remedial actions constitute the twelfth in a series of reports prepared annually for the US Department of Energy Remedial Action Programs. Citations to foreign and domestic literature of all types -- technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions -- have been included. The bibliography contains scientific, technical, economic, regulatory, and legal information pertinent to the US Department of Energy Remedial Action Programs. Major sections are (1) Decontamination and Decommissioning Program, (2) Nuclear Facilities Decommissioning, (3) Formerly Utilized Sites Remedial Action Program, (4) Facilities Contaminated with Naturally Occurring Radionuclides, (5) Uranium Mill Tailings Remedial Action Program, (6) Uranium Mill Tailings Management, (7) Technical Measurements Center, and (8) Environmental Restoration Program. Within these categories, references are arranged alphabetically by first author. Those references having no individual author are listed by corporate affiliation or by publication title. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, subject category, and key word. This report is a product of the Remedial Action Program Information Center (RAPIC), which selects, analyzes, and disseminates information on environmental restoration and remedial actions. RAPIC staff and resources are available to meet a variety of information needs. Contact the center at FTS 624-7764 or (615) 574-7764.

  16. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 12

    Energy Technology Data Exchange (ETDEWEB)

    Owen, P. T.; Webb, J. R.; Knox, N. P.; Goins, L. F.; Harrell, R. E.; Mallory, P. K.; Cravens, C. D.

    1991-09-01

    The 664 abstracted references on environmental restoration, nuclear facility decommissioning, uranium mill tailings management, and site remedial actions constitute the twelfth in a series of reports prepared annually for the US Department of Energy Remedial Action Programs. Citations to foreign and domestic literature of all types -- technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions -- have been included. The bibliography contains scientific, technical, economic, regulatory, and legal information pertinent to the US Department of Energy Remedial Action Programs. Major sections are (1) Decontamination and Decommissioning Program, (2) Nuclear Facilities Decommissioning, (3) Formerly Utilized Sites Remedial Action Program, (4) Facilities Contaminated with Naturally Occurring Radionuclides, (5) Uranium Mill Tailings Remedial Action Program, (6) Uranium Mill Tailings Management, (7) Technical Measurements Center, and (8) Environmental Restoration Program. Within these categories, references are arranged alphabetically by first author. Those references having no individual author are listed by corporate affiliation or by publication title. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, subject category, and key word. This report is a product of the Remedial Action Program Information Center (RAPIC), which selects, analyzes, and disseminates information on environmental restoration and remedial actions. RAPIC staff and resources are available to meet a variety of information needs. Contact the center at FTS 624-7764 or (615) 574-7764.

  17. SENSITIVITY OF MOLDS ISOLATED FROM WAREHOUSES OF FOOD PRODUCTION FACILITY ON SELECTED ESSENTIAL OILS

    Directory of Open Access Journals (Sweden)

    Łukasz Kręcidło

    2015-07-01

    Full Text Available Storage of raw materials is one of steps in food production chain. The aim of this study was to estimate the influence of selected essential oils on the growth of four fungal strains: Trichoderma viride, Rhizomucor miehei, Penicillium chrysogenum, Penicillium janthinellum. Strains were isolated from warehouses of the food production facility. Selected essential oils: thyme oil, rosewood oil and rosemary oil were used to assess antifungal activity. Chemical composition of essential oils was determined by Gas Chromatography-Mass Spectroscopy (GC-MS. Antifungal activity of essential oils was estimated in relative to peracetic acid (PAA and sterile water with Tween 80 (0,5%. The influence of essential oils on fungal growth was carried by medium poisoning method. Increment of fungal mycelium was measured every day by 10 days. The thyme essential oils totally inhibited fungal growth in the lowest concentration of 1 mm3·cm-3. The most resistant strain was Penicillium janthinellum.

  18. An overview of safety and environmental considerations in the selection of materials for fusion facilities

    International Nuclear Information System (INIS)

    Petti, D.A.; Piet, S.J.; Seki, Y.

    1996-01-01

    Safety and environmental considerations can play a large role in the selection of fusion materials. In this paper, we review the attributes of different structural, plasma facing, and breeding materials from a safety perspective and discuss some generic waste management issues as they relate to fusion materials in general. Specific safety concerns exist for each material that must be dealt with in fusion facility design. Low activation materials offer inherent safety benefits compared with conventional materials, but more work is needed before these materials have the requisite certified databases. In the interim, the international thermonuclear experimental reactor (ITER) has selected more conventional materials and is showing that the safety concerns with these materials can be addressed by proper attention to design. In the area of waste management disposal criteria differ by country. However, the criteria are all very strict making disposal of fusion components difficult. As a result, recycling has gained increasing attention. (orig.)

  19. Verification of dose rate calculation and selection study on low activation concrete in fusion facilities

    International Nuclear Information System (INIS)

    Oishi, Koji; Minami, Kiyoshi; Ikeda, Yujiro; Kosako, Kazuaki; Nakamura, Tomoo

    1991-01-01

    A concrete assembly was irradiated by D-T neutrons for 10 h, and dose rate measurement one day after shutdown has been carried out in order to provide a guide line for selection studies of low activation concrete. The experimental results were analyzed by the two dimensional calculation code DOT3.5 with its related nuclear data library GICX40 based on ENDF/B-III, however disagreement between experiment and calculation was observed in the deeper detector positions. Calculations were also performed using the nuclear data library based on ENDF/B-IV, and agreement within experimental errors was obtained at all detector positions. Selection studies for low activation concrete were performed using this nuclear data library. As a result, it was found that limestone concrete exhibited excellent properties as a low activation concrete in fusion facilities. (orig.)

  20. Site selection experience for a new low-level radioactive waste storage/disposal facility at the Savannah River Plant

    International Nuclear Information System (INIS)

    Towler, O.A.; Cook, J.R.; Helton, B.D.

    1985-10-01

    Preliminary performance criteria and site selection guides specific to the Savannah River Plant, were developed for a new low-level radioactive waste storage/disposal facility. These site selection guides were applied to seventeen potential sites identified at SRP. The potential site were ranked based on how well they met a set of characteristics considered important in site selection for a low-level radioactive waste disposal facility. The characteristics were given a weighting factor representing its relative importance in meeting site performance criteria. A candidate site was selected and will be the subject of a site characterization program

  1. Engineering study of generic site criteria for selected DOE plutonium facilities

    International Nuclear Information System (INIS)

    Kingsbury, R.J.; Greenwood, J.M.; Sandoval, M.D.

    1980-09-01

    The objectives of this study were to identify criteria that would be applied to selection of a site for plutonium facilities such as those at the Rocky Flats Plant, to establish the relative importance of these criteria, and to identify suitable areas within the United States for location of plutonium facilities with respect to these criteria. Sources of the site criteria identified include federal laws, federal agency regulations, state laws and regulations, and requirements associated with operations to be performed at the site. The criteria identified during the study were organized into 14 major categories. The relative importnace of each category and each criterion within the categories were established using group decision-making techniques. The major criteria categories, their assigned weight on a scale of 1 to 10, and their relative priority ranks are as follows: geology/seismicity; public safety; environmental impact; meteorology; hydrology; topography; transportation; utilities; personnel; safeguards/security; land area and availability; land use compatibility; and, public acceptance. A suitability analysis of the continental United States was performed using only those criteria that could be mapped at a national scale. Suitability was assessed with respect to each of these criteria, and individual suitability maps were prepared. A composite suitability map was generated using computerized overlay techniques. This map provides a starting point for identifying specific candidate sites if an actual site selection were to be conducted

  2. Using traffic light labels to improve food selection in recreation and sport facility eating environments.

    Science.gov (United States)

    Olstad, Dana Lee; Vermeer, Julianne; McCargar, Linda J; Prowse, Rachel J L; Raine, Kim D

    2015-08-01

    Many recreation and sports facilities have unhealthy food environments, however managers are reluctant to offer healthier foods because they perceive patrons will not purchase them. Preliminary evidence indicates that traffic light labeling (TLL) can increase purchase of healthy foods in away-from-home food retail settings. We examined the effectiveness of TLL of menus in promoting healthier food purchases by patrons of a recreation and sport facility concession, and among various sub-groups. TLL of all menu items was implemented for a 1-week period and sales were assessed for 1-week pre- and 1-week post-implementation of TLL (n = 2101 transactions). A subset of consumers completed a survey during the baseline (n = 322) and intervention (n = 313) periods. We assessed change in the proportion of patrons' purchases that were labeled with green, yellow and red lights from baseline to the TLL intervention, and association with demographic characteristics and other survey responses. Change in overall revenues was also assessed. There was an overall increase in sales of green (52.2% to 55.5%; p sales of red (30.4% to 27.2%; p revenues did not differ between the baseline and TLL periods. TLL of menus increased purchase of healthy, and reduced purchase of unhealthy foods in a publicly funded recreation and sport facility, with no loss of revenue. Policymakers should consider extending menu labeling laws to public buildings such as recreation and sports facilities to promote selection of healthier items. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Selection and design of ion sources for use at the Holifield radioactive ion beam facility

    International Nuclear Information System (INIS)

    Alton, G.D.; Haynes, D.L.; Mills, G.D.; Olsen, D.K.

    1994-01-01

    The Holifield Radioactive Ion Beam Facility now under construction at the Oak Ridge National Laboratory will use the 25 MV tandem accelerator for the acceleration of radioactive ion beams to energies appropriate for research in nuclear physics; negative ion beams are, therefore, required for injection into the tandem accelerator. Because charge exchange is an efficient means for converting initially positive ion beams to negative ion beams, both positive and negative ion sources are viable options for use at the facility. The choice of the type of ion source will depend on the overall efficiency for generating the radioactive species of interest. Although direct-extraction negative ion sources are clearly desirable, the ion formation efficiencies are often too low for practical consideration; for this situation, positive ion sources, in combination with charge exchange, are the logical choice. The high-temperature version of the CERN-ISOLDE positive ion source has been selected and a modified version of the source designed and fabricated for initial use at the facility because of its low emittance, relatively high ionization efficiencies, and species versatility, and because it has been engineered for remote installation, removal, and servicing as required for safe handling in a high-radiation-level ISOL facility. The source will be primarily used to generate ion beams from elements with intermediate to low electron affinities. Prototype plasma-sputter negative ion sources and negative surface-ionization sources are under design consideration for generating radioactive ion beams from high-electron-affinity elements. The design features of these sources and expected efficiencies and beam qualities (emittances) will be described in this report

  4. Nuclear facility decommissioning and site remedial actions: A selected bibliography, volume 9

    Energy Technology Data Exchange (ETDEWEB)

    Owen, P.T.; Knox, N.P.; Michelson, D.C.; Turmer, G.S.

    1988-09-01

    The 604 abstracted references on nuclear facility decommissioning, uranium mill tailings management, and site remedial actions constitute the ninth in a series of reports prepared annually for the US Department of Energy's Remedial Action Programs. Foreign and domestic literature of all types--technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions--has been included. The bibliography contains scientific, technical, economic, regulatory, and legal information pertinent to the US Department of Energy's remedial action programs. Major sections are (1) Surplus Facilities Management Program, (2) Nuclear Facilities Decommissioning, (3) Formerly Utilized Sites Remedial Action Program, (4) Facilities Contaminated with Naturally Occurring Radionuclides, (5) Uranium Mill Tailings Remedial Action Program, (6) Uranium Mill Tailings Management, (7) Technical Measurements Center, and (8) General Remedial Action Program Studies. Subsections for sections 1, 2, 5, and 6 include: Design, Planning, and Regulations; Environmental Studies and Site Surveys; Health, Safety, and Biomedical Studies; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. Within these categories, references are arranged alphabetically by first author. Those references having no individual author are listed by corporate affiliation or by publication description. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, and keywords. This report is a product of the Remedial Action Program Information Center (RAPIC), which selects and analyzes information on remedial actions and relevant radioactive waste management technologies. RAPIC staff and resources are available to meet a variety of information needs. Contact the center at (615) 576-0568 or FTS 626-0568.

  5. Nuclear facility decommissioning and site remedial actions: A selected bibliography, volume 9

    International Nuclear Information System (INIS)

    Owen, P.T.; Knox, N.P.; Michelson, D.C.; Turmer, G.S.

    1988-09-01

    The 604 abstracted references on nuclear facility decommissioning, uranium mill tailings management, and site remedial actions constitute the ninth in a series of reports prepared annually for the US Department of Energy's Remedial Action Programs. Foreign and domestic literature of all types--technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions--has been included. The bibliography contains scientific, technical, economic, regulatory, and legal information pertinent to the US Department of Energy's remedial action programs. Major sections are (1) Surplus Facilities Management Program, (2) Nuclear Facilities Decommissioning, (3) Formerly Utilized Sites Remedial Action Program, (4) Facilities Contaminated with Naturally Occurring Radionuclides, (5) Uranium Mill Tailings Remedial Action Program, (6) Uranium Mill Tailings Management, (7) Technical Measurements Center, and (8) General Remedial Action Program Studies. Subsections for sections 1, 2, 5, and 6 include: Design, Planning, and Regulations; Environmental Studies and Site Surveys; Health, Safety, and Biomedical Studies; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. Within these categories, references are arranged alphabetically by first author. Those references having no individual author are listed by corporate affiliation or by publication description. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, and keywords. This report is a product of the Remedial Action Program Information Center (RAPIC), which selects and analyzes information on remedial actions and relevant radioactive waste management technologies. RAPIC staff and resources are available to meet a variety of information needs. Contact the center at (615) 576-0568 or FTS 626-0568

  6. Equilibrium Strategy Based Recycling Facility Site Selection towards Mitigating Coal Gangue Contamination

    Directory of Open Access Journals (Sweden)

    Jiuping Xu

    2017-02-01

    Full Text Available Environmental pollution caused by coal gangue has been a significant challenge for sustainable development; thus, many coal gangue reduction approaches have been proposed in recent years. In particular, coal gangue facility (CGF construction has been considered as an efficient method for the control and recycling of coal gangue. Meanwhile, the identification and selection of suitable CGF sites is a fundamental task for the government. Therefore, based on the equilibrium strategy, a site selection approach under a fuzzy environment is developed to mitigate coal gangue contamination, which integrates a geographical information system (GIS technique and a bi-level model to identify candidate CGF sites and to select the most suitable one. In this situation, the GIS technique used to identify potential feasible sites is able to integrate a great deal of geographical data tofitwithpracticalcircumstances;thebi-levelmodelusedtoscreentheappropriatesitecanreasonably dealwiththeconflictsbetweenthelocalauthorityandthecolliery. Moreover,aKarush–Kuhn–Tucker (KKT condition-based approach is used to find an optimal solution, and a case study is given to demonstrate the effectiveness of the proposed method. The results across different scenarios show that appropriate site selection can achieve coal gangue reduction targets and that a suitable excess stack level can realize an environmental-economic equilibrium. Finally, some propositions and management recommendations are given.

  7. The Role of Distance and Quality on Facility Selection for Maternal and Child Health Services in Urban Kenya.

    Science.gov (United States)

    Escamilla, Veronica; Calhoun, Lisa; Winston, Jennifer; Speizer, Ilene S

    2018-02-01

    Universal access to health care requires service availability and accessibility for those most in need of maternal and child health services. Women often bypass facilities closest to home due to poor quality. Few studies have directly linked individuals to facilities where they sought maternal and child health services and examined the role of distance and quality on this facility choice. Using endline data from a longitudinal survey from a sample of women in five cities in Kenya, we examine the role of distance and quality on facility selection for women using delivery, facility-based contraceptives, and child health services. A survey of public and private facilities offering reproductive health services was also conducted. Distances were measured between household cluster location and both the nearest facility and facility where women sought care. A quality index score representing facility infrastructure, staff, and supply characteristics was assigned to each facility. We use descriptive statistics to compare distance and quality between the nearest available facility and visited facility among women who bypassed the nearest facility. Facility distance and quality comparisons were also stratified by poverty status. Logistic regression models were used to measure associations between the quality and distance to the nearest facility and bypassing for each outcome. The majority of women bypassed the nearest facility regardless of service sought. Women bypassing for delivery traveled the furthest and had the fewest facility options near their residential cluster. Poor women bypassing for delivery traveled 4.5 km further than non-poor women. Among women who bypassed, two thirds seeking delivery and approximately 46% seeking facility-based contraception or child health services bypassed to a public hospital. Both poor and non-poor women bypassed to higher quality facilities. Our findings suggest that women in five cities in Kenya prefer public hospitals and are

  8. Design and cost estimate for the SRL integrated hot off gas facility using selective adsorption

    International Nuclear Information System (INIS)

    Pence, D.T.; Kirstein, B.E.

    1981-07-01

    Based on the results of an engineering-scale demonstration program, a design and cost estimate were performed for a 25-m 3 /h (15-ft 3 /min) capacity pilot plant demonstration system using selective adsorption technology for installation at the Integrated Hot Off Gas Facility at the Savannah River Plant. The design includes provisions for the destruction of NO/sub x/ and the concentration and removal of radioisotopes of ruthenium, iodine-129, tritiated water vapor, carbon-14 contaminated carbon dioxide, and krypton-85. The nobel gases are separated by the use of selective adsorption on mordenite-type zeolites. The theory of noble gas adsorption on zeolites is essentially the same as that for the adsorption of noble gases on activated charcoals. Considerable detail is provided regarding the application of the theory to adsorbent bed designs and operation. The design is based on a comprehensive material balance and appropriate heat transfer calculations. Details are provided on techniques and procedures used for heating, cooling, and desorbing the adsorbent columns. Analyses are also given regarding component and arrangement selection and includes discussions on alternative arrangements. The estimated equipment costs for the described treatment system is about $1,400,000. The cost estimate includes a detailed equipment list of all the major component items in the design. Related technical issues and estimated system performance are also discussed

  9. Design and cost estimate for the SRL integrated hot off gas facility using selective adsorption

    Energy Technology Data Exchange (ETDEWEB)

    Pence, D T; Kirstein, B E

    1981-07-01

    Based on the results of an engineering-scale demonstration program, a design and cost estimate were performed for a 25-m/sup 3//h (15-ft/sup 3//min) capacity pilot plant demonstration system using selective adsorption technology for installation at the Integrated Hot Off Gas Facility at the Savannah River Plant. The design includes provisions for the destruction of NO/sub x/ and the concentration and removal of radioisotopes of ruthenium, iodine-129, tritiated water vapor, carbon-14 contaminated carbon dioxide, and krypton-85. The nobel gases are separated by the use of selective adsorption on mordenite-type zeolites. The theory of noble gas adsorption on zeolites is essentially the same as that for the adsorption of noble gases on activated charcoals. Considerable detail is provided regarding the application of the theory to adsorbent bed designs and operation. The design is based on a comprehensive material balance and appropriate heat transfer calculations. Details are provided on techniques and procedures used for heating, cooling, and desorbing the adsorbent columns. Analyses are also given regarding component and arrangement selection and includes discussions on alternative arrangements. The estimated equipment costs for the described treatment system is about $1,400,000. The cost estimate includes a detailed equipment list of all the major component items in the design. Related technical issues and estimated system performance are also discussed.

  10. ALARA engineering at Department of Energy facilities: Bibliography of selected readings in radiation protection and ALARA

    International Nuclear Information System (INIS)

    Dionne, B.J.; Khan, T.A.; Lane, S.G.; Baum, J.W.

    1991-03-01

    This report is the second in the series of bibliographies supporting the efforts at the Brookhaven National Laboratory ALARA Center on dose reduction at US Department of Energy (DOE) facilities. The BNL ALARA Center was originally established in 1983 under the sponsorship of the US Nuclear Regulatory Commission to monitor dose-reduction research and ALARA activities at nuclear power plants. This effort was expanded in 1988 by the DOE's Office of Environment, Safety and Health to include DOE nuclear facilities. Abstracts for this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy Data Base, and reprints of published articles provided by the authors. Information that the reader feels should be included in the next volume of this bibliography may be submitted to the BNL ALARA Center. These abstracts, which have a bearing on dose reduction, consolidates information from publications pertinent to Radiological Engineers and Operational Health Physicists. Volume 2 contains 127 abstracts numbered from 69 through 195 as well as author and subject indices. The subject index contains the abstract numbers from both the previous volume and the current volume, the latter being indicated in boldface

  11. Selection of a preferred initial access for the exploratory studies facility

    International Nuclear Information System (INIS)

    Boak, D.M.; Cikanek, E.M.; Elkins, N.Z.

    1995-06-01

    An issue of interest to the Yucca Mountain Site Characterization Project Office (YMPO) has been selection of the preferred location for initial access to the Exploratory Studies Facility (ESF) in the event that the U.S. Department of Energy (DOE) elected to proceed with a phased approach to facility development. A task force to conduct an assessment and prepare a recommendation of the preferred initial location (north or south) for starting underground in situ tests at Yucca Mountain was initiated by YMPO to address this issue. The task force addressed geotechnical issues associated with the presence of disqualifying conditions at the site, the inability of the site to meet qualifying conditions, and the potential for unexpected geologic conditions at the site. The task force compared the north and south ramp accesses of the ESF to determine whether either access would be more likely to provide relevant information about potential site unsuitability. The task force did not address issues such as design time or construction costs. Within the aforementioned context, a balanced evaluation of currently available geotechnical information and issues failed to provide a clear mandate for either ramp as the preferred initial ESF access. Neither access was clearly superior in providing geotechnical information to resolve site suitability issues. The task force therefore recommended that other appropriate programmatic factors, such as schedule, be used as a basis in determining the choice of a preferred, initial ESF access in the event of phased construction

  12. Development of a systematic methodology to select hazard analysis techniques for nuclear facilities

    Energy Technology Data Exchange (ETDEWEB)

    Vasconcelos, Vanderley de; Reis, Sergio Carneiro dos; Costa, Antonio Carlos Lopes da [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)]. E-mails: vasconv@cdtn.br; reissc@cdtn.br; aclc@cdtn.br; Jordao, Elizabete [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Faculdade de Engenharia Quimica]. E-mail: bete@feq.unicamp.br

    2008-07-01

    In order to comply with licensing requirements of regulatory bodies risk assessments of nuclear facilities should be carried out. In Brazil, such assessments are part of the Safety Analysis Reports, required by CNEN (Brazilian Nuclear Energy Commission), and of the Risk Analysis Studies, required by the competent environmental bodies. A risk assessment generally includes the identification of the hazards and accident sequences that can occur, as well as the estimation of the frequencies and effects of these unwanted events on the plant, people, and environment. The hazard identification and analysis are also particularly important when implementing an Integrated Safety, Health, and Environment Management System following ISO 14001, BS 8800 and OHSAS 18001 standards. Among the myriad of tools that help the process of hazard analysis can be highlighted: CCA (Cause- Consequence Analysis); CL (Checklist Analysis); ETA (Event Tree Analysis); FMEA (Failure Mode and Effects Analysis); FMECA (Failure Mode, Effects and Criticality Analysis); FTA (Fault Tree Analysis); HAZOP (Hazard and Operability Study); HRA (Human Reliability Analysis); Pareto Analysis; PHA (Preliminary Hazard Analysis); RR (Relative Ranking); SR (Safety Review); WI (What-If); and WI/CL (What-If/Checklist Analysis). The choice of a particular technique or a combination of techniques depends on many factors like motivation of the analysis, available data, complexity of the process being analyzed, expertise available on hazard analysis, and initial perception of the involved risks. This paper presents a systematic methodology to select the most suitable set of tools to conduct the hazard analysis, taking into account the mentioned involved factors. Considering that non-reactor nuclear facilities are, to a large extent, chemical processing plants, the developed approach can also be applied to analysis of chemical and petrochemical plants. The selected hazard analysis techniques can support cost

  13. Development of a systematic methodology to select hazard analysis techniques for nuclear facilities

    International Nuclear Information System (INIS)

    Vasconcelos, Vanderley de; Reis, Sergio Carneiro dos; Costa, Antonio Carlos Lopes da; Jordao, Elizabete

    2008-01-01

    In order to comply with licensing requirements of regulatory bodies risk assessments of nuclear facilities should be carried out. In Brazil, such assessments are part of the Safety Analysis Reports, required by CNEN (Brazilian Nuclear Energy Commission), and of the Risk Analysis Studies, required by the competent environmental bodies. A risk assessment generally includes the identification of the hazards and accident sequences that can occur, as well as the estimation of the frequencies and effects of these unwanted events on the plant, people, and environment. The hazard identification and analysis are also particularly important when implementing an Integrated Safety, Health, and Environment Management System following ISO 14001, BS 8800 and OHSAS 18001 standards. Among the myriad of tools that help the process of hazard analysis can be highlighted: CCA (Cause- Consequence Analysis); CL (Checklist Analysis); ETA (Event Tree Analysis); FMEA (Failure Mode and Effects Analysis); FMECA (Failure Mode, Effects and Criticality Analysis); FTA (Fault Tree Analysis); HAZOP (Hazard and Operability Study); HRA (Human Reliability Analysis); Pareto Analysis; PHA (Preliminary Hazard Analysis); RR (Relative Ranking); SR (Safety Review); WI (What-If); and WI/CL (What-If/Checklist Analysis). The choice of a particular technique or a combination of techniques depends on many factors like motivation of the analysis, available data, complexity of the process being analyzed, expertise available on hazard analysis, and initial perception of the involved risks. This paper presents a systematic methodology to select the most suitable set of tools to conduct the hazard analysis, taking into account the mentioned involved factors. Considering that non-reactor nuclear facilities are, to a large extent, chemical processing plants, the developed approach can also be applied to analysis of chemical and petrochemical plants. The selected hazard analysis techniques can support cost

  14. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Vol. 18. Part 2. Indexes

    International Nuclear Information System (INIS)

    1997-09-01

    This bibliography contains 3638 citations with abstracts of documents relevant to environmental restoration, nuclear facility decontamination and decommissioning (D ampersand D), uranium mill tailings management, and site remedial actions. This report is the eighteenth in a series of bibliographies prepared annually for the U.S. Department of Energy (DOE) Office of Environmental Restoration. Citations to foreign and domestic literature of all types - technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions - have been included in Part 1 of the report. The bibliography contains scientific, technical, financial, and regulatory information that pertains to DOE environmental restoration programs. The citations are separated by topic into 16 sections, including (1) DOE Environmental Restoration Program; (2) DOE D ampersand D Program; (3) Nuclear Facilities Decommissioning; (4) DOE Formerly Utilized Sites Remedial Action Programs; (5) NORM-Contaminated Site Restoration; (6) DOE Uranium Mill Tailings Remedial Action Project; (7) Uranium Mill Tailings Management; (8) DOE Site-Wide Remedial Actions; (9) DOE Onsite Remedial Action Projects; (10) Contaminated Site Remedial Actions; (11) DOE Underground Storage Tank Remediation; (12) DOE Technology Development, Demonstration, and Evaluations; (13) Soil Remediation; (14) Groundwater Remediation; (15) Environmental Measurements, Analysis, and Decision-Making; and (16) Environmental Management Issues. Within the 16 sections, the citations are sorted by geographic location. If a geographic location is not specified, the citations are sorted according to the document title. In Part 2 of the report, indexes are provided for author, author affiliation, selected title phrase, selected title word, publication description, geographic location, and keyword

  15. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Vol. 18. Part 2. Indexes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    This bibliography contains 3638 citations with abstracts of documents relevant to environmental restoration, nuclear facility decontamination and decommissioning (D&D), uranium mill tailings management, and site remedial actions. This report is the eighteenth in a series of bibliographies prepared annually for the U.S. Department of Energy (DOE) Office of Environmental Restoration. Citations to foreign and domestic literature of all types - technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions - have been included in Part 1 of the report. The bibliography contains scientific, technical, financial, and regulatory information that pertains to DOE environmental restoration programs. The citations are separated by topic into 16 sections, including (1) DOE Environmental Restoration Program; (2) DOE D&D Program; (3) Nuclear Facilities Decommissioning; (4) DOE Formerly Utilized Sites Remedial Action Programs; (5) NORM-Contaminated Site Restoration; (6) DOE Uranium Mill Tailings Remedial Action Project; (7) Uranium Mill Tailings Management; (8) DOE Site-Wide Remedial Actions; (9) DOE Onsite Remedial Action Projects; (10) Contaminated Site Remedial Actions; (11) DOE Underground Storage Tank Remediation; (12) DOE Technology Development, Demonstration, and Evaluations; (13) Soil Remediation; (14) Groundwater Remediation; (15) Environmental Measurements, Analysis, and Decision-Making; and (16) Environmental Management Issues. Within the 16 sections, the citations are sorted by geographic location. If a geographic location is not specified, the citations are sorted according to the document title. In Part 2 of the report, indexes are provided for author, author affiliation, selected title phrase, selected title word, publication description, geographic location, and keyword.

  16. DNA microarrays : a molecular cloning manual

    National Research Council Canada - National Science Library

    Sambrook, Joseph; Bowtell, David

    2002-01-01

    .... DNA Microarrays provides authoritative, detailed instruction on the design, construction, and applications of microarrays, as well as comprehensive descriptions of the software tools and strategies...

  17. Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

    Science.gov (United States)

    In the 2007 Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation (CNV) was analyzed ...

  18. Conflicting opinions: The controversy accompanying the site selection for a German reactor facility (1950-1955)

    International Nuclear Information System (INIS)

    Gleitsmann, R.J.

    1986-12-01

    The foundation and history of the Karlsruhe Nuclear Research Center (KfK) partly reflects the history of nuclear energy and the historical development of the German technology sector which in particular with respect to its topical implications (e.g. the acceptance of advanced technologies) is unfortunately still being underestimated in most cases. Studying the historical development of an institution such as Kfk reveals regional ties, municipal, district, neighbourhood and industrial ties which are normally buried and veiled. The history of its foundation and development bears evidence of the fact that Kfk is an integral part of the Karlsruhe technology region. The period from 1952 to 1955 was characterized by vehement disputes preceding the final site selection for the first nuclear reactor facility of the Federal Republic of Germany. Each endeavouring to be selected th competitors, i.e. the Free State of Bavaria represented by the city of Munich and the newly established Southwestern Baden-Wuerttemberg represented by the city of Karlsruhe virtually vied with one another for the most attractive proposals and bids. They were both fully aware of the fact that a positive decision would mean to assume obligations in the order of magnitude of enormous million sums. The slightest chance of being chosen the very region to house the promising and hopeful 'nuclear energy industry' of the Federal Republic of Germany evidently required rather high bids on both sides. (orig./HP) [de

  19. Facile synthesis of Bi/BiOCl composite with selective photocatalytic properties

    International Nuclear Information System (INIS)

    Chen, Dongling; Zhang, Min; Lu, Qiuju; Chen, Junfang; Liu, Bitao; Wang, Zhaofeng

    2015-01-01

    This paper presents a novel and facile method to fabricate Bi/BiOCl composites with dominant (001) facets in situ via a microwave reduction route. Different characterization techniques, including X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission scanning electron microscopy (TEM), UV–vis diffuse reflectance spectrometry (DRS), X-ray photoelectron spectroscopy (XPS), electron spin resonance spectroscopy (ESR), cathodoluminescence spectrum (CL), and lifetime, have been employed to investigate the structure, optical and electrical properties of the Bi/BiOCl composites. The experimental results show that the introduction of Bi particles can efficiently enhance the photocatalytic performance of BiOCl for the degradation of several dyes under ultraviolet (UV) light irradiation, especially for negative charged methyl orange (MO). Unlike the UV photocatalytic performance, such Bi/BiOCl composite shows higher degradation efficiency towards rhodamine B (RhB) than MO and methylene blue (MB) under visible light irradiation. This special photocatalytic performance can be ascribed to the synergistic effect between oxygen vacancies and Bi particles. This work provides new insights about the photodegradation mechanisms of MO, MB and RhB under UV and visible light irradiation, which would be helpful to guide the selection of an appropriate catalyst for other pollutants. - Highlights: • Bi/BiOCl composites were synthesized via a microwave reduction. • Tunable selectivity photocatalytic activity can be achieved. • Photodegradation mechanism under UV and visible light were proposed

  20. Selection of RIB targets using ion implantation at the Holifield radioactive ion beam facility

    International Nuclear Information System (INIS)

    Alton, G.D.; Dellwo, J.

    1995-01-01

    Among several major challenges posed by generating and accelerating adequate intensities of RIBs, selection of the most appropriate target material is perhaps the most difficult because of the requisite fast and selective thermal release of minute amounts of the short-lived product atoms from the ISOL target in the presence of bulk amounts of target material. Experimental studies are under way at the Oak Ridge National Laboratory (ORNL) which are designed to measure the time evolution of implanted elements diffused from refractory target materials which are candidates for forming radioactive ion beams (RIBs) at the Holifield Radioactive Ion Beam Facility (HRIBF). The diffusion coefficients are derived by comparing experimental data with numerical solutions to a one-dimensional form of Fick's second law for ion implanted distributions. In this report, we describe the experimental arrangement, experimental procedures, and provide time release data and diffusion coefficients for releasing ion implanted 37 Cl from Zr 5 Si 3 and 75 As, 79 Br, and 78 Se from Zr 5 Ge 3 and estimates of the diffusion coefficients for 35 Cl, 63 Cu, 65 Cu, 69 Ga and 71 Ga diffused from BN; 35 Cl, 63 Cu, 65 Cu, 69 Ga, 75 As, and 78 Se diffused from C; 35 Cl, 68 Cu, 69 Ga, 75 As, and 78 Se diffused from Ta

  1. General service and child immunization-specific readiness assessment of healthcare facilities in two selected divisions in Bangladesh.

    Science.gov (United States)

    Shawon, Md Shajedur Rahman; Adhikary, Gourab; Ali, Md Wazed; Shamsuzzaman, Md; Ahmed, Shahabuddin; Alam, Nurul; Shackelford, Katya A; Woldeab, Alexander; Lim, Stephen S; Levine, Aubrey; Gakidou, Emmanuela; Uddin, Md Jasim

    2018-01-25

    Service readiness of health facilities is an integral part of providing comprehensive quality healthcare to the community. Comprehensive assessment of general and service-specific (i.e. child immunization) readiness will help to identify the bottlenecks in healthcare service delivery and gaps in equitable service provision. Assessing healthcare facilities readiness also helps in optimal policymaking and resource allocation. A health facility survey was conducted between March 2015 and December 2015 in two purposively selected divisions in Bangladesh; i.e. Rajshahi division (high performing) and Sylhet division (low performing). A total of 123 health facilities were randomly selected from different levels of service, both public and private, with variation in sizes and patient loads from the list of facilities. Data on various aspects of healthcare facility were collected by interviewing key personnel. General service and child immunization specific service readiness were assessed using the Service Availability and Readiness Assessment (SARA) manual developed by World Health Organization (WHO). The analyses were stratified by division and level of healthcare facilities. The general service readiness index for pharmacies, community clinics, primary care facilities and higher care facilities were 40.6%, 60.5%, 59.8% and 69.5%, respectively in Rajshahi division and 44.3%, 57.8%, 57.5% and 73.4%, respectively in Sylhet division. Facilities at all levels had the highest scores for basic equipment (ranged between 51.7% and 93.7%) and the lowest scores for diagnostic capacity (ranged between 0.0% and 53.7%). Though facilities with vaccine storage capacity had very high levels of service readiness for child immunization, facilities without vaccine storage capacity lacked availability of many tracer items. Regarding readiness for newly introduced pneumococcal conjugate vaccine (PCV) and inactivated polio vaccine (IPV), most of the surveyed facilities reported lack of

  2. Structuring the Environmental Experience Design Research Framework through Selected Aged Care Facility Data Analyses in Victoria

    Directory of Open Access Journals (Sweden)

    Nan Ma

    2017-11-01

    Full Text Available Humans relate to the living environment physically and psychologically. Environmental psychology has a rich developed history while experience design emerged recently in the industrial design domain. Nonetheless, these approaches have barely been merged, understood or implemented in architectural design practices. This study explored the correlation between experience design and environmental psychology. Moreover, it conducted literature reviews on theories about emotion, user experience design, experience design and environmental psychology, followed by the analyses of spatial settings and environmental quality data of a selected aged care facility in Victoria, Australia, as a case study. Accordingly, this study led to proposing a research framework on environmental experience design (EXD. It can be defined as a deliberate attempt that affiliates experience design and environmental psychology with creation of the built environment that should accommodate user needs and demands. The EXD research framework proposed in this study was tailored for transforming related design functions into the solutions that contribute to improving the built environment for user health and wellbeing.

  3. Facile synthesis of surface-functionalized magnetic nanocomposites for effectively selective adsorption of cationic dyes

    Science.gov (United States)

    Hua, Yani; Xiao, Juan; Zhang, Qinqin; Cui, Chang; Wang, Chuan

    2018-04-01

    A new magnetic nano-adsorbent, polycatechol modified Fe3O4 magnetic nanoparticles (Fe3O4/PCC MNPs) were prepared by a facile chemical coprecipitation method using iron salts and catechol solution as precursors. Fe3O4/PCC MNPs owned negatively charged surface with oxygen-containing groups and showed a strong adsorption capacity and fast adsorption rates for the removal of cationic dyes in water. The adsorption capacity of methylene blue (MB), cationic turquoise blue GB (GB), malachite green (MG), crystal violet (CV) and cationic pink FG (FG) were 60.06 mg g- 1, 70.97 mg g- 1, 66.84 mg g- 1, 66.01 mg g- 1 and 50.27 mg g- 1, respectively. The adsorption mechanism was proposed by the analyses of the adsorption isotherms and adsorption kinetics of cationic dyes on Fe3O4/PCC MNPs. Moreover, the cationic dyes adsorbed on the MNPs as a function of contact time, pH value, temperature, coexisting cationic ions and ion strength were also investigated. These results suggested that the Fe3O4/PCC MNPs is promising to be used as a magnetic adsorbent for selective adsorption of cationic dyes in wastewater treatment.

  4. Application of GIS in site selection for nuclear waste disposal facility

    International Nuclear Information System (INIS)

    Sheng, G.; Luginaah, I.N.; Sorrell, J.

    1996-01-01

    Whether designing a new facility or investigating, potential contaminant migration at an existing site, proper characterization of the subsurface conditions and their interaction with surface features is critical to the process. The Atomic Energy Control Board, states in its regulatory document R-104 that, open-quotes For the long-term management of radioactive wastes, the preferred approach is disposal, a permanent method of management in which there is no intention of retrieval and which, ideally uses techniques and designs that do not rely for their success on long-term institutional control beyond a reasonable period of timeclose quotes. Thus although storage is safe, eventually disposal is necessary to avoid long-term reliance on continuing care and attention, such as monitoring and maintenance. In Canada, the concept being proposed by Atomic Energy of Canada Limited (AECL) involves disposal in deep underground repositories in intrusive igneous rock. The aim of this concept as a disposal method is to build multiple barriers that would protect humans and the natural environment from contaminants in the radioactive waste. The multiple barriers include the geosphere, which consists of the rock, any sediments overlying the rock, and the groundwater. Nevertheless, immediate, as well as long-term, consequences, including, risk involved with technological systems and the inherent uncertainty of any forecast, make the prediction and analysis tasks of increasing importance. This uncertainty in the area of nuclear waste disposal is leading to growing concerns about nuclear waste site selection

  5. Seroprevalence of yellow fever virus in selected health facilities in Western Kenya from 2010 to 2012.

    Science.gov (United States)

    Kwallah, Allan ole; Inoue, Shingo; Thairu-Muigai, Anne Wangari; Kuttoh, Nancy; Morita, Kouichi; Mwau, Matilu

    2015-01-01

    Yellow fever (YF), which is caused by a mosquito-borne virus, is an important viral hemorrhagic fever endemic in equatorial Africa and South America. Yellow fever virus (YFV) is the prototype of the family Flaviviridae and genus Flavivirus. The aim of this study was to determine the seroprevalence of YFV in selected health facilities in Western Kenya during the period 2010-2012. A total of 469 serum samples from febrile patients were tested for YFV antibodies using in-house IgM-capture ELISA, in-house indirect IgG ELISA, and 50% focus reduction neutralization test (FRNT50). The present study did not identify any IgM ELISA-positive cases, indicating absence of recent YFV infection in the area. Twenty-eight samples (6%) tested positive for YFV IgG, because of either YFV vaccination or past exposure to various flaviviruses including YFV. Five cases were confirmed by FRNT50; of these, 4 were either vaccination or natural infection during the YF outbreak in 1992-1993 or another period and 1 case was confirmed as a West Nile virus infection. Domestication and routine performance of arboviral differential diagnosis will help to address the phenomenon of pyrexia of unknown origin, contribute to arboviral research in developing countries, and enhance regular surveillance.

  6. Awareness regarding risk factors, symptoms and treatment facilities for cancer in selected states of India.

    Science.gov (United States)

    Raj, Sherin; Piang, Lam Khan; Nair, K S; Tiwari, V K; Kaur, H; Singh, Bacchu

    2012-01-01

    To study the level of awareness and knowledge about cancers and associated risk factors among households in selected states of India. In the study 3070 households were interviewed from six states viz, West Bengal, Kerala, Madhya Pradesh, Rajasthan and Mizoram. Knowledge of cancers other than those related to tobacco was very low (prostate 8%, colon 11% ) among the communities, with a poor awareness of warning signs and symptoms. The knowledge varied from state to state. It is found that the major source of information related to cancers was television (38%) followed by friends and relatives (36%). Only about 15 % of respondents had knowledge about cancer awareness camps organized in their districts but they did not have knowledge about the organizers of the camp. Findings suggested a strong need for strengthening of DCCP. It is important to create awareness among community through educational programs on cancer prevention, preventable cancer risk factors, benefits of early diagnosis, and availability of screening facilities. Integration of District Cancer Control activities with NRHM could be the most cost-effective strategy to prevent cancers and rural population.

  7. Selection of facility location under environmental damage priority and using ELECTRE method.

    Science.gov (United States)

    Gundogdu, Ceren Erdin

    2011-03-01

    In the recent years, the environmental problems have reached to a vital extent, which is pushing the boundaries and far beyond daily evaluations. Industrial plants, the energy sources and uncontrolled release of pollutant gases (SO2, CO2 etc.) in the production stage have the greatest share in the occurrence of unfavorable environmental conditions. For this reason, the dimension of the problems that may arise in the production stage of industrial plants is directly related to the selection of facility location. In this study, geographical regions (a total of 7 regions) of our country have been analyzed in terms of environmental values based on their basins and the unfavorable environmental problems that are currently being experienced. Considered as such, with the directives of an expert group composed of nature scientists, the criteria and alternative areas are determined using the data gathered on ecosystem, basin characteristics, and land types. Since the primary goal is to keep the environmental damages at the minimum level, comprehensive definition of the problem is constructed by consultation of the expert group and the criteria are determined. Considering the fact that it will prevent the drawbacks generated by making decisions depending on certain stereotypes toa great extent, ELECTRE (Elimination and Choice Translating Reality English - Elimination Et Choix Traduisant la Realite) method is used to determine in which geographic region our country's industrial plants should be located.

  8. Maternal and newborn morbidity by birth facility among selected United States 2006 low-risk births.

    Science.gov (United States)

    Wax, Joseph R; Pinette, Michael G; Cartin, Angelina; Blackstone, Jacquelyn

    2010-02-01

    We sought to evaluate perinatal morbidity by delivery location (hospital, freestanding birth center, and home). Selected 2006 US birth certificate data were accessed online from the Centers for Disease Control and Prevention. Low-risk maternal and newborn outcomes were tabulated and compared by birth facility. A total of 745,690 deliveries were included, of which 733,143 (97.0%) occurred in hospital, 4661 (0.6%) at birth centers, and 7427 (0.9%) at home. Compared with hospital deliveries, home and birthing center deliveries were associated with more frequent prolonged and precipitous labors. Home births experienced more frequent 5-minute Apgar scores home and birthing center deliveries were associated with less frequent chorioamnionitis, fetal intolerance of labor, meconium staining, assisted ventilation, neonatal intensive care unit admission, and birthweight Home births are associated with a number of less frequent adverse perinatal outcomes at the expense of more frequent abnormal labors and low 5-minute Apgar scores. Copyright 2010 Mosby, Inc. All rights reserved.

  9. Summary of selected health statistics for counties with nuclear facilities, New York State excluding New York City, 1960--1975

    International Nuclear Information System (INIS)

    Burometto, E.; Therriault, G.; Logrillo, V.

    1977-08-01

    A previous report of the Office of Biostatistics of the New York State Department of Health, issued in 1971, summarized selected health statistics for the period 1960 through 1969, comparing counties in Upstate New York (New York State exclusive of New York City) in which nuclear facilities are located with counties without such facilities. This report will present comparisons extending the analysis of the previous study through 1975. At various times during the period from 1960 to 1975 nuclear facilities were operating in 12 of the 57 Upstate counties. Westchester, Wayne and Oswego counties are the sites for the three commercial power plants operating in Upstate New York. A nuclear fuel reprocessing plant is located in Cattaraugus County. Facilities with testing, training or research reactors are located in eight other Upstate counties

  10. A Java-based tool for the design of classification microarrays.

    Science.gov (United States)

    Meng, Da; Broschat, Shira L; Call, Douglas R

    2008-08-04

    Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays-and mixed-plasmid microarrays in particular-it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm), several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text), and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff). Weights generated using stepwise discriminant analysis can be stored for

  11. Emerging use of gene expression microarrays in plant physiology.

    Science.gov (United States)

    Wullschleger, Stan D; Difazio, Stephen P

    2003-01-01

    Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

  12. Emerging Use of Gene Expression Microarrays in Plant Physiology

    Directory of Open Access Journals (Sweden)

    Stephen P. Difazio

    2006-04-01

    Full Text Available Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

  13. Advanced spot quality analysis in two-colour microarray experiments

    Directory of Open Access Journals (Sweden)

    Vetter Guillaume

    2008-09-01

    Full Text Available Abstract Background Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information. Findings We evaluated the performance of two image analysis packages MAIA and GenePix (GP using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5% than GP with default spot filtering conditions. Conclusion Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions.

  14. 38 CFR 21.294 - Selecting the training or rehabilitation facility.

    Science.gov (United States)

    2010-07-01

    ... AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Vocational Rehabilitation and Employment Under... the veteran's preference for a particular training or rehabilitation facility but VA has final...

  15. Design of a covalently bonded glycosphingolipid microarray

    DEFF Research Database (Denmark)

    Arigi, Emma; Blixt, Klas Ola; Buschard, Karsten

    2012-01-01

    , the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release...... of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2...

  16. Facile hyphenation of gas chromatography and a microcantilever array sensor for enhanced selectivity.

    Science.gov (United States)

    Chapman, Peter J; Vogt, Frank; Dutta, Pampa; Datskos, Panos G; Devault, Gerald L; Sepaniak, Michael J

    2007-01-01

    The very simple coupling of a standard, packed-column gas chromatograph with a microcantilever array (MCA) is demonstrated for enhanced selectivity and potential analyte identification in the analysis of volatile organic compounds (VOCs). The cantilevers in MCAs are differentially coated on one side with responsive phases (RPs) and produce bending responses of the cantilevers due to analyte-induced surface stresses. Generally, individual components are difficult to elucidate when introduced to MCA systems as mixtures, although pattern recognition techniques are helpful in identifying single components, binary mixtures, or composite responses of distinct mixtures (e.g., fragrances). In the present work, simple test VOC mixtures composed of acetone, ethanol, and trichloroethylene (TCE) in pentane and methanol and acetonitrile in pentane are first separated using a standard gas chromatograph and then introduced into a MCA flow cell. Significant amounts of response diversity to the analytes in the mixtures are demonstrated across the RP-coated cantilevers of the array. Principal component analysis is used to demonstrate that only three components of a four-component VOC mixture could be identified without mixture separation. Calibration studies are performed, demonstrating a good linear response over 2 orders of magnitude for each component in the primary study mixture. Studies of operational parameters including column temperature, column flow rate, and array cell temperature are conducted. Reproducibility studies of VOC peak areas and peak heights are also carried out showing RSDs of less than 4 and 3%, respectively, for intra-assay studies. Of practical significance is the facile manner by which the hyphenation of a mature separation technique and the burgeoning sensing approach is accomplished, and the potential to use pattern recognition techniques with MCAs as a new type of detector for chromatography with analyte-identifying capabilities.

  17. Classification across gene expression microarray studies

    Directory of Open Access Journals (Sweden)

    Kuner Ruprecht

    2009-12-01

    Full Text Available Abstract Background The increasing number of gene expression microarray studies represents an important resource in biomedical research. As a result, gene expression based diagnosis has entered clinical practice for patient stratification in breast cancer. However, the integration and combined analysis of microarray studies remains still a challenge. We assessed the potential benefit of data integration on the classification accuracy and systematically evaluated the generalization performance of selected methods on four breast cancer studies comprising almost 1000 independent samples. To this end, we introduced an evaluation framework which aims to establish good statistical practice and a graphical way to monitor differences. The classification goal was to correctly predict estrogen receptor status (negative/positive and histological grade (low/high of each tumor sample in an independent study which was not used for the training. For the classification we chose support vector machines (SVM, predictive analysis of microarrays (PAM, random forest (RF and k-top scoring pairs (kTSP. Guided by considerations relevant for classification across studies we developed a generalization of kTSP which we evaluated in addition. Our derived version (DV aims to improve the robustness of the intrinsic invariance of kTSP with respect to technologies and preprocessing. Results For each individual study the generalization error was benchmarked via complete cross-validation and was found to be similar for all classification methods. The misclassification rates were substantially higher in classification across studies, when each single study was used as an independent test set while all remaining studies were combined for the training of the classifier. However, with increasing number of independent microarray studies used in the training, the overall classification performance improved. DV performed better than the average and showed slightly less variance. In

  18. APPLICATION OF CDNA MICROARRAY TECHNOLOGY TO IN VITRO TOXICOLOGY AND THE SELECTION OF GENES FOR A REAL TIME RT-PCR-BASED SCREEN FOR OXIDATIVE STRESS IN HEP-G2 CELLS

    Science.gov (United States)

    Large-scale analysis of gene expression using cDNA microarrays promises therapid detection of the mode of toxicity for drugs and other chemicals. cDNAmicroarrays were used to examine chemically-induced alterations of geneexpression in HepG2 cells exposed to oxidative ...

  19. Life-Cycle Assessments of Selected NASA Ground-Based Test Facilities

    Science.gov (United States)

    Sydnor, George Honeycutt

    2012-01-01

    In the past two years, two separate facility-specific life cycle assessments (LCAs) have been performed as summer student projects. The first project focused on 13 facilities managed by NASA s Aeronautics Test Program (ATP), an organization responsible for large, high-energy ground test facilities that accomplish the nation s most advanced aerospace research. A facility inventory was created for each facility, and the operational-phase carbon footprint and environmental impact were calculated. The largest impacts stemmed from electricity and natural gas used directly at the facility and to generate support processes such as compressed air and steam. However, in specialized facilities that use unique inputs like R-134a, R-14, jet fuels, or nitrogen gas, these sometimes had a considerable effect on the facility s overall environmental impact. The second LCA project was conducted on the NASA Ames Arc Jet Complex and also involved creating a facility inventory and calculating the carbon footprint and environmental impact. In addition, operational alternatives were analyzed for their effectiveness at reducing impact. Overall, the Arc Jet Complex impact is dominated by the natural-gas fired boiler producing steam on-site, but alternatives were provided that could reduce the impact of the boiler operation, some of which are already being implemented. The data and results provided by these LCA projects are beneficial to both the individual facilities and NASA as a whole; the results have already been used in a proposal to reduce carbon footprint at Ames Research Center. To help future life cycle projects, several lessons learned have been recommended as simple and effective infrastructure improvements to NASA, including better utility metering and data recording and standardization of modeling choices and methods. These studies also increased sensitivity to and appreciation for quantifying the impact of NASA s activities.

  20. Polyadenylation state microarray (PASTA) analysis.

    Science.gov (United States)

    Beilharz, Traude H; Preiss, Thomas

    2011-01-01

    Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly(A) tail length control in a transcriptome, we developed the polyadenylation state microarray (PASTA) method. It involves the purification of mRNA based on poly(A) tail length using thermal elution from poly(U) sepharose, followed by microarray analysis of the resulting fractions. In this chapter we detail our PASTA approach and describe some methods for bulk and mRNA-specific poly(A) tail length measurements of use to monitor the procedure and independently verify the microarray data.

  1. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 13: Part 2, Indexes

    Energy Technology Data Exchange (ETDEWEB)

    Goins, L.F.; Webb, J.R.; Cravens, C.D.; Mallory, P.K.

    1992-09-01

    This is part 2 of a bibliography on nuclear facility decommissioning and site remedial action. This report contains indexes on the following: authors, corporate affiliation, title words, publication description, geographic location, subject category, and key word.

  2. 76 FR 55886 - Selection Criteria-Transportation Infrastructure Improvements Associated With Medical Facilities...

    Science.gov (United States)

    2011-09-09

    ... applicants for funding from the Office of Economic Adjustment (OEA) for construction of Transportation... be passed through another Federal agency for implementation. Response: For direct OEA construction... accident (negative factor) of an existing or proposed transportation facility. Response: The commenter...

  3. A successful case site selection for low-and intermediate-level radioactive waste disposal facility

    International Nuclear Information System (INIS)

    Lee, Bongwoo

    2007-01-01

    Korea decided on Gyeongju-si as the site of low-and intermediate-level radioactive waste disposal facility by referendum in November, 2005. Five success factors are considered; 1) the mayor and municipal assembly leaded the public opinion of inhabitants, 2) an invitation group was formed by citizen, social and religious group, 3) Gyeongju-si has operated the nuclear power plant since 20 years ago, and this radioactive waste disposal facility brings large financial support, 4) many kinds of public information means were used for invitation agreement and 5) the preconception, a nuclear facility is danger, was removed by visiting citizen, social group and local inhabitants at the nuclear power plant facility. Promotion process of the project, invitation process of Gyeongju-si and success factors, construction of an invitation promotion group and development of public information activities, publicity of financial effects and safety of radioactive waste disposal facility, increase of general acceptance among inhabitants by many kinds of public information means, and P.R. of safety of nuclear power plant facility by visiting leadership layers are reported. (S.Y.)

  4. The benefits of Outsourcing facility services when selecting right service provider for a hotel:Case Kämp Group Oy

    OpenAIRE

    Paudyal, Manoj; Acharya, Saroj

    2015-01-01

    This research paper examines about the outsourcing of facility services in the Kämp group of hotels. The scope of the study includes Facility Management, outsourcing facilities services, and the selection process of the service providers for a hotel. The research was carried at the hotels of Kämp group Oy in the Metropolitan Area of Helsinki. Facility management includes wide ranges of non-core functions such as Property management, real estates, design and technology. Activities such as secu...

  5. Occupational dose reduction at Department of Energy contractor facilities: Bibliography of selected readings in radiation protection and ALARA

    International Nuclear Information System (INIS)

    Dionne, B.J.; Lane, S.G.; Baum, J.W.

    1991-11-01

    Promoting the exchange of information related to implementation of the As Low as Reasonably Achievable (ALARA) philosophy is a continuing objective for the Department of Energy (DOE). This report, prepared by the Brookhaven National Laboratory (BNL) ALARA Center for the DOE Office of Health, contains the third in a series of bibliographies on dose reduction at DOE facilities. This report also contains abstracts from the two previous volumes. The BNL ALARA Center was originally established in 1983 under the sponsorship of the Nuclear Regulatory Commission to monitor dose-reduction research and ALARA activities at nuclear power plants. This effort was expanded in 1988 by the DOE's Office of Environment, Safety and Health to include DOE nuclear facilities. This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose-reduction activities, with a specific focus on DOE facilities. Abstracts included in this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy Data Base, and reprints of published articles provided by the authors. Facility types and activities covered in the scope of this report include: radioactive waste, uranium enrichment, fuel fabrication, storage, and reprocessing, facility decommissioning, hot laboratories, tritium production, research, test and production reactors, weapons fabrication and testing, and accelerators. Material on improved shielding design, decontamination, containments, robotics, job planning, improved operational techniques, and other topics are also included

  6. Emergency preparedness hazards assessment for selected 100 Area Bechtel Hanford, Inc. facilities

    International Nuclear Information System (INIS)

    1997-07-01

    The emergency preparedness hazards assessment for Bechtel Hanford Inc. (BHI) facilities in the 100 Areas of the Hanford Site. The purpose of a hazards assessment is to identify the hazardous material at each facility, identify the conditions that could release the hazardous material, and calculate the consequences of the releases. The hazards assessment is the technical basis for the facility emergency plans and procedures. There are many other buildings and past- practice burial grounds, trenches, cribs, etc., in the 100 Areas that may contain hazardous materials. Undisturbed buried waste sites that are not near the Columbia River are outside the scope of emergency preparedness hazards assessments because there is no mechanism for acute release to the air or ground water. The sites near the Columbia River are considered in a separate flood hazards assessment. This hazards assessment includes only the near-term soil remediation projects that involve intrusive activities

  7. Direct calibration of PICKY-designed microarrays

    Directory of Open Access Journals (Sweden)

    Ronald Pamela C

    2009-10-01

    Full Text Available Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

  8. Current Knowledge on Microarray Technology - An Overview

    African Journals Online (AJOL)

    Erah

    This paper reviews basics and updates of each microarray technology and serves to .... through protein microarrays. Protein microarrays also known as protein chips are nothing but grids that ... conditioned media, patient sera, plasma and urine. Clontech ... based antibody arrays) is similar to membrane-based antibody ...

  9. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.

    2005-01-01

    DNA microarrays have changed the field of biomedical sciences over the past 10 years. For several reasons, antibody and other protein microarrays have not developed at the same rate. However, protein and antibody arrays have emerged as a powerful tool to complement DNA microarrays during the post...

  10. ALARA engineering at Department of Energy facilities: Bibliography of selected readings in radiation protection and ALARA

    International Nuclear Information System (INIS)

    Dionne, B.J.; Khan, T.A.; Lane, S.G.; Baum, J.W.

    1991-05-01

    Promoting the exchange of information related to implementation of the As Low As Reasonably Achievable (ALARA) philosophy is a continuing objective for the Department of Energy (DOE). This report, prepared by the Brookhaven National Laboratory (BNL) ALARA Center for the DOE Office of Health, is the second in a series of bibliographies on dose reduction at DOE facilities. This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose reduction activities, with a specific focus towards DOE facilities. Facility types and activities covered in the scope of this report include: radioactive waste; uranium enrichment; fuel fabrication, storage, and reprocessing; facility decommissioning; hot laboratories; tritium production; research, test and production reactors; weapons fabrication and testing; and accelerators. Material on improved shielding design, decontamination, containments, robotics, job planning, improved operational techniques, and other topics has also been included. This volume (Volume 2 of the series) contains 127 abstracts numbered from 69 through 195, as well as author and subject indices. The subject index contains the abstract numbers from both the previous volume and the current volume, the latter being indicated in boldface. Information that the reader feels should be included in the next volume of this bibliography should be submitted to the BNL ALARA Center

  11. Production facility site selection factors for Texas value-added wood producers

    Science.gov (United States)

    Judd H. Michael; Joanna Teitel; James E. Granskog

    1998-01-01

    Value-added wood products manufacturers serve an important role in the economies of many U.S. regions and are therefore sought after by entities such as economic development agencies. The reasons why certain locations for a prospective prodution facility would be more attractive to secondary wood industry producers are not clearly understood. Therefore, this research...

  12. How to Investigate Drug Use in Health Facilities. Selected Drug Use ...

    African Journals Online (AJOL)

    This short WHO manual outlines methods for evaluating drug use indicators in health facilities. The broad areas of ... Washington: American Psychiatric Press, Inc. 1991. ISBN 0-88048-114-5. This book is ... discussion of different symptom categories using the DSM. (Diagnostic Statistical Manual) as a base. The definition of.

  13. Nuclear facility decommissioning and site remedial actions: A selected bibliography: Volume 7

    International Nuclear Information System (INIS)

    Owen, P.T.; Michelson, D.C.; Knox, N.P.; Fowler, J.W.

    1986-09-01

    The 644 abstracted references on nuclear facility decommissioning, uranium mill tailings management, and site remedial actions constitute the seventh in a series of reports prepared annually for the US Department of Energy's Remedial Action Programs. Foreign and domestic literature of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - has been included. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's remedial action program. Major chapters are (1) Surplus Facilities Management Program, (2) Nuclear Facilities Decommissioning, (3) Formerly Utilized Sites Remedial Action Program, (4) Facilities Contaminated with Naturally Occurring Radionuclides, (5) Uranium Mill Tailings Remedial Action Program, (6) Grand Junction Remedial Action Program, (7) Uranium Mill Tailings Management, (8) Technical Measurements Center, and (9) General Remedial Action Program Studies. Chapter sections for chapters 1, 2, 5, and 7 include Design, Planning, and Regulations; Environmental Studies and Site Surveys; Health, Safety, and Biomedical Studies; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. References are arranged alphabetically by leading author. Those references having no individual author are listed by corporate affiliation or by publication description. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, and keywords. The appendix contains a list of frequently used acronyms and abbreviations

  14. Nuclear Facilities Decommissioning and site remedial actions: a selected bibliography. Vol. 2

    International Nuclear Information System (INIS)

    Owen, P.T.; Fielden, J.M.; Knox, N.P.; Trotter, ES.

    1981-10-01

    This bibliography of 643 references represents the second in a series on nuclear facility decommissioning and site remedial actions to be produced by the Radiation Effects Information Center (REIC) within the Information Center Complex, Information Division, Oak Ridge National Laboratory. The bibliography contains scientific, technical, economic, and regulatory information pertaining to the US Department of Energy's Remedial Action Program. Major chapters are: Surplus Facilities Management Program; Nuclear Facilities Decommissioning; Formerly Utilized Sites Remedial Action Program; and Uranium Mill Tailings Management. The references within each chapter are arranged alphabetically by leading author. References having no individual author are arranged by corporate affiliation or by title. Indexes are provided for: (1) author; (2) corporate affiliation; (3) title; (4) publication description; (5) geographic location; and (6) keywords. The bibliography was compiled from a specialized data base established and maintained by REIC to provide information support for the US Department of Energy's Remedial Action Program, under the cosponsorship of its four major components: Surplus Facilities Management Program; Formerly Utilized Sites Remedial Action Program; Uranium Mill Tailings Remedial Action Program; and the Grand Junction Remedial Action Program

  15. Nuclear facility decommissioning and site remedial actions. Volume 6. A selected bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Owen, P.T.; Michelson, D.C.; Knox, N.P.

    1985-09-01

    This bibliography of 683 references with abstracts on the subject of nuclear facility decommissioning, uranium mill tailings management, and site remedial actions is the sixth in a series of annual reports prepared for the US Department of Energy's Remedial Action Programs. Foreign as well as domestic literature of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - has been included. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's remedial action program. Major chapters are: (1) Surplus Facilities Management Program; (2) Nuclear Facilities Decommissioning; (3) Formerly Utilized Sites Remedial Action Program; (4) Facilities Contaminated with Natural Radioactivity; (5) Uranium Mill Tailings Remedial Action Program; (6) Grand Junction Remedial Action Program; (7) Uranium Mill Tailings Management; (8) Technical Measurements Center; and (9) General Remedial Action Program Studies. Chapter sections for chapters 1, 2, 5, and 7 include Design, Planning, and Regulations; Environmental Studies and Site Surveys; Health, Safety, and Biomedical Studies; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. The references within each chapter or section are arranged alphabetically by leading author. References having no individual author are arranged by corporate affiliation or by publication description.

  16. Nuclear facility decommissioning and site remedial actions: A selected bibliography: Volume 8

    Energy Technology Data Exchange (ETDEWEB)

    Owen, P.T.; Michelson, D.C.; Knox, N.P.

    1987-09-01

    The 553 abstracted references on nuclear facility decommissioning, uranium mill tailings management, and site remedial actions constitute the eighth in a series of reports. Foreign and domestic literature of all types - technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions - has been included. The bibliography contains scientific, technical, economic, regulatory, and legal information pertinent to the US Department of energy's remedial action program. Major chapters are Surplus Facilities Management Program, Nuclear Facilities Decommissioning, Formerly Utilized Sites Remedial Action Program, Facilities Contaminated with Naturally Occurring Radionuclides, Uranium Mill Tailings Remedial Action Program, Uranium Mill Tailings Management, Technical Measurements Center, and General Remedial Action Program Studies. Chapter sections for chapters 1, 2, 5, and 6 include Design, Planning, and Regulations; Environmental Studies and Site Surveys; Health, Safety, and Biomedical Studies; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. Within these categories, references are arranged alphabetically by first author. Those references having no individual author are listed by corporate affiliation or by publication description. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, and keywords. The appendix contains a list of frequently used acronyms and abbreviations.

  17. Nuclear facility decommissioning and site remedial actions. Volume 6. A selected bibliography

    International Nuclear Information System (INIS)

    Owen, P.T.; Michelson, D.C.; Knox, N.P.

    1985-09-01

    This bibliography of 683 references with abstracts on the subject of nuclear facility decommissioning, uranium mill tailings management, and site remedial actions is the sixth in a series of annual reports prepared for the US Department of Energy's Remedial Action Programs. Foreign as well as domestic literature of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - has been included. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's remedial action program. Major chapters are: (1) Surplus Facilities Management Program; (2) Nuclear Facilities Decommissioning; (3) Formerly Utilized Sites Remedial Action Program; (4) Facilities Contaminated with Natural Radioactivity; (5) Uranium Mill Tailings Remedial Action Program; (6) Grand Junction Remedial Action Program; (7) Uranium Mill Tailings Management; (8) Technical Measurements Center; and (9) General Remedial Action Program Studies. Chapter sections for chapters 1, 2, 5, and 7 include Design, Planning, and Regulations; Environmental Studies and Site Surveys; Health, Safety, and Biomedical Studies; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. The references within each chapter or section are arranged alphabetically by leading author. References having no individual author are arranged by corporate affiliation or by publication description

  18. Nuclear facility decommissioning and site remedial actions: A selected bibliography: Volume 8

    International Nuclear Information System (INIS)

    Owen, P.T.; Michelson, D.C.; Knox, N.P.

    1987-09-01

    The 553 abstracted references on nuclear facility decommissioning, uranium mill tailings management, and site remedial actions constitute the eighth in a series of reports. Foreign and domestic literature of all types - technical reports, progress reports, journal articles, symposia proceedings, theses, books, patents, legislation, and research project descriptions - has been included. The bibliography contains scientific, technical, economic, regulatory, and legal information pertinent to the US Department of energy's remedial action program. Major chapters are Surplus Facilities Management Program, Nuclear Facilities Decommissioning, Formerly Utilized Sites Remedial Action Program, Facilities Contaminated with Naturally Occurring Radionuclides, Uranium Mill Tailings Remedial Action Program, Uranium Mill Tailings Management, Technical Measurements Center, and General Remedial Action Program Studies. Chapter sections for chapters 1, 2, 5, and 6 include Design, Planning, and Regulations; Environmental Studies and Site Surveys; Health, Safety, and Biomedical Studies; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. Within these categories, references are arranged alphabetically by first author. Those references having no individual author are listed by corporate affiliation or by publication description. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, and keywords. The appendix contains a list of frequently used acronyms and abbreviations

  19. Selected publications related to the experimental facilities of the Advanced Photon Source, 1987--1991

    International Nuclear Information System (INIS)

    1992-01-01

    This report contain papers on work related to the experimental facilities of the Advanced Photon Source. The general topics of these papers are: insertion devices; front ends; high heat load x-ray optics; novel optics and techniques; and radiation safety, interlocks, and personnel safety

  20. Morbidity profile of elderly outpatients attending selected sub-district Siddha health facilities in Tamil Nadu, India

    Science.gov (United States)

    Selvaraj, Kalaiselvi; Srinivasan, Manikandan; Duraisamy, Venkatachalam; Ramaswamy, Gomathi; Venugopal, Vinayagamurthy; Chinnakali, Palanivel

    2016-01-01

    Background: Recently, under National Health Mission alternate systems of Medicine are mainstreamed in public health care system. Effective action plan generation, logistic arrangement and roll out of these alternate systems of Medicine needs understanding on profile of morbidities among attendees who come to these facilities. Objectives: This study was planned to report profile of morbidities, age and sex differentials in specific morbidities among geriatric attendees in secondary level siddha health facilities. Materials and Methods: A facility based cross sectional study was conducted among elderly person (60 years and above) attending Siddha outpatient department (OPD) from two of the randomly selected sub district level siddha facilities in Erode district, Tamil Nadu, India. Information on socio-demographic variables like age, gender, education and clinical profile (diagnosis) were collected from records already maintained in the siddha OPD. Morbidities were summarized in terms of proportions based on age and gender. Age and sex specific differentials on specific morbidities were compared using ‘z’ test. Results: Of 2710 patients who visited these two siddha facilities during the reference period, 763 (28.1%) patients were elderly. Arthritis (45.2%), neuritis (8.8%), diabetes (6.6%), bronchial asthma (5.2%), hemiplegia (3.7%) were the top five morbidities diagnosed and treated among elderly attending the siddha OPD. There was a predilection towards elderly male for morbidities such as bronchial asthma and hemiplegia compared to elderly female. Similarly, higher proportions of lumbar spondylosis, hypertension and fungal skin diseases were reported among aged 80 years or more compared to elderly aged 60-79 years. Conclusion: Elderly constitute more than one fourth of outpatients load from siddha health facilities. Degenerative diseases like arthritis and non-communicable diseases were the common morbidities in this age group. Geriatric clinics and mobile

  1. Comparing transformation methods for DNA microarray data

    Directory of Open Access Journals (Sweden)

    Zwinderman Aeilko H

    2004-06-01

    Full Text Available Abstract Background When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include subtraction of an estimated background signal, subtracting the reference signal, smoothing (to account for nonlinear measurement effects, and more. Different authors use different approaches, and it is generally not clear to users which method they should prefer. Results We used the ratio between biological variance and measurement variance (which is an F-like statistic as a quality measure for transformation methods, and we demonstrate a method for maximizing that variance ratio on real data. We explore a number of transformations issues, including Box-Cox transformation, baseline shift, partial subtraction of the log-reference signal and smoothing. It appears that the optimal choice of parameters for the transformation methods depends on the data. Further, the behavior of the variance ratio, under the null hypothesis of zero biological variance, appears to depend on the choice of parameters. Conclusions The use of replicates in microarray experiments is important. Adjustment for the null-hypothesis behavior of the variance ratio is critical to the selection of transformation method.

  2. Assessment of radiation dose due to fluoroscopic procedures in patients at some selected facilities in the Greater Accra Region, Ghana

    International Nuclear Information System (INIS)

    Gyasi, E.

    2013-07-01

    Radiation doses to 182 adults patients who underwent barium enema, barium meal, barium swallow, myelogram, hysterosalpingography and urethrogram examination collectively at facilities A and B were investigated. Radiation dose was measured using kerma-area-product (KAP) meter. From the KAP readings, patient's data and other relevant information from the control console, effective dose and selective organ doses were estimated using Monte Carlo program software (PCXMC version 1.5). Quality control tests performed on the two fluoroscopy machines were found to be within the acceptance criteria. Mean effective doses were found to be 8.45 ± 0.38mSv, 7.628 ± 0.42 mSv, 1.46 ± 0.13 mSv, 2.02 ± 0.16 mSv, 0.32 ± 0.03 mSv for barium enema, barium meal, barium swallow, myelogram and urethrogram examinations respectively at Facility A. At Facility B the mean effective dose were found to be 4.12 ± 0.15 mSv, 1.83 ± 0.10 mSv, 0.81 ± 0.04 mSv, 0.53 ± 0.036 mSv and 0.27 ± 0.01 mSv for barium enema, barium meal, barium swallow, myelogram, hysterosalpingography and urethrogram examination respectively. Thymus received the highest organ dose of 29.19± 2.07mGy during barium meal studies at Facility A of all the procedures in the two hospitals. Magnitude of organ doses was observed to to be in relation with the closeness to or in the direction of the primary beam of radiation. Organ and effective doses from Facility A were relatively higher than those from Facility B in comparison by a factor of a about 2 with the exception of the barium meal examination at Facility A which was by a factor of about 4. The measured KAP readings fro the two facilities were below the international accepted reference levels with the exception of barium meal examination at Facility A which recorded a higher value of 25.96 ± 1.83 Gy.cm 2 as compared to ICRP (2001) reference value of 25 Gy.cm 2 . Longer radiation beam on time, high number of radiographs taken per patient, wide exposure beam area on

  3. Influences on the start, selection and duration of treatment with antibiotics in long-term care facilities.

    Science.gov (United States)

    Daneman, Nick; Campitelli, Michael A; Giannakeas, Vasily; Morris, Andrew M; Bell, Chaim M; Maxwell, Colleen J; Jeffs, Lianne; Austin, Peter C; Bronskill, Susan E

    2017-06-26

    Understanding the extent to which current antibiotic prescribing behaviour is influenced by clinicians' historical patterns of practice will help target interventions to optimize antibiotic use in long-term care. Our objective was to evaluate whether clinicians' historical prescribing behaviours influence the start, prolongation and class selection for treatment with antibiotics in residents of long-term care facilities. We conducted a retrospective cohort study of all physicians who prescribed to residents in long-term care facilities in Ontario between Jan. 1 and Dec. 31, 2014. We examined variability in antibiotic prescribing among physicians for 3 measures: start of treatment with antibiotics, use of prolonged durations exceeding 7 days and selection of fluoroquinolones. Funnel plots with control limits were used to determine the extent of variation and characterize physicians as extreme low, low, average, high and extreme high prescribers for each tendency. Multivariable logistic regression was used to assess whether a clinician's prescribing tendency in the previous year predicted current prescribing patterns, after accounting for residents' demographics, comorbidity, functional status and indwelling devices. Among 1695 long-term care physicians, who prescribed for 93 132 residents, there was wide variability in the start of antibiotic treatment (median 45% of patients, interquartile range [IQR] 32%-55%), use of prolonged treatment durations (median 30% of antibiotic prescriptions, IQR 19%-46%) and selection of fluoroquinolones (median 27% of antibiotic prescriptions, IQR 18%-37%). Prescribing tendencies for antibiotics by physicians in 2014 correlated strongly with tendencies in the previous year. After controlling for individual resident characteristics, prior prescribing tendency was a significant predictor of current practice. Physicians prescribing antibiotics exhibited individual, measurable and historical tendencies toward start of antibiotic treatment

  4. Descriptions of selected accidents that have occurred at nuclear reactor facilities

    Energy Technology Data Exchange (ETDEWEB)

    Bertini, H.W.

    1980-04-01

    This report was prepared at the request of the President's Commission on the Accident at Three Mile Island to provide the members of the Commission with some insight into the nature and significance of accidents that have occurred at nuclear reactor facilities in the past. Toward that end, this report presents a brief description of 44 accidents which have occurred throughout the world and which meet at least one of the severity criteria that were established.

  5. Descriptions of selected accidents that have occurred at nuclear reactor facilities

    International Nuclear Information System (INIS)

    Bertini, H.W.

    1980-04-01

    This report was prepared at the request of the President's Commission on the Accident at Three Mile Island to provide the members of the Commission with some insight into the nature and significance of accidents that have occurred at nuclear reactor facilities in the past. Toward that end, this report presents a brief description of 44 accidents which have occurred throughout the world and which meet at least one of the severity criteria that were established

  6. Nuclear facility decommissioning and site remedial actions: a selected bibliography. Volume 5

    International Nuclear Information System (INIS)

    Owen, P.T.; Knox, N.P.; Chilton, B.D.; Baldauf, M.F.

    1984-09-01

    This bibliography of 756 references with abstracts on the subject of nuclear facility decommissioning, uranium mill tailings management, and site remedial actions is the fifth in a series of annual reports prepared for the US Department of Energy, Division of Remedial Action Projects. Foreign as well as domestic literature of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - has been included in this publication. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's Remedial Action Program. Major chapters are: (1) Surplus Facilities Management Program; (2) Nuclear Facilities Decommissioning; (3) Formerly Utilized Sites Remedial Action Program; (4) Uranium Mill Tailings Remedial Action Program; (5) Grand Junction Remedial Action Program; (6) Uranium Mill Tailings Management; and (7) Technical Measurements Center. Chapter sections for chapters 1, 2, 4, and 6 include Design, Planning, and Regulations; Environmental Studies and Site Surveys; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. The references within each chapter or section are arranged alphabetically by leading author. References having no individual author are arranged by corporate author or by title. Indexes are provided for the categories of author, corporate affiliation, title, publication description, geographic location, and keywords. The Appendix contains a list of frequently used acronyms

  7. Nuclear facility decommissioning and site remedial actions: a selected bibliography. Volume 5

    Energy Technology Data Exchange (ETDEWEB)

    Owen, P.T.; Knox, N.P.; Chilton, B.D.; Baldauf, M.F.

    1984-09-01

    This bibliography of 756 references with abstracts on the subject of nuclear facility decommissioning, uranium mill tailings management, and site remedial actions is the fifth in a series of annual reports prepared for the US Department of Energy, Division of Remedial Action Projects. Foreign as well as domestic literature of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - has been included in this publication. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's Remedial Action Program. Major chapters are: (1) Surplus Facilities Management Program; (2) Nuclear Facilities Decommissioning; (3) Formerly Utilized Sites Remedial Action Program; (4) Uranium Mill Tailings Remedial Action Program; (5) Grand Junction Remedial Action Program; (6) Uranium Mill Tailings Management; and (7) Technical Measurements Center. Chapter sections for chapters 1, 2, 4, and 6 include Design, Planning, and Regulations; Environmental Studies and Site Surveys; Decontamination Studies; Dismantlement and Demolition; Site Stabilization and Reclamation; Waste Disposal; Remedial Action Experience; and General Studies. The references within each chapter or section are arranged alphabetically by leading author. References having no individual author are arranged by corporate author or by title. Indexes are provided for the categories of author, corporate affiliation, title, publication description, geographic location, and keywords. The Appendix contains a list of frequently used acronyms.

  8. A multi-objective optimization approach for the selection of working fluids of geothermal facilities: Economic, environmental and social aspects.

    Science.gov (United States)

    Martínez-Gomez, Juan; Peña-Lamas, Javier; Martín, Mariano; Ponce-Ortega, José María

    2017-12-01

    The selection of the working fluid for Organic Rankine Cycles has traditionally been addressed from systematic heuristic methods, which perform a characterization and prior selection considering mainly one objective, thus avoiding a selection considering simultaneously the objectives related to sustainability and safety. The objective of this work is to propose a methodology for the optimal selection of the working fluid for Organic Rankine Cycles. The model is presented as a multi-objective approach, which simultaneously considers the economic, environmental and safety aspects. The economic objective function considers the profit obtained by selling the energy produced. Safety was evaluated in terms of individual risk for each of the components of the Organic Rankine Cycles and it was formulated as a function of the operating conditions and hazardous properties of each working fluid. The environmental function is based on carbon dioxide emissions, considering carbon dioxide mitigation, emission due to the use of cooling water as well emissions due material release. The methodology was applied to the case of geothermal facilities to select the optimal working fluid although it can be extended to waste heat recovery. The results show that the hydrocarbons represent better solutions, thus among a list of 24 working fluids, toluene is selected as the best fluid. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Occupational dose reduction at Department of Energy contractor facilities: Bibliography of selected readings in radiation protection and ALARA; Volume 5

    Energy Technology Data Exchange (ETDEWEB)

    Dionne, B.J.; Sullivan, S.G.; Baum, J.W. [Brookhaven National Lab., Upton, NY (United States)

    1994-01-01

    Promoting the exchange of information related to implementation of the As Low as Reasonably Achievable (ALARA) philosophy is a continuing objective for the Department of Energy (DOE). This report was prepared by the Brookhaven National Laboratory (BNL) ALARA Center for the DOE Office of Health. It contains the fifth in a series of bibliographies on dose reduction at DOE facilities. The BNL ALARA Center was originally established in 1983 under the sponsorship of the Nuclear Regulatory Commission to monitor dose-reduction research and ALARA activities at nuclear power plants. This effort was expanded in 1988 by the DOE`s Office of Environment, Safety and Health, to include DOE nuclear facilities. This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose-reduction activities, with a specific focus on DOE facilities. Abstracts included in this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy, Science and Technology Database (in general, the citation and abstract information is presented as obtained from this database), and reprints of published articles provided by the authors. Facility types and activities covered in the scope of this report include: radioactive waste, uranium enrichment, fuel fabrication, spent fuel storage and reprocessing, facility decommissioning, hot laboratories, tritium production, research, test and production reactors, weapons fabrication and testing, fusion, uranium and plutonium processing, radiography, and accelerators. Information on improved shielding design, decontamination, containments, robotics, source prevention and control, job planning, improved operational and design techniques, as well as on other topics, has been included. In addition, DOE/EH reports not included in previous volumes of the bibliography are in this volume (abstracts 611 to 684). This volume (Volume 5 of the series) contains 217 abstracts.

  10. Occupational dose reduction at Department of Energy contractor facilities: Bibliography of selected readings in radiation protection and ALARA; Volume 5

    International Nuclear Information System (INIS)

    Dionne, B.J.; Sullivan, S.G.; Baum, J.W.

    1994-01-01

    Promoting the exchange of information related to implementation of the As Low as Reasonably Achievable (ALARA) philosophy is a continuing objective for the Department of Energy (DOE). This report was prepared by the Brookhaven National Laboratory (BNL) ALARA Center for the DOE Office of Health. It contains the fifth in a series of bibliographies on dose reduction at DOE facilities. The BNL ALARA Center was originally established in 1983 under the sponsorship of the Nuclear Regulatory Commission to monitor dose-reduction research and ALARA activities at nuclear power plants. This effort was expanded in 1988 by the DOE's Office of Environment, Safety and Health, to include DOE nuclear facilities. This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose-reduction activities, with a specific focus on DOE facilities. Abstracts included in this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy, Science and Technology Database (in general, the citation and abstract information is presented as obtained from this database), and reprints of published articles provided by the authors. Facility types and activities covered in the scope of this report include: radioactive waste, uranium enrichment, fuel fabrication, spent fuel storage and reprocessing, facility decommissioning, hot laboratories, tritium production, research, test and production reactors, weapons fabrication and testing, fusion, uranium and plutonium processing, radiography, and accelerators. Information on improved shielding design, decontamination, containments, robotics, source prevention and control, job planning, improved operational and design techniques, as well as on other topics, has been included. In addition, DOE/EH reports not included in previous volumes of the bibliography are in this volume (abstracts 611 to 684). This volume (Volume 5 of the series) contains 217 abstracts

  11. AMDA: an R package for the automated microarray data analysis

    Directory of Open Access Journals (Sweden)

    Foti Maria

    2006-07-01

    Full Text Available Abstract Background Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and new experiments are constantly being performed. In spite of this fact, few and limited tools exist for quickly and easily analyzing the results. Microarray analysis can be challenging for researchers without the necessary training and it can be time-consuming for service providers with many users. Results To address these problems we have developed an automated microarray data analysis (AMDA software, which provides scientists with an easy and integrated system for the analysis of Affymetrix microarray experiments. AMDA is free and it is available as an R package. It is based on the Bioconductor project that provides a number of powerful bioinformatics and microarray analysis tools. This automated pipeline integrates different functions available in the R and Bioconductor projects with newly developed functions. AMDA covers all of the steps, performing a full data analysis, including image analysis, quality controls, normalization, selection of differentially expressed genes, clustering, correspondence analysis and functional evaluation. Finally a LaTEX document is dynamically generated depending on the performed analysis steps. The generated report contains comments and analysis results as well as the references to several files for a deeper investigation. Conclusion AMDA is freely available as an R package under the GPL license. The package as well as an example analysis report can be downloaded in the Services/Bioinformatics section of the Genopolis http://www.genopolis.it/

  12. Nuclear facility decommissioning and site remedial actions: a selected bibliography. Volume 4

    International Nuclear Information System (INIS)

    Owen, P.T.; Knox, N.P.; Fielden, J.M.; Faust, R.A.

    1983-09-01

    This bibliography of 657 references with abstracts on the subject of nuclear facility decommissioning, uranium mill tailings management, and site remedial actions is the fourth in a series of annual reports prepared for the US Department of Energy, Division of Remedial Action Projects. Foreign as well as domestic documents of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - have been references in this publication. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's Remedial Action Program. Major chapters are: (1) Surplus Facilities Management Program; (2) Nuclear Facilities Decommissioning; (3) Formerly Utilized Sites Remedial Action Program; (4) Uranium Mill Tailings Remedial Action Program; (5) Grand Junction Remedial Action Program; and (6) Uranium Mill Tailings Management. Chapter sections for chapters 1 and 2 include: Design, Planning, and Regulations; Site Surveys; Decontamination Studies; Dismantlement and Demolition; Land Decontamination and Reclamation; Waste Disposal; and General studies. The references within each chapter or section are arranged alphabetically by leading author. References having no individual author are arranged by corporate author, or by title. Indexes are provided for the categories of author, corporate affiliation, title, publication description, geographic location, and keywords. Appendix A lists 264 bibliographic references to literature identified during this reporting period but not abstracted due to time constraints. Title and publication description indexes are given for this appendix. Appendix B defines frequently used acronyms, and Appendix C lists the recipients of this report according to their corporate affiliation

  13. Nuclear facility decommissioning and site remedial actions: a selected bibliography. Volume 4

    Energy Technology Data Exchange (ETDEWEB)

    Owen, P.T.; Knox, N.P.; Fielden, J.M.; Faust, R.A.

    1983-09-01

    This bibliography of 657 references with abstracts on the subject of nuclear facility decommissioning, uranium mill tailings management, and site remedial actions is the fourth in a series of annual reports prepared for the US Department of Energy, Division of Remedial Action Projects. Foreign as well as domestic documents of all types - technical reports, progress reports, journal articles, conference papers, symposium proceedings, theses, books, patents, legislation, and research project descriptions - have been references in this publication. The bibliography contains scientific (basic research as well as applied technology), economic, regulatory, and legal literature pertinent to the US Department of Energy's Remedial Action Program. Major chapters are: (1) Surplus Facilities Management Program; (2) Nuclear Facilities Decommissioning; (3) Formerly Utilized Sites Remedial Action Program; (4) Uranium Mill Tailings Remedial Action Program; (5) Grand Junction Remedial Action Program; and (6) Uranium Mill Tailings Management. Chapter sections for chapters 1 and 2 include: Design, Planning, and Regulations; Site Surveys; Decontamination Studies; Dismantlement and Demolition; Land Decontamination and Reclamation; Waste Disposal; and General studies. The references within each chapter or section are arranged alphabetically by leading author. References having no individual author are arranged by corporate author, or by title. Indexes are provided for the categories of author, corporate affiliation, title, publication description, geographic location, and keywords. Appendix A lists 264 bibliographic references to literature identified during this reporting period but not abstracted due to time constraints. Title and publication description indexes are given for this appendix. Appendix B defines frequently used acronyms, and Appendix C lists the recipients of this report according to their corporate affiliation.

  14. 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

  15. Approaches of selecting options for upgrading of safety of near surface facilities

    International Nuclear Information System (INIS)

    Goldammer, W.

    2003-01-01

    General principle of optimization using cost-benefit analysis and multi-attribute utility analysis and considering the radiological and ecological risks are discussed. Alternative scenarios (unplanned events) are also considered. Comparison of options for interim storage facility is made in the example of Uranium mining. The conclusions from the example are: Quantitative optimisation necessary in order to arrive at conclusion (higher financial expenditures yield lower risks); Only inclusion of failure scenarios reveals that passive safety of wet option is not satisfactory; Probabilistic simulation allows for keeping track of uncertainties and assessing their consequences within the decision-making process; Optimisation analysis can be refined in the course of further reclamation planning to allow for questions on detailed design to be addressed. Pragmatic (non-quantitative) assessment cannot reveal how safe is safe enough. Different options for the waste storage in an interim storage facility are analysed. The methodology includes: Estimate of cost components; Discounting of long-term costs; Estimate of risks; Assessment of qualitative factors; Definition of weighting factors; Application of multi-attribute utility analysis; Deterministic sensitivity analysis for important parameters.The examples show the importance of the incorporation of qualitative factors, weighting of parameters and sensitivity analysis in the decision making

  16. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 13: Part 1, Main text

    Energy Technology Data Exchange (ETDEWEB)

    Goins, L.F.; Webb, J.R.; Cravens, C.D.; Mallory, P.K.

    1992-09-01

    This publication contains 1035 abstracted references on environmental restoration, nuclear facility decommissioning, uranium mill tailings management, and site remedial actions. These citations constitute the thirteenth in a series of reports prepared annually for the US Department of Energy (DOE) Environmental Restoration programs. Citations to foreign and domestic literature of all types. There are 13 major sections of the publication, including: (1) DOE Decontamination and Decommissioning Program; (2) Nuclear Facilities Decommissioning; (3) DOE Formerly Utilized Sites Remedial Action Program; (4) DOE Uranium Mill Tailings Remedial Action Project; (5) Uranium Mill Tailings Management; (6) DOE Environmental Restoration Program; (7) DOE Site-Specific Remedial Actions; (8) Contaminated Site Restoration; (9) Remediation of Contaminated Soil and Groundwater; (10) Environmental Data Measurements, Management, and Evaluation; (11) Remedial Action Assessment and Decision-Making; (12) Technology Development and Evaluation; and (13) Environmental and Waste Management Issues. Bibliographic references are arranged in nine subject categories by geographic location and then alphabetically by first author, corporate affiliation, or publication title. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, subject category, and key word.

  17. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 13: Part 1, Main text

    International Nuclear Information System (INIS)

    Goins, L.F.; Webb, J.R.; Cravens, C.D.; Mallory, P.K.

    1992-09-01

    This publication contains 1035 abstracted references on environmental restoration, nuclear facility decommissioning, uranium mill tailings management, and site remedial actions. These citations constitute the thirteenth in a series of reports prepared annually for the US Department of Energy (DOE) Environmental Restoration programs. Citations to foreign and domestic literature of all types. There are 13 major sections of the publication, including: (1) DOE Decontamination and Decommissioning Program; (2) Nuclear Facilities Decommissioning; (3) DOE Formerly Utilized Sites Remedial Action Program; (4) DOE Uranium Mill Tailings Remedial Action Project; (5) Uranium Mill Tailings Management; (6) DOE Environmental Restoration Program; (7) DOE Site-Specific Remedial Actions; (8) Contaminated Site Restoration; (9) Remediation of Contaminated Soil and Groundwater; (10) Environmental Data Measurements, Management, and Evaluation; (11) Remedial Action Assessment and Decision-Making; (12) Technology Development and Evaluation; and (13) Environmental and Waste Management Issues. Bibliographic references are arranged in nine subject categories by geographic location and then alphabetically by first author, corporate affiliation, or publication title. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, subject category, and key word

  18. Occupational dose reduction at Department of Energy contractor facilities: Bibliography of selected readings in radiation protection and ALARA

    Energy Technology Data Exchange (ETDEWEB)

    Dionne, B.J.; Sullivan, S.G.; Baum, J.W.

    1993-12-01

    This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose reduction activities, with a focus on DOE facilities. Abstracts included in this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy, Science and Technology Database (in general, the citation and abstract information is presented as obtained from this database), and reprints of published articles provided by the authors. Facility types and activities covered in the scope of this report include: radioactive waste, uranium enrichment, fuel fabrication, spent fuel storage and reprocessing, facility decommissioning, hot laboratories, tritium production, research, test and production reactors, weapons fabrication and testing, fusion, uranium and plutonium processing, radiography, and aocelerators. Information on improved shielding design, decontamination, containments, robotics, source prevention and control, job planning, improved operational and design techniques, as well as on other topics, has been included. In addition, DOE/EH reports not included in previous volumes of the bibliography are in this volume (abstracts 611 to 684). This volume (Volume 5 of the series) contains 217 abstracts. An author index and a subject index are provided to facilitate use. Both indices contain the abstract numbers from previous volumes, as well as the current volume. Information that the reader feels might be included in the next volume of this bibliography should be submitted to the BNL ALARA Center.

  19. Occupational dose reduction at Department of Energy contractor facilities: Bibliography of selected readings in radiation protection and ALARA

    International Nuclear Information System (INIS)

    Dionne, B.J.; Sullivan, S.G.; Baum, J.W.

    1993-03-01

    This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose-reduction activities, with a specific focus on DOE facilities. Abstracts included in this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy, Science and Technology Database (in general, the citation and abstract information is presented as obtained from this database), and reprints of published articles provided by the authors. Facility types and activities covered in the scope of this report include: radioactive waste, uranium enrichment, fuel fabrication, spent fuel storage and reprocessing, facility decommissioning, hot laboratories, tritium production, research, test and production reactors, weapons fabrication and testing, fusion, uranium and plutonium processing, radiography, and accelerators. Information on improved shielding design, decontamination, containments, robotics, source prevention and control, job planning, improved operational and design techniques, as well other topics, has been included. This volume (Volume 4 of the series) contains 209 abstracts. An author index and a subject index are provided to facilitate use. The subject index contains the abstract numbers from previous volumes, as well as the current volume

  20. Cryogenic implications of orbit selection of the Space Infrared Telescope Facility (SIRTF)

    International Nuclear Information System (INIS)

    Lee, J.H.; Brooke, W.F.; Maa, S.

    1986-01-01

    The Infrared Astronomical Satellite (IRAS) which completed the first all sky survey in the infrared demonstrated the tremendous advantage of space-based infrared astronomy. The ability to cool the telescope optics and focal plane to liquid helium temperatures and the absence of atmospheric disturbances which cause ''seeing'' effects resulted in the discovery of 250,000 IR sources and many interesting phenomena including dust clouds around Vega and the infrared ''cirrus'' at 100 μm. To realize the true benefit of space infrared astronomy, NASA is now studying the Space Infrared Telescope Facility, a long-life space-based observatory, to follow up on the survey results of IRAS. The choice of orbits is a critical program decision. The objective of this paper is to compare the performance of an all superfluid helium SIRTF system in the two possible orbit inclinations, polar orbit (99 0 ) and the low inclination orbit (28.5 0 )

  1. Selected Laws Relating to the Construction and Repair of Public School Facilities in North Carolina.

    Science.gov (United States)

    North Carolina State Dept. of Public Instruction, Raleigh.

    Schools in North Carolina are governed by numerous laws pertaining to construction and repair. A selection of these laws is presented. Financial concerns constitute the bulk of these statutes, covering areas such as bids (financial outlay, advertisement, rejecting bids, and withdrawing bids); sources of state funds; the selling or buying of school…

  2. Improving the food waste composting facilities site selection for sustainable development using a hybrid modified MADM model.

    Science.gov (United States)

    Liu, Kung-Ming; Lin, Sheng-Hau; Hsieh, Jing-Chzi; Tzeng, Gwo-Hshiung

    2018-05-01

    With the growth of population and the development of urbanization, waste management has always been a critical global issue. Recently, more and more countries have found that food waste constitutes the majority of municipal waste, if they are disposed of properly, will bring more benefits in sustainable development. Regarding the issue of selecting and improving the location to make the disposal facility towards achieving the aspiration level for sustainable development, since it involves multiple and complicated interaction factors about environment, society, and economy which have to be considered properly in the decision-making process of mutual influence relationship. It is basically a multiple attribute decision making (MADM) issue, a difficult problem which has been obsessing the governments of many countries is widely studied and discussed. This study uses the new hybrid modified MADM model, as follows, first to build an influential network relation map (INRM) via DEMATEL technique, next to confirm the influential weightings via DANP (DEMATEL-based ANP), and then to construct a decision-making model via a hybrid modified VIKOR method to improve and select the location for remaining the best disposal facilities. Finally, an empirical case study is illustrated to demonstrate that the proposed model can be effective and useful. In finding the process of decision making, environmental pollution is the main concern of many people in the area, but actually it is the resistance by the general public that has to be considered with first priority. Copyright © 2018. Published by Elsevier Ltd.

  3. Universal ligation-detection-reaction microarray applied for compost microbes

    Directory of Open Access Journals (Sweden)

    Romantschuk Martin

    2008-12-01

    Full Text Available Abstract Background Composting is one of the methods utilised in recycling organic communal waste. The composting process is dependent on aerobic microbial activity and proceeds through a succession of different phases each dominated by certain microorganisms. In this study, a ligation-detection-reaction (LDR based microarray method was adapted for species-level detection of compost microbes characteristic of each stage of the composting process. LDR utilises the specificity of the ligase enzyme to covalently join two adjacently hybridised probes. A zip-oligo is attached to the 3'-end of one probe and fluorescent label to the 5'-end of the other probe. Upon ligation, the probes are combined in the same molecule and can be detected in a specific location on a universal microarray with complementary zip-oligos enabling equivalent hybridisation conditions for all probes. The method was applied to samples from Nordic composting facilities after testing and optimisation with fungal pure cultures and environmental clones. Results Probes targeted for fungi were able to detect 0.1 fmol of target ribosomal PCR product in an artificial reaction mixture containing 100 ng competing fungal ribosomal internal transcribed spacer (ITS area or herring sperm DNA. The detection level was therefore approximately 0.04% of total DNA. Clone libraries were constructed from eight compost samples. The LDR microarray results were in concordance with the clone library sequencing results. In addition a control probe was used to monitor the per-spot hybridisation efficiency on the array. Conclusion This study demonstrates that the LDR microarray method is capable of sensitive and accurate species-level detection from a complex microbial community. The method can detect key species from compost samples, making it a basis for a tool for compost process monitoring in industrial facilities.

  4. Checking the special professional qualification of selected personnel of Czechoslovak nuclear power facilities

    International Nuclear Information System (INIS)

    Kovar, P.; Bahnova, V.

    1990-01-01

    The system of examinations of selected staff members of Czechoslovak nuclear power plants for their special professional quanlification is described in detail. This selected personnel includes secondary circuit operators, primary circuit operators, graduate shift leaders as well as reactor unit managers. Attention is paid to the structure, methodology, contents and criteria of evaluation of the written, oral and practical parts of the examination, which is sat for before the State Examination Commission. Based on the results of the examinations, the Czechoslovak Atomic Energy Commission grants, prolongs or cancels licenses for the particular functions. Over the period from 1985 to March 1989, 394 new licenses were issued, 93 licenses were prolonged and 4 were withdrawn. (Z.M.). 7 figs., 3 tabs., 3 refs

  5. Effects of solvent-extraction contactor selection on flowsheet and facility design

    International Nuclear Information System (INIS)

    Whatley, M.E.

    1982-01-01

    The notion is developed that the selection of a solvent extraction contactor is part of a more general development of principles and philosophy guiding the overall plant design. Specifically, the requirements and constraints placed on the plant by the solvent extraction system must be consistent with those imposed by the other operations, which generally are more expensive and more complicated. Were a conservative philosophy employed throughout the plant, the choice of pulsed columns seem correct. Were the plant intended to employ modern techniques and state-of-the-art technology, particularly in remote maintenance and process control, the selection of centrifugal contactors seems appropriate. The process improvements attainable from employing more stages in a more tightly controlled solvent extraction system seem marginal at present when applied to conventional flowsheets, although the cost-benefit may be attractive in a modern plant. The potential for improvement through major flowsheet modification can not presently be assessed quantitatively

  6. Technical investigation in solid waste to energy facilities and selection of suitable incineration technology for Tehran

    International Nuclear Information System (INIS)

    Mokarizdeh, V.; Lari, H.R.

    2001-01-01

    Incineration is another way for producing electrical energy. There are various methods for incineration as Stoker Fired, Suspension Fired, Rotary Kiln, Cyclone and Fluidized Bed; that each one has it's own advantages and disadvantages. Selecting suitable one for establishment in Tehran depends on many parameters like technical, economical and environmental factors. Comparing the various technologies due to the mentioned parameters by Multi Criteria Decision Making method shows that stoker-fired incinerator is the best one for the Capital City

  7. Dimension reduction methods for microarray data: a review

    Directory of Open Access Journals (Sweden)

    Rabia Aziz

    2017-03-01

    Full Text Available Dimension reduction has become inevitable for pre-processing of high dimensional data. “Gene expression microarray data” is an instance of such high dimensional data. Gene expression microarray data displays the maximum number of genes (features simultaneously at a molecular level with a very small number of samples. The copious numbers of genes are usually provided to a learning algorithm for producing a complete characterization of the classification task. However, most of the times the majority of the genes are irrelevant or redundant to the learning task. It will deteriorate the learning accuracy and training speed as well as lead to the problem of overfitting. Thus, dimension reduction of microarray data is a crucial preprocessing step for prediction and classification of disease. Various feature selection and feature extraction techniques have been proposed in the literature to identify the genes, that have direct impact on the various machine learning algorithms for classification and eliminate the remaining ones. This paper describes the taxonomy of dimension reduction methods with their characteristics, evaluation criteria, advantages and disadvantages. It also presents a review of numerous dimension reduction approaches for microarray data, mainly those methods that have been proposed over the past few years.

  8. Broad spectrum microarray for fingerprint-based bacterial species identification

    Directory of Open Access Journals (Sweden)

    Frey Jürg E

    2010-02-01

    Full Text Available Abstract Background Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. Results A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. Conclusions These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

  9. Employing image processing techniques for cancer detection using microarray images.

    Science.gov (United States)

    Dehghan Khalilabad, Nastaran; Hassanpour, Hamid

    2017-02-01

    Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes. Finally, via the extracted data, cancerous cell is recognized. To evaluate the performance of the proposed system, microarray database is employed which includes Breast cancer, Myeloid Leukemia and Lymphomas from the Stanford Microarray Database. The results indicate that the proposed system is able to identify the type of cancer from the data set with an accuracy of 95.45%, 94.11%, and 100%, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. "Harshlighting" small blemishes on microarrays

    Directory of Open Access Journals (Sweden)

    Wittkowski Knut M

    2005-03-01

    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs. Results We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.

  11. A guide for the selection of computer assisted mapping (CAM) and facilities informations systems

    Energy Technology Data Exchange (ETDEWEB)

    Haslin, S.; Baxter, P.; Jarvis, L.

    1980-12-01

    Many distribution engineers are now aware that computer assisted mapping (CAM) and facilities informations systems are probably the most significant breakthrough to date in computer applications for distribution engineering. The Canadian Electrical Asociation (CEA) recognized this and requested engineers of B.C. Hydro make a study of the state of the art in Canadian utilities and the progress of CAM systems on an international basis. The purpose was to provide a guide to assist Canadian utility distribution engineers faced with the problem of studying the application of CAM systems as an alternative to present methods, consideration being given to the long-term and other benefits that were perhaps not apparent for those approaching this field for the first time. It soon became apparent that technology was developing at a high rate and competition in the market was very strong. Also a number of publications were produced by other sources which adequately covered the scope of this study. This report is thus a collection of references to reports, manuals, and other documents with a few considerations provided for those companies interested in exploring further the use of interactive graphics. 24 refs.

  12. Lipid Microarray Biosensor for Biotoxin Detection.

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Anup K.; Throckmorton, Daniel J.; Moran-Mirabal, Jose C.; Edel, Joshua B.; Meyer, Grant D.; Craighead, Harold G.

    2006-05-01

    We present the use of micron-sized lipid domains, patterned onto planar substrates and within microfluidic channels, to assay the binding of bacterial toxins via total internal reflection fluorescence microscopy (TIRFM). The lipid domains were patterned using a polymer lift-off technique and consisted of ganglioside-populated DSPC:cholesterol supported lipid bilayers (SLBs). Lipid patterns were formed on the substrates by vesicle fusion followed by polymer lift-off, which revealed micron-sized SLBs containing either ganglioside GT1b or GM1. The ganglioside-populated SLB arrays were then exposed to either Cholera toxin subunit B (CTB) or Tetanus toxin fragment C (TTC). Binding was assayed on planar substrates by TIRFM down to 1 nM concentration for CTB and 100 nM for TTC. Apparent binding constants extracted from three different models applied to the binding curves suggest that binding of a protein to a lipid-based receptor is strongly affected by the lipid composition of the SLB and by the substrate on which the bilayer is formed. Patterning of SLBs inside microfluidic channels also allowed the preparation of lipid domains with different compositions on a single device. Arrays within microfluidic channels were used to achieve segregation and selective binding from a binary mixture of the toxin fragments in one device. The binding and segregation within the microfluidic channels was assayed with epifluorescence as proof of concept. We propose that the method used for patterning the lipid microarrays on planar substrates and within microfluidic channels can be easily adapted to proteins or nucleic acids and can be used for biosensor applications and cell stimulation assays under different flow conditions. KEYWORDS. Microarray, ganglioside, polymer lift-off, cholera toxin, tetanus toxin, TIRFM, binding constant.4

  13. Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes.

    Science.gov (United States)

    Jahandeh, Nadia; Ranjbar, Reza; Behzadi, Payam; Behzadi, Elham

    2015-01-01

    The pathotypes of uropathogenic Escherichia coli (UPEC) cause different types of urinary tract infections (UTIs). The presence of a wide range of virulence genes in UPEC enables us to design appropriate DNA microarray probes. These probes, which are used in DNA microarray technology, provide us with an accurate and rapid diagnosis and definitive treatment in association with UTIs caused by UPEC pathotypes. The main goal of this article is to introduce the UPEC virulence genes as invaluable approaches for designing DNA microarray probes. Main search engines such as Google Scholar and databases like NCBI were searched to find and study several original pieces of literature, review articles, and DNA gene sequences. In parallel with in silico studies, the experiences of the authors were helpful for selecting appropriate sources and writing this review article. There is a significant variety of virulence genes among UPEC strains. The DNA sequences of virulence genes are fabulous patterns for designing microarray probes. The location of virulence genes and their sequence lengths influence the quality of probes. The use of selected virulence genes for designing microarray probes gives us a wide range of choices from which the best probe candidates can be chosen. DNA microarray technology provides us with an accurate, rapid, cost-effective, sensitive, and specific molecular diagnostic method which is facilitated by designing microarray probes. Via these tools, we are able to have an accurate diagnosis and a definitive treatment regarding UTIs caused by UPEC pathotypes.

  14. Instruction texts and problems for the training and examination of selected personnel at research nuclear facilities

    International Nuclear Information System (INIS)

    Matejka, K.; Fleischhans, J.; Hejzlar, R.

    1994-01-01

    The publication comprises 6 separate brochures: (1) Selected chapters in reactor theory; (2) Experimental education methods; (3) Research and experimental reactors; (4.1) Technical description of the LVR-15 reactor; (4.2) Technical description of the LR-0 reactor; (4.3) Technical description of the VR-1 reactor; (5) Research reactor safety and operation; and (6) Database of problems for qualification examinations. Brochure No. 4 consists of 3 separate parts. The publication is intended for the training and examination of the following research reactor staff: reactor operator, shift engineer, control physicist, and start-up group head. (J.B.)

  15. The January 17, 1994 Northridge Earthquake: Effects on selected industrial facilities and lifelines

    Energy Technology Data Exchange (ETDEWEB)

    Eli, M.W.; Sommer, S.C. [Lawrence Livermore National Lab., CA (United States); Roche, T.R.; Merz, K.L.

    1995-02-01

    Revision 0 of this report is being published in February 1995 to closely mark the one-year anniversary of the Northridge Earthquake. A September 1994 Draft version of the report was reviewed by DOE and NRC, and many of the review comments are incorporated into Revision 0. While this revision of the report is not entirely complete, it is being made available for comment, review, and evaluation. Since the report was written by several authors, sections of the report have slightly different styles. Several sections of Revision 0 are not complete, but are planned to be completed in Revision 1. The primary unfinished section is Section 3.3 on Electric Power Transmission. Other sections of Revision 0, such as Section 4.5.2 on the Energy Technology Engineering Center and 3.2 on Electric Power Generation, will be enhanced with further detailed information as it becomes available. In addition, further data, including processed response spectra for investigated facilities and cataloging of relay performance, will be added to Revision 1 depending upon investigation support. While Revision 0 of this report is being published by LLNL, Revision 1 is planned to be published by EPRI. The anticipated release date for Revision 1 is December 1995. Unfortunately, the one-year anniversary of the Northridge Earthquake was also marked by the devastating Hyogo-Ken Nanbu (or Hanshin-Awaji) Earthquake in Kobe, Japan. As compared to the Northridge Earthquake, there were many more deaths, collapsed structures, destroyed lifelines, and fires following the Kobe Earthquake. Lessons from the Kobe Earthquake will both reemphasize topics discussed in this report and provide further issues to be addressed when designing and retrofitting structures, systems, and components for seismic strong motion.

  16. Performance comparisons of selected personnel-dosimetry systems in use at Department of Energy facilities

    International Nuclear Information System (INIS)

    Roberson, P.L; Holbrook, K.L.; Yoder, R.C.; Fox, R.A.; Hadley, R.T.; Hogan, B.T.; Hooker, C.D.

    1983-10-01

    Dosimeter performance data were collected to help develop a uniform approach to the calibration and use of personnel dosimetry systems for Department of Energy (DOE) laboratories. Eleven DOE laboratories participated in six months of testing using the American National Draft Standard, Criteria for Testing Personnel Dosimetry Performance, ANSI N13.11, and additional testing categories. The tests described in ANSI N13.11 used a pass/fail system to determine compliance with the draft standard. Recalculation to PNL irradiations showed that the 137 Cs, 90 Sr/ 90 Y, and 252 Cf categories can be recalibrated to have acceptable performance for nearly all participant systems. Deficient dosimeter design or handling techniques caused poor performance in the x-ray category for nearly half of the participants. Too little filtration for the deep-dose element caused poor performance in the beta/photon mixture category for one participant. Two participants had excessively high standard deviations in the neutron category due to dosimeter design or handling deficiencies. The participating dosimetry systems were separated into three categories on their dose evaluation procedure for low-energy photons. These were film dosimeters, fixed-calibration thermoluminescent (TL) dosimeters, and variable-calibration TL dosimeters. The performance of the variable-calibration design was best while the film dosimeters performed considerably worse than either TL dosimeter design. Beta energy dependence studies confirmed a strong correlation between sensitive element thickness, shallow element filtration and low-energy beta response. Studies of neutron calibration conditions for each participant suggested a relationship between response and calibration facility design

  17. Pilot study risk assessment for selected problems at three US Department of Energy Facilities

    International Nuclear Information System (INIS)

    Hamilton, L.D.; Holtzman, S.; Meinhold, A.F.; Morris, S.C.; Pardi, R.; Rowe, M.D.; Sun, C.; Anspaugh, L.R.; Bogen, K.T.; Daniels, J.I.

    1994-01-01

    Objective and realistic human health risk assessments were performed for environmental problems at the Savannah River Site (SRS), the Fernald Environmental Management Project (FEMP), and the Nevada Test Site (NTS). At the SRS, cancer mortality risks were analyzed for projected public exposure to 3 H and 137 Cs released into the Savannah River. For annual human exposures to SRS tritium in Savannah River water, calculated incremental individual lifetime risks in two human receptor populations were small (8x10 -7 ; upper 95 percentile point of the distribution). The 95th percentile point of the distribution for incremental individual lifetime risks from one year's exposure to 137 Cs is less than 10 -8 . No deaths are expected in either populations as a result of exposures to tritium or cesium released to the Savannah River. Routine releases of radon and radon progeny from the K-65 silos at FEMP resulted in individual lifetime risks greater than 1x10 -4 only for onsite workers and fenceline residents. Assessment of risks from exposure to uranium in ground water released by the FEMP predicted no toxic effects for human receptors. All estimated cancer risks were small. The largest predicted individual lifetime risk was for a well close to the facility. For various above-ground shot sites at the NTS, highest predicted lifetime cancer risks are for a resident farmer. At 50,000 and 100,000 y in the future, the predicted cancer risks are all below 10 -6 . In the assessment of exposure to radionuclides in ground water at the NTS, for an individual onsite near the site boundary, the geometric mean of the maximum potential excess lifetime risk of cancer mortality for an individual is 7x10 -3 . For an individual using water offsite, the geometric mean of the maximum potential excess lifetime risk of cancer mortality is 7x10 -7 . 40 refs., 6 figs., 2 tabs

  18. Selection of Liner Materials and Design of Hazardous Water Facilities in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Sahel N. Abduljauwad

    2001-12-01

    Full Text Available Rapid development in Saudi Arabia has produced a broad spectrum of wastes.  In the last two decades, several refineries and petrochemical industries have been established. These industries have produced sludges and other toxic wastes which need proper planning for their handling and disposal. This paper covers design and selection of liner materials for two hazardous waste disposal sites. One of them is located in the Eastern Province of Saudi Arabia, while the second one is located in the Western part. The paper will present complete design details of the natural compacted and geosynthetic soil liners and the leachate collection and removal system for primary liners and leak detection/leachate collection and removal system for secondary liners.

  19. Cleanup and treatment of radioactively contaminated land including areas near nuclear facilities. A selected bibliography

    International Nuclear Information System (INIS)

    Fore, C.S.; Faust, R.A.; Brewster, R.H.

    1982-09-01

    This annotated bibliography of 337 references summarizes the literature published on the cleanup and treatment of radioactively contaminated land. Specifically, this bibliography focuses on literature concerned with the methods of cleanup and treatment being applied - chemical, physical, or vegetative stabilization; the types of equipment being used; and the influence of climatic conditions on the method selected for use. The emphasis in such literature is placed on hazardous site cleanup efforts that have been completed as well as those that are in progress and are being planned. Appendix A includes 135 additional references to literature identified but not included in the bibliography because of time and funding constraints. Appendix B consists of a table that identifies the cleanup and treatment research conducted at specific sites. All of the information included in this bibliography is stored in a computerized form that is readily available upon request

  20. Translating microarray data for diagnostic testing in childhood leukaemia

    International Nuclear Information System (INIS)

    Hoffmann, Katrin; Firth, Martin J; Beesley, Alex H; Klerk, Nicholas H de; Kees, Ursula R

    2006-01-01

    Recent findings from microarray studies have raised the prospect of a standardized diagnostic gene expression platform to enhance accurate diagnosis and risk stratification in paediatric acute lymphoblastic leukaemia (ALL). However, the robustness as well as the format for such a diagnostic test remains to be determined. As a step towards clinical application of these findings, we have systematically analyzed a published ALL microarray data set using Robust Multi-array Analysis (RMA) and Random Forest (RF). We examined published microarray data from 104 ALL patients specimens, that represent six different subgroups defined by cytogenetic features and immunophenotypes. Using the decision-tree based supervised learning algorithm Random Forest (RF), we determined a small set of genes for optimal subgroup distinction and subsequently validated their predictive power in an independent patient cohort. We achieved very high overall ALL subgroup prediction accuracies of about 98%, and were able to verify the robustness of these genes in an independent panel of 68 specimens obtained from a different institution and processed in a different laboratory. Our study established that the selection of discriminating genes is strongly dependent on the analysis method. This may have profound implications for clinical use, particularly when the classifier is reduced to a small set of genes. We have demonstrated that as few as 26 genes yield accurate class prediction and importantly, almost 70% of these genes have not been previously identified as essential for class distinction of the six ALL subgroups. Our finding supports the feasibility of qRT-PCR technology for standardized diagnostic testing in paediatric ALL and should, in conjunction with conventional cytogenetics lead to a more accurate classification of the disease. In addition, we have demonstrated that microarray findings from one study can be confirmed in an independent study, using an entirely independent patient cohort

  1. Advanced microarray technologies for clinical diagnostics

    NARCIS (Netherlands)

    Pierik, Anke

    2011-01-01

    DNA microarrays become increasingly important in the field of clinical diagnostics. These microarrays, also called DNA chips, are small solid substrates, typically having a maximum surface area of a few cm2, onto which many spots are arrayed in a pre-determined pattern. Each of these spots contains

  2. Analysis of the application of selected physico-chemical methods in eliminating odor nuisance of municipal facilities

    Directory of Open Access Journals (Sweden)

    Miller Urszula

    2018-01-01

    Full Text Available Operation of municipal management facilities is inseparable from the problem of malodorous compounds emissions to the atmospheric air. In that case odor nuisance is related to the chemical composition of waste, sewage and sludge as well as to the activity of microorganisms whose products of life processes can be those odorous compounds. Significant reduction of odorant emission from many sources can be achieved by optimizing parameters and conditions of processes. However, it is not always possible to limit the formation of odorants. In such cases it is best to use appropriate deodorizing methods. The choice of the appropriate method is based on in terms of physical parameters, emission intensity of polluted gases and their composition, if it is possible to determine. Among the solutions used in municipal economy, there can be distinguished physico-chemical methods such as sorption and oxidation. In cases where the source of the emission is not encapsulated, odor masking techniques are used, which consists of spraying preparations that neutralize unpleasant odors. The paper presents the characteristics of selected methods of eliminating odor nuisance and evaluation of their applicability in municipal management facilities.

  3. Analysis of the application of selected physico-chemical methods in eliminating odor nuisance of municipal facilities

    Science.gov (United States)

    Miller, Urszula; Grzelka, Agnieszka; Romanik, Elżbieta; Kuriata, Magdalena

    2018-01-01

    Operation of municipal management facilities is inseparable from the problem of malodorous compounds emissions to the atmospheric air. In that case odor nuisance is related to the chemical composition of waste, sewage and sludge as well as to the activity of microorganisms whose products of life processes can be those odorous compounds. Significant reduction of odorant emission from many sources can be achieved by optimizing parameters and conditions of processes. However, it is not always possible to limit the formation of odorants. In such cases it is best to use appropriate deodorizing methods. The choice of the appropriate method is based on in terms of physical parameters, emission intensity of polluted gases and their composition, if it is possible to determine. Among the solutions used in municipal economy, there can be distinguished physico-chemical methods such as sorption and oxidation. In cases where the source of the emission is not encapsulated, odor masking techniques are used, which consists of spraying preparations that neutralize unpleasant odors. The paper presents the characteristics of selected methods of eliminating odor nuisance and evaluation of their applicability in municipal management facilities.

  4. Identification of potential biomarkers from microarray experiments using multiple criteria optimization

    International Nuclear Information System (INIS)

    Sánchez-Peña, Matilde L; Isaza, Clara E; Pérez-Morales, Jaileene; Rodríguez-Padilla, Cristina; Castro, José M; Cabrera-Ríos, Mauricio

    2013-01-01

    Microarray experiments are capable of determining the relative expression of tens of thousands of genes simultaneously, thus resulting in very large databases. The analysis of these databases and the extraction of biologically relevant knowledge from them are challenging tasks. The identification of potential cancer biomarker genes is one of the most important aims for microarray analysis and, as such, has been widely targeted in the literature. However, identifying a set of these genes consistently across different experiments, researches, microarray platforms, or cancer types is still an elusive endeavor. Besides the inherent difficulty of the large and nonconstant variability in these experiments and the incommensurability between different microarray technologies, there is the issue of the users having to adjust a series of parameters that significantly affect the outcome of the analyses and that do not have a biological or medical meaning. In this study, the identification of potential cancer biomarkers from microarray data is casted as a multiple criteria optimization (MCO) problem. The efficient solutions to this problem, found here through data envelopment analysis (DEA), are associated to genes that are proposed as potential cancer biomarkers. The method does not require any parameter adjustment by the user, and thus fosters repeatability. The approach also allows the analysis of different microarray experiments, microarray platforms, and cancer types simultaneously. The results include the analysis of three publicly available microarray databases related to cervix cancer. This study points to the feasibility of modeling the selection of potential cancer biomarkers from microarray data as an MCO problem and solve it using DEA. Using MCO entails a new optic to the identification of potential cancer biomarkers as it does not require the definition of a threshold value to establish significance for a particular gene and the selection of a normalization

  5. Carbohydrate Microarrays in Plant Science

    DEFF Research Database (Denmark)

    Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.

    2012-01-01

    Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important...... industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high...... for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities....

  6. The EADGENE Microarray Data Analysis Workshop

    DEFF Research Database (Denmark)

    de Koning, Dirk-Jan; Jaffrézic, Florence; Lund, Mogens Sandø

    2007-01-01

    Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from...... 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays...... statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful...

  7. Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei

    OpenAIRE

    Zirlinger, M.; Kreiman, Gabriel; Anderson, D. J.

    2001-01-01

    Microarray technology represents a potentially powerful method for identifying cell type- and regionally restricted genes expressed in the brain. Here we have combined a microarray analysis of differential gene expression among five selected brain regions, including the amygdala, cerebellum, hippocampus, olfactory bulb, and periaqueductal gray, with in situ hybridization. On average, 0.3% of the 34,000 genes interrogated were highly enriched in each of the five regions...

  8. Dynamic, electronically switchable surfaces for membrane protein microarrays.

    Science.gov (United States)

    Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J

    2006-02-01

    Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.

  9. Cesium and strontium sorption by selected tropical and subtropical soils around nuclear facilities

    International Nuclear Information System (INIS)

    Chiang, P.N.; Wang, M. K.; Huang, P.M.; Wang, J.J.; Chiu, C.Y.

    2010-01-01

    The dynamics of Cs and Sr sorption by soils, especially in the subtropics and tropics, as influenced by soil components are not fully understood. The rates and capacities of Cs and Sr sorption by selected subtropical and tropical soils in Taiwan were investigated to facilitate our understanding of the transformation and dynamics of Cs and Sr in soils developed under highly weathering intensity. The Langmuir isotherms and kinetic rates of Cs and Sr sorption on the Ap1 and Bt1 horizons of the Long-Tan (Lt) and the A and Bt1 horizons of the Kuan-Shan (Kt), Mao-Lin (Tml) and Chi-Lo (Cl) soils were selected for this study. Air-dried soil ( -5 to 1.88 x 10 -3 M of CsCl (pH 4.0) or 1.14 x 10 -4 to 2.85 x 10 -3 M of SrCl 2 (pH 4.0) solutions at 25 deg. C. The sorption maximum capacity (q m ) of Cs by the Ap1 and Bt1 horizons of the Lt soil (62.24 and 70.70 mmol Cs kg -1 soil) were significantly (p -1 soil in Kt soil and 34.83 and 29.96 mmol Cs kg -1 soil in Cl soil, respectively), however, the sorption maximum capacity values of the Lt and Tml soils did not show significant differences. The amounts of pyrophosphate extractable Fe (Fe p ) were correlated significantly with the Cs and Sr sorption capacities (for Cs sorption, r 2 = 0.97, p -4 ; for Sr sorption, r 2 = 0.82, p -3 ). The partition coefficient of radiocesium sorbed on soil showed the following order: Cl soil >> Kt soil > Tml soil > Lt soil. It was due to clay minerals. The second-order kinetic model was applied to the Cs and Sr sorption data. The rate constant of Cs or Sr sorption on the four soils was substantiality increased with increasing temperature. This is attributable to the availability of more energy for bond breaking and bond formation brought about by the higher temperatures. The rate constant of Cs sorption at 308 K was 1.39-2.09 times higher than that at 278 K in the four soils. The activation energy of Cs and Sr sorbed by the four soils ranged from 7.2 to 16.7 kJ mol -1 and from 15.2 to 22.4 kJ mol

  10. Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

    Directory of Open Access Journals (Sweden)

    Tong Weida

    2010-10-01

    Full Text Available Abstract Background The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. In addition, it was not clear whether the two human reference RNA samples established by the MAQC project in 2005 still maintained their transcriptome integrity over a period of four years. Experiments were conducted to answer these questions. Results Microarray data were generated in 2009 in three replicates for each of the two MAQC samples with either expired Affymetrix U133A or unexpired U133Plus2 microarrays. These results were compared with data obtained in 2005 on the U133Plus2 microarray. The percentage of overlap between the lists of differentially expressed genes (DEGs from U133Plus2 microarray data generated in 2009 and in 2005 was 97.44%. While there was some degree of fold change compression in the expired U133A microarrays, the percentage of overlap between the lists of DEGs from the expired and unexpired microarrays was as high as 96.99%. Moreover, the microarray data generated using the expired U133A microarrays in 2009 were highly concordant with microarray and TaqMan® data generated by the MAQC project in 2005. Conclusions Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer’s expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the

  11. Assessment of laboratory logistics management information system practice for HIV/AIDS and tuberculosis laboratory commodities in selected public health facilities in Addis Ababa, Ethiopia

    OpenAIRE

    Desale, Adino; Taye, Bineyam; Belay, Getachew; Nigatu, Alemayehu

    2013-01-01

    Introduction Logistics management information system for health commodities remained poorly implemented in most of developing countries. To assess the status of laboratory logistics management information system for HIV/AIDS and tuberculosis laboratory commodities in public health facilities in Addis Ababa. Methods A cross-sectional descriptive study was conducted from September 2010-January 2011 at selected public health facilities. A stratified random sampling method was used to include a t...

  12. A Java-based tool for the design of classification microarrays

    Directory of Open Access Journals (Sweden)

    Broschat Shira L

    2008-08-01

    Full Text Available Abstract Background Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. Results The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. Conclusion In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays–and mixed-plasmid microarrays in particular–it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm, several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text, and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff. Weights

  13. MARS: Microarray analysis, retrieval, and storage system

    Directory of Open Access Journals (Sweden)

    Scheideler Marcel

    2005-04-01

    Full Text Available Abstract Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS, a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

  14. Annotating breast cancer microarray samples using ontologies

    Science.gov (United States)

    Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

    2008-01-01

    As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108

  15. Simulation of microarray data with realistic characteristics

    Directory of Open Access Journals (Sweden)

    Lehmussola Antti

    2006-07-01

    Full Text Available Abstract Background Microarray technologies have become common tools in biological research. As a result, a need for effective computational methods for data analysis has emerged. Numerous different algorithms have been proposed for analyzing the data. However, an objective evaluation of the proposed algorithms is not possible due to the lack of biological ground truth information. To overcome this fundamental problem, the use of simulated microarray data for algorithm validation has been proposed. Results We present a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization. After all these steps are taken into account, the simulated data has realistic biological and statistical characteristics. The applicability of the proposed model is demonstrated by several examples. Conclusion The proposed microarray simulation model is modular and can be used in different kinds of applications. It includes several error models that have been proposed earlier and it can be used with different types of input data. The model can be used to simulate both spotted two-channel and oligonucleotide based single-channel microarrays. All this makes the model a valuable tool for example in validation of data analysis algorithms.

  16. Radioactive cDNA microarray in neurospsychiatry

    International Nuclear Information System (INIS)

    Choe, Jae Gol; Shin, Kyung Ho; Lee, Min Soo; Kim, Meyoung Kon

    2003-01-01

    Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen leading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with cell lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA in fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high quality rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. In summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most

  17. Radioactive cDNA microarray in neurospsychiatry

    Energy Technology Data Exchange (ETDEWEB)

    Choe, Jae Gol; Shin, Kyung Ho; Lee, Min Soo; Kim, Meyoung Kon [Korea University Medical School, Seoul (Korea, Republic of)

    2003-02-01

    Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen leading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with cell lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA in fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high quality rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. In summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most

  18. Fuzzy support vector machine for microarray imbalanced data classification

    Science.gov (United States)

    Ladayya, Faroh; Purnami, Santi Wulan; Irhamah

    2017-11-01

    DNA microarrays are data containing gene expression with small sample sizes and high number of features. Furthermore, imbalanced classes is a common problem in microarray data. This occurs when a dataset is dominated by a class which have significantly more instances than the other minority classes. Therefore, it is needed a classification method that solve the problem of high dimensional and imbalanced data. Support Vector Machine (SVM) is one of the classification methods that is capable of handling large or small samples, nonlinear, high dimensional, over learning and local minimum issues. SVM has been widely applied to DNA microarray data classification and it has been shown that SVM provides the best performance among other machine learning methods. However, imbalanced data will be a problem because SVM treats all samples in the same importance thus the results is bias for minority class. To overcome the imbalanced data, Fuzzy SVM (FSVM) is proposed. This method apply a fuzzy membership to each input point and reformulate the SVM such that different input points provide different contributions to the classifier. The minority classes have large fuzzy membership so FSVM can pay more attention to the samples with larger fuzzy membership. Given DNA microarray data is a high dimensional data with a very large number of features, it is necessary to do feature selection first using Fast Correlation based Filter (FCBF). In this study will be analyzed by SVM, FSVM and both methods by applying FCBF and get the classification performance of them. Based on the overall results, FSVM on selected features has the best classification performance compared to SVM.

  19. Tumour auto-antibody screening: performance of protein microarrays using SEREX derived antigens

    International Nuclear Information System (INIS)

    Stempfer, René; Weinhäusel, Andreas; Syed, Parvez; Vierlinger, Klemens; Pichler, Rudolf; Meese, Eckart; Leidinger, Petra; Ludwig, Nicole; Kriegner, Albert; Nöhammer, Christa

    2010-01-01

    The simplicity and potential of minimal invasive testing using serum from patients make auto-antibody based biomarkers a very promising tool for use in diagnostics of cancer and auto-immune disease. Although several methods exist for elucidating candidate-protein markers, immobilizing these onto membranes and generating so called macroarrays is of limited use for marker validation. Especially when several hundred samples have to be analysed, microarrays could serve as a good alternative since processing macro membranes is cumbersome and reproducibility of results is moderate. Candidate markers identified by SEREX (serological identification of antigens by recombinant expression cloning) screenings of brain and lung tumour were used for macroarray and microarray production. For microarray production recombinant proteins were expressed in E. coli by autoinduction and purified His-tag (histidine-tagged) proteins were then used for the production of protein microarrays. Protein arrays were hybridized with the serum samples from brain and lung tumour patients. Methods for the generation of microarrays were successfully established when using antigens derived from membrane-based selection. Signal patterns obtained by microarrays analysis of brain and lung tumour patients' sera were highly reproducible (R = 0.92-0.96). This provides the technical foundation for diagnostic applications on the basis of auto-antibody patterns. In this limited test set, the assay provided high reproducibility and a broad dynamic range to classify all brain and lung samples correctly. Protein microarray is an efficient means for auto-antibody-based detection when using SEREX-derived clones expressing antigenic proteins. Protein microarrays are preferred to macroarrays due to the easier handling and the high reproducibility of auto-antibody testing. Especially when using only a few microliters of patient samples protein microarrays are ideally suited for validation of auto

  20. Characterization of stormwater at selected South Carolina Department of Transportation maintenance yards and section shed facilities in Ballentine, Conway, and North Charleston, South Carolina, 2010-12

    Science.gov (United States)

    Journey, Celeste A.; Conlon, Kevin J.

    2014-01-01

    Increased impervious surfaces (driveways, parking lots, and buildings) and human activities (residential, industrial, and commercial) have been linked to substantial changes in both the quality and quantity of stormwater on a watershed scale (Brabec and others, 2002; Pitt and Maestre, 2005). Small-scale storage and equipment repair facilities increase impervious surfaces that prevent infiltration of stormwater, and these facilities accommodate activities that can introduce trace metals, organic compounds, and other contaminants to the facility’s grounds. Thus, these small facilities may contribute pollutants to the environment during storm events (U.S. Environmental Protection Agency, 1992). The South Carolina Department of Transportation (SCDOT) operates section shed and maintenance yard facilities throughout the State. Prior to this investigation, the SCDOT had no data to define the quality of stormwater leaving these facilities. To provide these data, the U.S. Geological Survey (USGS), in cooperation with the SCDOT, conducted an investigation to identify and quantify constituents that are transported in stormwater from two maintenance yards and a section shed in three different areas of South Carolina. The two maintenance yards, in North Charleston and Conway, S.C., were selected because they represent facilities where equipment and road maintenance materials are stored and complete equipment repair operations are conducted. The section shed, in Ballentine, S.C., was selected because it is a facility that stores equipment and road maintenance material. Characterization of the constituents that were transported in stormwater from these representative SCDOT maintenance facilities may be used by the SCDOT in the development of stormwater management plans for similar section shed and maintenance yard facilities throughout the State to improve stormwater quality.

  1. Gene Expression and Microarray Investigation of Dendrobium ...

    African Journals Online (AJOL)

    blood glucose > 16.7 mmol/L were used as the model group and treated with Dendrobium mixture. (DEN ... Keywords: Diabetes, Gene expression, Dendrobium mixture, Microarray testing ..... homeostasis in airway smooth muscle. Am J.

  2. Estimates of external dose-rate conversion factors and internal dose conversion factors for selected radionuclides released from fusion facilities

    Energy Technology Data Exchange (ETDEWEB)

    Homma, Toshimitsu; Togawa, Orihiko [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1996-11-01

    This report provides a tabulation of both external dose-rate conversion factors and internal dose conversion factors using radioactive decay data in the updated Evaluated Nuclear Structure Data File (ENSDF) for selected 26 radionuclides and all their daughter radionuclides of potential importance in safety assessments of fusion facilities. The external dose-rate conversion factors for 21 target organs are tabulated for three exposure modes that are immersion in contaminated air, irradiation at a height of 1 m above a contaminated ground surface and immersion contaminated water. For internal exposure, committed dose equivalents, based on the methodology of ICRP Publication 30, in the same target organs per intake of unit activity are given for the inhalation and ingestion exposure pathways. The data presented here is intended to be generally used for safety assessments of fusion reactors. Comparisons of external effective dose-rate conversion factors and committed effective dose equivalents are made with the previous data from the independent data bases to provide quality assurance on our calculated results. There is generally good agreement among data from the independent data bases. The differences in the values of both effective dose-rate and dose conversion factors appeared are primarily due to differences in calculational methodology, the use of different radioactive decay data, and compilation errors. (author)

  3. Delivery Practices and Associated Factors among Mothers Seeking Child Welfare Services in Selected Health Facilities in Nyandarua South District, Kenya

    Directory of Open Access Journals (Sweden)

    Wanjira Carol

    2011-05-01

    Full Text Available Abstract Background A measure of the proportion of deliveries assisted by skilled attendants is one of the indicators of progress towards achieving Millennium Development Goal (MDG 5, which aims at improving maternal health. This study aimed at establishing delivery practices and associated factors among mothers seeking child welfare services at selected health facilities in Nyandarua South district, Kenya to determine whether mothers were receiving appropriate delivery care. Methods A hospital-based cross-sectional survey among women who had recently delivered while in the study area was carried out between August and October 2009. Binary Logistic regression was used to identify factors that predicted mothers' delivery practice. Results Among the 409 mothers who participated in the study, 1170 deliveries were reported. Of all the deliveries reported, 51.8% were attended by unskilled birth attendants. Among the deliveries attended by unskilled birth attendants, 38.6% (452/1170 were by neighbors and/or relatives. Traditional Birth Attendants attended 1.5% (17/1170 of the deliveries while in 11.7% (137/1170 of the deliveries were self administered. Mothers who had unskilled birth attendance were more likely to have Conclusion Among the mothers interviewed, utilization of skilled delivery attendance services was still low with a high number of deliveries being attended by unqualified lay persons. There is need to implement cost effective and sustainable measures to improve the quality of maternal health services with an aim of promoting safe delivery and hence reducing maternal mortality.

  4. Facile synthesis of N-acetyl-L-cysteine capped CdHgSe quantum dots and selective determination of hemoglobin.

    Science.gov (United States)

    Wang, Qingqing; Zhan, Guoqing; Li, Chunya

    2014-01-03

    Using N-acetyl-L-cysteine (NAC) as a stabilizer, well water-dispersed, high-quality and stable CdHgSe quantum dots were facilely synthesized via a simple aqueous phase method. The as-prepared NAC capped CdHgSe quantum dots were thoroughly characterized by fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and transmission electron microscopy. A novel method for the selective determination of hemoglobin (Hb) was developed based on fluorescence quenching of the NAC capped CdHgSe quantum dots. A number of key factors including pH value of phosphate buffer solution, quantum dots concentration, the adding sequence of reagents and reaction time that influence the analytical performance of the NAC capped CdHgSe quantum dots in Hb determination were investigated. Under the optimal experimental conditions, the change of fluorescence intensity (ΔI) was linearly proportional to the concentration of Hb in the range of 4.0×10(-9)-4.4×10(-7) mol L(-1) with a detection limit of 2.0×10(-9) mol L(-1). The developed method has been successfully employed to determine Hb in human urine samples. Copyright © 2013. Published by Elsevier B.V.

  5. Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays

    Directory of Open Access Journals (Sweden)

    Wu Xiaogang

    2012-06-01

    Full Text Available In many cases, crucial genes show relatively slight changes between groups of samples (e.g. normal vs. disease, and many genes selected from microarray differential analysis by measuring the expression level statistically are also poorly annotated and lack of biological significance. In this paper, we present an innovative approach - network expansion and pathway enrichment analysis (NEPEA for integrative microarray analysis. We assume that organized knowledge will help microarray data analysis in significant ways, and the organized knowledge could be represented as molecular interaction networks or biological pathways. Based on this hypothesis, we develop the NEPEA framework based on network expansion from the human annotated and predicted protein interaction (HAPPI database, and pathway enrichment from the human pathway database (HPD. We use a recently-published microarray dataset (GSE24215 related to insulin resistance and type 2 diabetes (T2D as case study, since this study provided a thorough experimental validation for both genes and pathways identified computationally from classical microarray analysis and pathway analysis. We perform our NEPEA analysis for this dataset based on the results from the classical microarray analysis to identify biologically significant genes and pathways. Our findings are not only consistent with the original findings mostly, but also obtained more supports from other literatures.

  6. Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential

    DEFF Research Database (Denmark)

    Grønlund, Hugo Ahlm; Riber, Leise; Vigre, Håkan

    2011-01-01

    Bacterial food-borne infections in humans caused by Salmonella spp. are considered a crucial food safety issue. Therefore, it is important for the risk assessments of Salmonella to consider the genomic variationamong different isolates in order to control pathogen-induced infections. Microarray...... critical methodology parameters that differed between the two labs were identified. These related to printing facilities, choice of hybridization buffer,wash buffers used following the hybridization and choice of procedure for purifying genomic DNA. Critical parameters were randomized in a four......DNA and different wash buffers. However, less agreement (Kappa=0.2–0.6) between microarray results were observed when using different hybridization buffers, indicating this parameter as being highly criticalwhen transferring a standard microarray assay between laboratories. In conclusion, this study indicates...

  7. Supervised group Lasso with applications to microarray data analysis

    Directory of Open Access Journals (Sweden)

    Huang Jian

    2007-02-01

    Full Text Available Abstract Background A tremendous amount of efforts have been devoted to identifying genes for diagnosis and prognosis of diseases using microarray gene expression data. It has been demonstrated that gene expression data have cluster structure, where the clusters consist of co-regulated genes which tend to have coordinated functions. However, most available statistical methods for gene selection do not take into consideration the cluster structure. Results We propose a supervised group Lasso approach that takes into account the cluster structure in gene expression data for gene selection and predictive model building. For gene expression data without biological cluster information, we first divide genes into clusters using the K-means approach and determine the optimal number of clusters using the Gap method. The supervised group Lasso consists of two steps. In the first step, we identify important genes within each cluster using the Lasso method. In the second step, we select important clusters using the group Lasso. Tuning parameters are determined using V-fold cross validation at both steps to allow for further flexibility. Prediction performance is evaluated using leave-one-out cross validation. We apply the proposed method to disease classification and survival analysis with microarray data. Conclusion We analyze four microarray data sets using the proposed approach: two cancer data sets with binary cancer occurrence as outcomes and two lymphoma data sets with survival outcomes. The results show that the proposed approach is capable of identifying a small number of influential gene clusters and important genes within those clusters, and has better prediction performance than existing methods.

  8. Design issues in toxicogenomics using DNA microarray experiment

    International Nuclear Information System (INIS)

    Lee, Kyoung-Mu; Kim, Ju-Han; Kang, Daehee

    2005-01-01

    The methods of toxicogenomics might be classified into omics study (e.g., genomics, proteomics, and metabolomics) and population study focusing on risk assessment and gene-environment interaction. In omics study, microarray is the most popular approach. Genes falling into several categories (e.g., xenobiotics metabolism, cell cycle control, DNA repair etc.) can be selected up to 20,000 according to a priori hypothesis. The appropriate type of samples and species should be selected in advance. Multiple doses and varied exposure durations are suggested to identify those genes clearly linked to toxic response. Microarray experiments can be affected by numerous nuisance variables including experimental designs, sample extraction, type of scanners, etc. The number of slides might be determined from the magnitude and variance of expression change, false-positive rate, and desired power. Instead, pooling samples is an alternative. Online databases on chemicals with known exposure-disease outcomes and genetic information can aid the interpretation of the normalized results. Gene function can be inferred from microarray data analyzed by bioinformatics methods such as cluster analysis. The population study often adopts hospital-based or nested case-control design. Biases in subject selection and exposure assessment should be minimized, and confounding bias should also be controlled for in stratified or multiple regression analysis. Optimal sample sizes are dependent on the statistical test for gene-to-environment or gene-to-gene interaction. The design issues addressed in this mini-review are crucial in conducting toxicogenomics study. In addition, integrative approach of exposure assessment, epidemiology, and clinical trial is required

  9. Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

    DEFF Research Database (Denmark)

    Novak, Jaroslav P; Kim, Seon-Young; Xu, Jun

    2006-01-01

    BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have...

  10. Nanotechnology: moving from microarrays toward nanoarrays.

    Science.gov (United States)

    Chen, Hua; Li, Jun

    2007-01-01

    Microarrays are important tools for high-throughput analysis of biomolecules. The use of microarrays for parallel screening of nucleic acid and protein profiles has become an industry standard. A few limitations of microarrays are the requirement for relatively large sample volumes and elongated incubation time, as well as the limit of detection. In addition, traditional microarrays make use of bulky instrumentation for the detection, and sample amplification and labeling are quite laborious, which increase analysis cost and delays the time for obtaining results. These problems limit microarray techniques from point-of-care and field applications. One strategy for overcoming these problems is to develop nanoarrays, particularly electronics-based nanoarrays. With further miniaturization, higher sensitivity, and simplified sample preparation, nanoarrays could potentially be employed for biomolecular analysis in personal healthcare and monitoring of trace pathogens. In this chapter, it is intended to introduce the concept and advantage of nanotechnology and then describe current methods and protocols for novel nanoarrays in three aspects: (1) label-free nucleic acids analysis using nanoarrays, (2) nanoarrays for protein detection by conventional optical fluorescence microscopy as well as by novel label-free methods such as atomic force microscopy, and (3) nanoarray for enzymatic-based assay. These nanoarrays will have significant applications in drug discovery, medical diagnosis, genetic testing, environmental monitoring, and food safety inspection.

  11. Integrative missing value estimation for microarray data.

    Science.gov (United States)

    Hu, Jianjun; Li, Haifeng; Waterman, Michael S; Zhou, Xianghong Jasmine

    2006-10-12

    Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS) imputation algorithm by up to 15% improvement in our benchmark tests. We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  12. Integrative missing value estimation for microarray data

    Directory of Open Access Journals (Sweden)

    Zhou Xianghong

    2006-10-01

    Full Text Available Abstract Background Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. Results We present the integrative Missing Value Estimation method (iMISS by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS imputation algorithm by up to 15% improvement in our benchmark tests. Conclusion We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  13. Decree of the Czechoslovak Atomic Energy Commission No. 191/1989 on procedures, terms and conditions for examining special professional qualification and competence of selected nuclear facility personnel

    International Nuclear Information System (INIS)

    1995-01-01

    The procedures, terms and conditions for examining special professional competence of selected nuclear facility personnel are specified, including conditions for professional training and for issuing licenses qualifying the personnel for their work. Nuclear safety-related jobs at nuclear facilities are listed. Professional licenses with a two-year term of validity are granted by the Czechoslovak Atomic Energy Agency (CSAEC) to candidates who have passed examination before the State Examination Commission. Personnel training may only be performed by bodies authorized for that by the CSAEC. The Decree entered into force on 1 January 1990. (J.B.)

  14. Discovering biological progression underlying microarray samples.

    Directory of Open Access Journals (Sweden)

    Peng Qiu

    2011-04-01

    Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

  15. Role of the State Office for Nuclear Safety in testing special professional competence of selected personnel of nuclear facilities and selected personnel handling ionizing radiation sources

    International Nuclear Information System (INIS)

    Kovar, P.

    2003-01-01

    The laws and regulations governing the title topic are identified. The following terms are defined and their context highlighted: professional competence; special professional competence; selected personnel; requirements for selected personnel; requirements for selected personnel training; examination boards; and licensing procedure. (P.A.)

  16. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 13: Part 2, Indexes. Environmental Restoration Program

    Energy Technology Data Exchange (ETDEWEB)

    Goins, L.F.; Webb, J.R.; Cravens, C.D.; Mallory, P.K.

    1992-09-01

    This is part 2 of a bibliography on nuclear facility decommissioning and site remedial action. This report contains indexes on the following: authors, corporate affiliation, title words, publication description, geographic location, subject category, and key word.

  17. An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays

    Directory of Open Access Journals (Sweden)

    Laurenzi Ian J

    2009-12-01

    Full Text Available Abstract Background Although oligonucleotide microarray technology is ubiquitous in genomic research, reproducibility and standardization of expression measurements still concern many researchers. Cross-hybridization between microarray probes and non-target ssDNA has been implicated as a primary factor in sensitivity and selectivity loss. Since hybridization is a chemical process, it may be modeled at a population-level using a combination of material balance equations and thermodynamics. However, the hybridization reaction network may be exceptionally large for commercial arrays, which often possess at least one reporter per transcript. Quantification of the kinetics and equilibrium of exceptionally large chemical systems of this type is numerically infeasible with customary approaches. Results In this paper, we present a robust and computationally efficient algorithm for the simulation of hybridization processes underlying microarray assays. Our method may be utilized to identify the extent to which nucleic acid targets (e.g. cDNA will cross-hybridize with probes, and by extension, characterize probe robustnessusing the information specified by MAGE-TAB. Using this algorithm, we characterize cross-hybridization in a modified commercial microarray assay. Conclusions By integrating stochastic simulation with thermodynamic prediction tools for DNA hybridization, one may robustly and rapidly characterize of the selectivity of a proposed microarray design at the probe and "system" levels. Our code is available at http://www.laurenzi.net.

  18. The use of microarrays in microbial ecology

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  19. 3D Biomaterial Microarrays for Regenerative Medicine

    DEFF Research Database (Denmark)

    Gaharwar, Akhilesh K.; Arpanaei, Ayyoob; Andresen, Thomas Lars

    2015-01-01

    Three dimensional (3D) biomaterial microarrays hold enormous promise for regenerative medicine because of their ability to accelerate the design and fabrication of biomimetic materials. Such tissue-like biomaterials can provide an appropriate microenvironment for stimulating and controlling stem...... for tissue engineering and drug screening applications....... cell differentiation into tissue-specifi c lineages. The use of 3D biomaterial microarrays can, if optimized correctly, result in a more than 1000-fold reduction in biomaterials and cells consumption when engineering optimal materials combinations, which makes these miniaturized systems very attractive...

  20. An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

    Science.gov (United States)

    2012-01-01

    Background The combination of chromatin immunoprecipitation with two-channel microarray technology enables genome-wide mapping of binding sites of DNA-interacting proteins (ChIP-on-chip) or sites with methylated CpG di-nucleotides (DNA methylation microarray). These powerful tools are the gateway to understanding gene transcription regulation. Since the goals of such studies, the sample preparation procedures, the microarray content and study design are all different from transcriptomics microarrays, the data pre-processing strategies traditionally applied to transcriptomics microarrays may not be appropriate. Particularly, the main challenge of the normalization of "regulation microarrays" is (i) to make the data of individual microarrays quantitatively comparable and (ii) to keep the signals of the enriched probes, representing DNA sequences from the precipitate, as distinguishable as possible from the signals of the un-enriched probes, representing DNA sequences largely absent from the precipitate. Results We compare several widely used normalization approaches (VSN, LOWESS, quantile, T-quantile, Tukey's biweight scaling, Peng's method) applied to a selection of regulation microarray datasets, ranging from DNA methylation to transcription factor binding and histone modification studies. Through comparison of the data distributions of control probes and gene promoter probes before and after normalization, and assessment of the power to identify known enriched genomic regions after normalization, we demonstrate that there are clear differences in performance between normalization procedures. Conclusion T-quantile normalization applied separately on the channels and Tukey's biweight scaling outperform other methods in terms of the conservation of enriched and un-enriched signal separation, as well as in identification of genomic regions known to be enriched. T-quantile normalization is preferable as it additionally improves comparability between microarrays. In

  1. Development and application of a microarray meter tool to optimize microarray experiments

    Directory of Open Access Journals (Sweden)

    Rouse Richard JD

    2008-07-01

    Full Text Available Abstract Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a a measure of variability in the signal intensities, b a measure of the signal dynamic range and c a measure of variability of the spot morphologies.

  2. Evaluation of a commercial microarray as a confirmation test for the presence of extended-spectrum beta-lactamases in isolates from the routine clinical setting.

    NARCIS (Netherlands)

    Platteel, T.N.; Stuart, J.W.; Voets, G.M.; Scharringa, J.; Sande, N. van de; Fluit, A.C.; Leverstein-van Hall, M.A.; Sturm, P.D.J.; et al.,

    2011-01-01

    Since the diagnostic characteristics of the Check-KPC ESBL microarray as a confirmation test on isolates obtained in a routine clinical setting have not been determined, we evaluated the microarray in a random selection of 346 clinical isolates with a positive ESBL screen test (MIC >1 mg/L for

  3. ALARA [as low as reasonably achievable] engineering at Department of Energy facilities: Bibliography of selected readings in radiation protection and ALARA

    International Nuclear Information System (INIS)

    Daniel, S.W.; Kaplan, E.; Dionne, B.J.; Khan, T.A.; Lane, S.G.; Baum, J.W.

    1989-09-01

    This report is the first in the series of bibliographies supporting the efforts at the Brookhaven National Laboratory ALARA Center on dose reduction at DOE facilities. Abstracts for this bibliography were selected from proceedings of technical meetings, journals, research reports, and searches of the DOE Energy Data Base. The abstracts included in this report relate to operational health physics as well as other subjects which have a bearing on dose reduction. Facilities covered include: radioactive waste, uranium enrichment, fabrication, unirradiated fissile materials storage, irradiated fissile material storage, reprocessing, decommissioning, recovery, hot laboratories, tritium production, reactors (research, test and production but not power reactors), and accelerators. We have also included material in improved design, materials selection, planning, and other topics which are related to dose-reduction efforts. The report contains 68 abstracts as well as subject and author indices

  4. Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

    Science.gov (United States)

    Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

    2012-06-08

    Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

  5. Fuzzy C-means method for clustering microarray data.

    Science.gov (United States)

    Dembélé, Doulaye; Kastner, Philippe

    2003-05-22

    Clustering analysis of data from DNA microarray hybridization studies is essential for identifying biologically relevant groups of genes. Partitional clustering methods such as K-means or self-organizing maps assign each gene to a single cluster. However, these methods do not provide information about the influence of a given gene for the overall shape of clusters. Here we apply a fuzzy partitioning method, Fuzzy C-means (FCM), to attribute cluster membership values to genes. A major problem in applying the FCM method for clustering microarray data is the choice of the fuzziness parameter m. We show that the commonly used value m = 2 is not appropriate for some data sets, and that optimal values for m vary widely from one data set to another. We propose an empirical method, based on the distribution of distances between genes in a given data set, to determine an adequate value for m. By setting threshold levels for the membership values, genes which are tigthly associated to a given cluster can be selected. Using a yeast cell cycle data set as an example, we show that this selection increases the overall biological significance of the genes within the cluster. Supplementary text and Matlab functions are available at http://www-igbmc.u-strasbg.fr/fcm/

  6. Principles of gene microarray data analysis.

    Science.gov (United States)

    Mocellin, Simone; Rossi, Carlo Riccardo

    2007-01-01

    The development of several gene expression profiling methods, such as comparative genomic hybridization (CGH), differential display, serial analysis of gene expression (SAGE), and gene microarray, together with the sequencing of the human genome, has provided an opportunity to monitor and investigate the complex cascade of molecular events leading to tumor development and progression. The availability of such large amounts of information has shifted the attention of scientists towards a nonreductionist approach to biological phenomena. High throughput technologies can be used to follow changing patterns of gene expression over time. Among them, gene microarray has become prominent because it is easier to use, does not require large-scale DNA sequencing, and allows for the parallel quantification of thousands of genes from multiple samples. Gene microarray technology is rapidly spreading worldwide and has the potential to drastically change the therapeutic approach to patients affected with tumor. Therefore, it is of paramount importance for both researchers and clinicians to know the principles underlying the analysis of the huge amount of data generated with microarray technology.

  7. LNA-modified isothermal oligonucleotide microarray for ...

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... the advent of DNA microarray techniques (Lee et al. 2007). ... atoms of ribose to form a bicyclic ribosyl structure. It is the .... 532 nm and emission at 570 nm. The signal ..... sis and validation using real-time PCR. Nucleic Acids ...

  8. Gene Expression Analysis Using Agilent DNA Microarrays

    DEFF Research Database (Denmark)

    Stangegaard, Michael

    2009-01-01

    Hybridization of labeled cDNA to microarrays is an intuitively simple and a vastly underestimated process. If it is not performed, optimized, and standardized with the same attention to detail as e.g., RNA amplification, information may be overlooked or even lost. Careful balancing of the amount ...

  9. Microarrays (DNA Chips) for the Classroom Laboratory

    Science.gov (United States)

    Barnard, Betsy; Sussman, Michael; BonDurant, Sandra Splinter; Nienhuis, James; Krysan, Patrick

    2006-01-01

    We have developed and optimized the necessary laboratory materials to make DNA microarray technology accessible to all high school students at a fraction of both cost and data size. The primary component is a DNA chip/array that students "print" by hand and then analyze using research tools that have been adapted for classroom use. The…

  10. Comparing transformation methods for DNA microarray data

    NARCIS (Netherlands)

    Thygesen, Helene H.; Zwinderman, Aeilko H.

    2004-01-01

    Background: When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include

  11. Design of a system for examinations of the history of operation of selected WWER primary circuit facilities. Stage I: requirements

    International Nuclear Information System (INIS)

    Brumovsky, M.; Kraus, V.; Ruscak, M.; Vejvoda, S.

    1994-01-01

    A survey is presented of data required for the evaluation and control of nuclear power plant aging and service life, and a data acquisition and record-keeping system is proposed. The data fall in 3 classes: (i) information on the initial status, including design data and status data at the beginning of the operational lifetime of the facilities; (ii) data on the history of operation, including operating conditions at the level of the corresponding system and facility, as well as operating test and failure data; and (iii) data on the history of maintenance, including data on the monitoring of the facility condition and on maintenance. Basic information requirements for the evaluation of the service life of the pressure vessel, steam generator, pressurizer, and main circulation pipe are given; the way of processing this information is outlined. (J.B.). 2 figs

  12. Microarray analysis identified Puccinia striiformis f. sp. tritici genes involved in infection and sporulation.

    Science.gov (United States)

    Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, one of the most important diseases of wheat worldwide. To identify Pst genes involved in infection and sporulation, a custom oligonucleotide Genechip was made using sequences of 442 genes selected from Pst cDNA libraries. Microarray analy...

  13. Transcription analysis of apple fruit development using cDNA microarrays

    NARCIS (Netherlands)

    Soglio, V.; Costa, F.; Molthoff, J.W.; Weemen-Hendriks, M.; Schouten, H.J.; Gianfranceschi, L.

    2009-01-01

    The knowledge of the molecular mechanisms underlying fruit quality traits is fundamental to devise efficient marker-assisted selection strategies and to improve apple breeding. In this study, cDNA microarray technology was used to identify genes whose expression changes during fruit development and

  14. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    2010-09-01

    Full Text Available International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  15. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  16. Facile one-step direct electrodeposition of bismuth nanowires on glassy carbon electrode for selective determination of folic acid

    International Nuclear Information System (INIS)

    Ananthi, Arjunan; Kumar, Shanmugam Senthil; Phani, Kanala Lakshminarasimha

    2015-01-01

    Highlights: • BiNWs prepared through simple, fast one step electrochemical route. • BiNWs showed more catalytic activity and sensitivity than GC towards FA reduction. • Selective detection of FA was achieved with low limit of detection (9.53 × 10 −9 mol L −1 ). • Real sample analysis was successfully demonstrated using FA pharmaceutical tablets. • BiNWs based sensor matrix is inexpensive, and more suitable for FA real application. - Abstract: In the present work, we have developed a facile one step route to electrodeposition of stabilizer-free bismuth nanowires (BiNWs) on glassy carbon (GC) substrates by using a simple potentiostatic method. Formation of BiNWs on GC substrate was confirmed by field emission scanning electron microscopy (FE-SEM). The growth of BiNWs on the GC substrate was monitored by cyclic voltammetry and found that continuous in-situ generation of hydrogen bubbles during electrodeposition provides a stagnant template for the formation of BiNWs on the GC substrate. Phase-purity of the deposited BiNWs on GC substrate studied by XRD indicates no other oxide formation. The electrodeposited BiNWs on GC substrate was used for electro-reduction of folic acid (FA) and its quantitative determination in Britton-Robinson buffer of pH 4.5 solutions. The observed cyclic voltammetric reduction current of FA on BiNWs/GC is almost 15 times higher with 0.015 V less negative overpotential compared to bare GC substrate alone. This result clearly reveals the electrocatalytic activity of the deposited BiNWs. In addition, square wave voltammetry (SWV) showed a perfectly linear response in the concentration range of 1 × 10 −8 –15 × 10 −8 mol L −1 with a correlation coefficient of 0.9956. The limit of detection (LOD) and limit of quantitation (LOQ) are determined to be 9.53 × 10 −9 and 31.68 × 10 −9 mol L −1 respectively. The response of the BiNWs/GC sensor matrix is not affected by any usual interference from excess concentrations of

  17. Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jianping Hua

    2004-01-01

    Full Text Available This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney test-based algorithm to segment cDNA microarray images, and performs postprocessing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with the background adjustment, are then used for independent compression of the foreground and background. We introduce a new distortion measurement for cDNA microarray image compression and devise a coding scheme by modifying the embedded block coding with optimized truncation (EBCOT algorithm (Taubman, 2000 to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that the bit rate required to ensure sufficiently accurate gene expression measurement varies and depends on the quality of cDNA microarray images. For homogeneously hybridized cDNA microarray images, BASICA is able to provide from a bit rate as low as 5 bpp the gene expression data that are 99% in agreement with those of the original 32 bpp images.

  18. Morbidity profile of elderly outpatients attending selected sub-district Siddha health facilities in Tamil Nadu, India

    Directory of Open Access Journals (Sweden)

    Kalaiselvi Selvaraj

    2016-01-01

    Conclusion: Elderly constitute more than one fourth of outpatients load from siddha health facilities. Degenerative diseases like arthritis and non-communicable diseases were the common morbidities in this age group. Geriatric clinics and mobile clinics under siddha system may help in improving health care services.

  19. Factors determining the concentration and chemical composition of particulate matter in the air of selected service facilities

    Science.gov (United States)

    Rogula-Kopiec, Patrycja; Pastuszka, Józef; Mathews, Barbara; Widziewicz, Kamila

    2018-01-01

    The link between increased morbidity and mortality and increasing concentrations of particulate matter (PM) resulted in great attention being paid to the presence and physicochemical properties of PM in closed rooms, where people spends most of their time. The least recognized group of such indoor environments are small service facilities. The aim of this study was to identify factors which determine the concentration, chemical composition and sources of PM in the air of different service facilities: restaurant kitchen, printing office and beauty salon. The average PM concentration measured in the kitchen was 5-fold (PM4, particle fraction ≥ 4 μm) and 5.3-fold (TSP, total PM) greater than the average concentration of these PM fractions over the same period. During the same measurement period in the printing office and in the beauty salon, the mean PM concentration was 10- and 4-fold (PM4) and 8- and 3-fold (TSP) respectively greater than the mean concentration of these PM fractions in outdoor air. In both facilities the main source of PM macro-components, especially organic carbon, were chemicals, which are normally used in such places - solvents, varnishes, paints, etc. The influence of some metals inflow from the outdoor air into indoor environment of those facilities was also recognized.

  20. Assessment of laboratory logistics management information system practice for HIV/AIDS and tuberculosis laboratory commodities in selected public health facilities in Addis Ababa, Ethiopia.

    Science.gov (United States)

    Desale, Adino; Taye, Bineyam; Belay, Getachew; Nigatu, Alemayehu

    2013-01-01

    Logistics management information system for health commodities remained poorly implemented in most of developing countries. To assess the status of laboratory logistics management information system for HIV/AIDS and tuberculosis laboratory commodities in public health facilities in Addis Ababa. A cross-sectional descriptive study was conducted from September 2010-January 2011 at selected public health facilities. A stratified random sampling method was used to include a total of 43 facilities which, were investigated through quantitative methods using structured questionnaires interviews. Focus group discussion with the designated supply chain managers and key informant interviews were conducted for the qualitative method. There exists a well-designed logistics system for laboratory commodities with trained pharmacy personnel, distributed standard LMIS formats and established inventory control procedures. However, majority of laboratory professionals were not trained in LMIS. Majority of the facilities (60.5%) were stocked out for at least one ART monitoring and TB laboratory reagents and the highest stock out rate was for chemistry reagents. Expired ART monitoring laboratory commodities were found in 25 (73.5%) of facilities. Fifty percent (50%) of the assessed hospitals and 54% of health centers were currently using stock/bin cards for all HIV/AIDS and TB laboratory commodities in main pharmacy store, among these only 25% and 20.8% of them were updated with accurate information matching with the physical count done at the time of visit for hospitals and health centers respectively. Even though there exists a well designed laboratory LMIS, keeping quality stock/bin cards and LMIS reports were very low. Key ART monitoring laboratory commodities were stock out at many facilities at the day of visit and during the past six months. Based on findings, training of laboratory personnel's managing laboratory commodities and keeping accurate inventory control procedures

  1. Assessment of laboratory logistics management information system practice for HIV/AIDS and tuberculosis laboratory commodities in selected public health facilities in Addis Ababa, Ethiopia

    Science.gov (United States)

    Desale, Adino; Taye, Bineyam; Belay, Getachew; Nigatu, Alemayehu

    2013-01-01

    Introduction Logistics management information system for health commodities remained poorly implemented in most of developing countries. To assess the status of laboratory logistics management information system for HIV/AIDS and tuberculosis laboratory commodities in public health facilities in Addis Ababa. Methods A cross-sectional descriptive study was conducted from September 2010-January 2011 at selected public health facilities. A stratified random sampling method was used to include a total of 43 facilities which, were investigated through quantitative methods using structured questionnaires interviews. Focus group discussion with the designated supply chain managers and key informant interviews were conducted for the qualitative method. Results There exists a well-designed logistics system for laboratory commodities with trained pharmacy personnel, distributed standard LMIS formats and established inventory control procedures. However, majority of laboratory professionals were not trained in LMIS. Majority of the facilities (60.5%) were stocked out for at least one ART monitoring and TB laboratory reagents and the highest stock out rate was for chemistry reagents. Expired ART monitoring laboratory commodities were found in 25 (73.5%) of facilities. Fifty percent (50%) of the assessed hospitals and 54% of health centers were currently using stock/bin cards for all HIV/AIDS and TB laboratory commodities in main pharmacy store, among these only 25% and 20.8% of them were updated with accurate information matching with the physical count done at the time of visit for hospitals and health centers respectively. Conclusion Even though there exists a well designed laboratory LMIS, keeping quality stock/bin cards and LMIS reports were very low. Key ART monitoring laboratory commodities were stock out at many facilities at the day of visit and during the past six months. Based on findings, training of laboratory personnel's managing laboratory commodities and keeping

  2. SEISMIC DESIGN REQUIREMENTS SELECTION METHODOLOGY FOR THE SLUDGE TREATMENT and M-91 SOLID WASTE PROCESSING FACILITIES PROJECTS

    International Nuclear Information System (INIS)

    RYAN GW

    2008-01-01

    In complying with direction from the U.S. Department of Energy (DOE), Richland Operations Office (RL) (07-KBC-0055, 'Direction Associated with Implementation of DOE-STD-1189 for the Sludge Treatment Project,' and 08-SED-0063, 'RL Action on the Safety Design Strategy (SDS) for Obtaining Additional Solid Waste Processing Capabilities (M-91 Project) and Use of Draft DOE-STD-I 189-YR'), it has been determined that the seismic design requirements currently in the Project Hanford Management Contract (PHMC) will be modified by DOE-STD-1189, Integration of Safety into the Design Process (March 2007 draft), for these two key PHMC projects. Seismic design requirements for other PHMC facilities and projects will remain unchanged. Considering the current early Critical Decision (CD) phases of both the Sludge Treatment Project (STP) and the Solid Waste Processing Facilities (M-91) Project and a strong intent to avoid potentially costly re-work of both engineering and nuclear safety analyses, this document describes how Fluor Hanford, Inc. (FH) will maintain compliance with the PHMC by considering both the current seismic standards referenced by DOE 0 420.1 B, Facility Safety, and draft DOE-STD-1189 (i.e., ASCE/SEI 43-05, Seismic Design Criteria for Structures, Systems, and Components in Nuclear Facilities, and ANSI ANS 2.26-2004, Categorization of Nuclear Facility Structures, Systems and Components for Seismic Design, as modified by draft DOE-STD-1189) to choose the criteria that will result in the most conservative seismic design categorization and engineering design. Following the process described in this document will result in a conservative seismic design categorization and design products. This approach is expected to resolve discrepancies between the existing and new requirements and reduce the risk that project designs and analyses will require revision when the draft DOE-STD-1189 is finalized

  3. The evaluation of the performance of the automatic exposure control system of some selected mammography facilities in the Greater Accra Region, Ghana

    International Nuclear Information System (INIS)

    Amesimenu, R.

    2013-07-01

    Mammography aids in the early detection of breast cancer. X-rays has an associated risk of inducing cancer though very useful and as such mammography procedures should be optimized through the appropriate processes such as the selection of exposure factors for an optimum image and minimal dose to patients. The automatic exposure control (AEC) aids in the selection of exposure factors thus controlling the amount of radiation to the breast and automatically compensates for differences in the breast thickness and density. The performance of the automatic exposure control system of mammography equipment and the status of quality management systems including quality assurance and quality controls of four (4) mammography facilities within the Greater Accra Region were assessed. In assessing the performance of the automatic exposure control system, the short term reproducibility test, thickness and voltage compensation test were carried out using breast equivalent phantom of various thicknesses. Half value layer test, film reject analysis and patient dose assessment were also performed. Analysis of the responses of the questionnaire administered to radiographers and supervisors of the selected facilities revealed that three (3) of the facilities have some aspect of quality management system programme in place but not effectively implemented. Measured optical densities from the various tests performed to evaluate the performance of the automatic exposure control systems revealed that the AEC compensates for the different phantom thickness and tube voltage (KV) by producing comparable optical densities for the various phantom thickness and tube voltages. Some of the measured optical densities were within the recommended optical density range of 1.5 OD - 1.9 OD. The highest optical density value was 0.13 OD above the highest limit of 1.9 OD. The film reject analysis showed that patient motion accounted for the large part (28%) of film rejects. Other factors such as too light

  4. Screening for C3 deficiency in newborns using microarrays.

    Directory of Open Access Journals (Sweden)

    Magdalena Janzi

    Full Text Available BACKGROUND: Dried blood spot samples (DBSS from newborns are widely used in neonatal screening for selected metabolic diseases and diagnostic possibilities for additional disorders are continuously being evaluated. Primary immunodeficiency disorders comprise a group of more than one hundred diseases, several of which are fatal early in life. Yet, a majority of the patients are not diagnosed due to lack of high-throughput screening methods. METHODOLOGY/PRINCIPAL FINDINGS: We have previously developed a system using reverse phase protein microarrays for analysis of IgA levels in serum samples. In this study, we extended the applicability of the method to include determination of complement component C3 levels in eluates from DBSS collected at birth. Normal levels of C3 were readily detected in 269 DBSS from healthy newborns, while no C3 was detected in sera and DBSS from C3 deficient patients. CONCLUSIONS/SIGNIFICANCE: The findings suggest that patients with deficiencies of specific serum proteins can be identified by analysis of DBSS using reverse phase protein microarrays.

  5. Microarray Dot Electrodes Utilizing Dielectrophoresis for Cell Characterization

    Directory of Open Access Journals (Sweden)

    Fatimah Ibrahim

    2013-07-01

    Full Text Available During the last three decades; dielectrophoresis (DEP has become a vital tool for cell manipulation and characterization due to its non-invasiveness. It is very useful in the trend towards point-of-care systems. Currently, most efforts are focused on using DEP in biomedical applications, such as the spatial manipulation of cells, the selective separation or enrichment of target cells, high-throughput molecular screening, biosensors and immunoassays. A significant amount of research on DEP has produced a wide range of microelectrode configurations. In this paper; we describe the microarray dot electrode, a promising electrode geometry to characterize and manipulate cells via DEP. The advantages offered by this type of microelectrode are also reviewed. The protocol for fabricating planar microelectrodes using photolithography is documented to demonstrate the fast and cost-effective fabrication process. Additionally; different state-of-the-art Lab-on-a-Chip (LOC devices that have been proposed for DEP applications in the literature are reviewed. We also present our recently designed LOC device, which uses an improved microarray dot electrode configuration to address the challenges facing other devices. This type of LOC system has the capability to boost the implementation of DEP technology in practical settings such as clinical cell sorting, infection diagnosis, and enrichment of particle populations for drug development.

  6. Healthcare waste management status in Lagos State, Nigeria: a case study from selected healthcare facilities in Ikorodu and Lagos metropolis.

    Science.gov (United States)

    Longe, Ezechiel O

    2012-06-01

    A survey of healthcare waste management practices and their implications for health and the environment was carried out. The study assessed waste management practices in 20 healthcare facilities ranging in capacity from 40 to 600 beds in Ikorodu and metropolitan Lagos, Lagos State, Nigeria. The prevailing healthcare waste management status was analysed. Management issues on quantities and proportion of different constituents of waste, segregation, collection, handling, transportation, treatment and disposal methods were assessed. The waste generation averaged 0.631 kg bed(-1) day(-1) over the survey area. The waste stream from the healthcare facilities consisted of general waste (59.0%), infectious waste (29.7%), sharps and pathological (8.9%), chemical (1.45%) and others (0.95%). Sharps/pathological waste includes disposable syringes. In general, the waste materials were collected in a mixed form, transported and disposed of along with municipal solid waste with attendant risks to health and safety. Most facilities lacked appropriate treatment systems for a variety of reasons that included inadequate funding and little or no priority for healthcare waste management as well as a lack of professionally competent waste managers among healthcare providers. Hazards associated with healthcare waste management and shortcomings in the existing system were identified.

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

    Directory of Open Access Journals (Sweden)

    Stear Michael

    2003-03-01

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

  8. DNA Microarrays in Comparative Genomics and Transcriptomics

    DEFF Research Database (Denmark)

    Willenbrock, Hanni

    2007-01-01

    at identifying the exact breakpoints where DNA has been gained or lost. In this thesis, three popular methods are compared and a realistic simulation model is presented for generating artificial data with known breakpoints and known DNA copy number. By using simulated data, we obtain a realistic evaluation......During the past few years, innovations in the DNA sequencing technology has led to an explosion in available DNA sequence information. This has revolutionized biological research and promoted the development of high throughput analysis methods that can take advantage of the vast amount of sequence...... data. For this, the DNA microarray technology has gained enormous popularity due to its ability to measure the presence or the activity of thousands of genes simultaneously. Microarrays for high throughput data analyses are not limited to a few organisms but may be applied to everything from bacteria...

  9. Immobilization Techniques for Microarray: Challenges and Applications

    Directory of Open Access Journals (Sweden)

    Satish Balasaheb Nimse

    2014-11-01

    Full Text Available The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

  10. Mining meiosis and gametogenesis with DNA microarrays.

    Science.gov (United States)

    Schlecht, Ulrich; Primig, Michael

    2003-04-01

    Gametogenesis is a key developmental process that involves complex transcriptional regulation of numerous genes including many that are conserved between unicellular eukaryotes and mammals. Recent expression-profiling experiments using microarrays have provided insight into the co-ordinated transcription of several hundred genes during mitotic growth and meiotic development in budding and fission yeast. Furthermore, microarray-based studies have identified numerous loci that are regulated during the cell cycle or expressed in a germ-cell specific manner in eukaryotic model systems like Caenorhabditis elegans, Mus musculus as well as Homo sapiens. The unprecedented amount of information produced by post-genome biology has spawned novel approaches to organizing biological knowledge using currently available information technology. This review outlines experiments that contribute to an emerging comprehensive picture of the molecular machinery governing sexual reproduction in eukaryotes.

  11. Facilitating RNA structure prediction with microarrays.

    Science.gov (United States)

    Kierzek, Elzbieta; Kierzek, Ryszard; Turner, Douglas H; Catrina, Irina E

    2006-01-17

    Determining RNA secondary structure is important for understanding structure-function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2'-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve the prediction of that secondary structure. When experimental constraints from hybridization results are added to a free-energy minimization algorithm, the prediction of the secondary structure of Escherichia coli 5S rRNA improves from 27 to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2'-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.

  12. Plasmonically amplified fluorescence bioassay with microarray format

    Science.gov (United States)

    Gogalic, S.; Hageneder, S.; Ctortecka, C.; Bauch, M.; Khan, I.; Preininger, Claudia; Sauer, U.; Dostalek, J.

    2015-05-01

    Plasmonic amplification of fluorescence signal in bioassays with microarray detection format is reported. A crossed relief diffraction grating was designed to couple an excitation laser beam to surface plasmons at the wavelength overlapping with the absorption and emission bands of fluorophore Dy647 that was used as a label. The surface of periodically corrugated sensor chip was coated with surface plasmon-supporting gold layer and a thin SU8 polymer film carrying epoxy groups. These groups were employed for the covalent immobilization of capture antibodies at arrays of spots. The plasmonic amplification of fluorescence signal on the developed microarray chip was tested by using interleukin 8 sandwich immunoassay. The readout was performed ex situ after drying the chip by using a commercial scanner with high numerical aperture collecting lens. Obtained results reveal the enhancement of fluorescence signal by a factor of 5 when compared to a regular glass chip.

  13. 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....

  14. Factors affecting acceptance of provider-initiated HIV testing and counseling services among outpatient clients in selected health facilities in Harar Town, Eastern Ethiopia

    Directory of Open Access Journals (Sweden)

    Abdurahman S

    2015-05-01

    Full Text Available Sami Abdurahman,1 Berhanu Seyoum,2 Lemessa Oljira,2 Fitsum Weldegebreal2 1Harari Regional Health Bureau, 2Haramaya University, College of Health and Medical Sciences, Harar, Ethiopia Purpose: To improve the slow uptake of HIV counseling and testing, the World Health Organization (WHO and the Joint United Nations Programme on HIV/AIDS (UNAIDS have developed draft guidelines on provider-initiated testing and counseling (PITC. Both in low- and high-income countries, mainly from outpatient clinics and tuberculosis settings, indicates that the direct offer of HIV testing by health providers can result in significant improvements in test uptake. In Ethiopia, there were limited numbers of studies conducted regarding PITC in outpatient clinics. Therefore, in this study, we have assessed the factors affecting the acceptance of PITC among outpatient clients in selected health facilities in Harar, Harari Region State, Ethiopia. Materials and methods: Institutional-based, cross-sectional quantitative and qualitative studies were conducted from February 12–30, 2011 in selected health facilities in Harar town, Harari Region State, Ethiopia. The study participants were recruited from the selected health facilities of Harar using a systematic random sampling technique. The collected data were double entered into a data entry file using Epi Info version 3.5.1. The data were transferred to SPSS software version 16 and analyzed according to the different variables. Results: A total of 362 (70.6% clients accepted PITC, and only 39.4% of clients had heard of PITC in the outpatient department service. Age, occupation, marital status, anyone who wanted to check their HIV status, and the importance of PITC were the variables that showed significant associations with the acceptance of PITC upon bivariate and multivariate analyses. The main reasons given for not accepting the tests were self-trust, not being at risk for HIV, not being ready, needing to consult their

  15. Geiger mode avalanche photodiodes for microarray systems

    Science.gov (United States)

    Phelan, Don; Jackson, Carl; Redfern, R. Michael; Morrison, Alan P.; Mathewson, Alan

    2002-06-01

    New Geiger Mode Avalanche Photodiodes (GM-APD) have been designed and characterized specifically for use in microarray systems. Critical parameters such as excess reverse bias voltage, hold-off time and optimum operating temperature have been experimentally determined for these photon-counting devices. The photon detection probability, dark count rate and afterpulsing probability have been measured under different operating conditions. An active- quench circuit (AQC) is presented for operating these GM- APDs. This circuit is relatively simple, robust and has such benefits as reducing average power dissipation and afterpulsing. Arrays of these GM-APDs have already been designed and together with AQCs open up the possibility of having a solid-state microarray detector that enables parallel analysis on a single chip. Another advantage of these GM-APDs over current technology is their low voltage CMOS compatibility which could allow for the fabrication of an AQC on the same device. Small are detectors have already been employed in the time-resolved detection of fluorescence from labeled proteins. It is envisaged that operating these new GM-APDs with this active-quench circuit will have numerous applications for the detection of fluorescence in microarray systems.

  16. Facile and Selective Synthesis of 2-Substituted Benzimidazoles Catalyzed by FeCl3/ Al2O3

    Directory of Open Access Journals (Sweden)

    Guo-Feng Chen

    2012-01-01

    Full Text Available 2-Substituted benzimidazoles were synthesized in a single pot from aromatic aldehydes and o-phenylenediamine catalyzed by FeCl3/ Al2O3 in DMF at ambient temperature attained good yields and high selectivity.

  17. Seismic assessment of selected buildings and equipment contents of a DOE facility in UBC zone 2A

    International Nuclear Information System (INIS)

    Tong, W.H.; Deneff, C.; Griffin, M.J.

    1991-01-01

    A preliminary seismic risk assessment for selected buildings and representative equipment contents in Allied-Signal Kansas City Division was performed to identify potential seismic hazard and weakness. The site is located in the Uniform Building Code Zone 2A. The selected building structures were constructed between 1940s to 1980s. The performance goal was to qualitatively assess the potential for loss of toxic or hazardous materials and injury to plant personnel due to an earthquake event

  18. Use of strategic environmental assessment in the site selection process for a radioactive waste disposal facility in Slovenia.

    Science.gov (United States)

    Dermol, Urška; Kontić, Branko

    2011-01-01

    The benefits of strategic environmental considerations in the process of siting a repository for low- and intermediate-level radioactive waste (LILW) are presented. The benefits have been explored by analyzing differences between the two site selection processes. One is a so-called official site selection process, which is implemented by the Agency for radwaste management (ARAO); the other is an optimization process suggested by experts working in the area of environmental impact assessment (EIA) and land-use (spatial) planning. The criteria on which the comparison of the results of the two site selection processes has been based are spatial organization, environmental impact, safety in terms of potential exposure of the population to radioactivity released from the repository, and feasibility of the repository from the technical, financial/economic and social point of view (the latter relates to consent by the local community for siting the repository). The site selection processes have been compared with the support of the decision expert system named DEX. The results of the comparison indicate that the sites selected by ARAO meet fewer suitability criteria than those identified by applying strategic environmental considerations in the framework of the optimization process. This result stands when taking into account spatial, environmental, safety and technical feasibility points of view. Acceptability of a site by a local community could not have been tested, since the formal site selection process has not yet been concluded; this remains as an uncertain and open point of the comparison. Copyright © 2010 Elsevier Ltd. All rights reserved.

  19. Serious limitations of the QTL/Microarray approach for QTL gene discovery

    Directory of Open Access Journals (Sweden)

    Warden Craig H

    2010-07-01

    Full Text Available Abstract Background It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL. However, the effectiveness of this approach has not been assessed. Results Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons between congenic and background strains. Three studies led to the identification of an underlying QTL gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of QTL regulated in cis (cis eQTL showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP. Conclusions The literature shows limited successes from the QTL/microarray approach to identify QTL genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select cis-eQTL over trans-eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false cis-eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes

  20. Scientific Symposium “Small Solution for Big Water-Related Problems: Innovative Microarrays and Small Sensors to Cope with Water Quality and Food Security”

    Directory of Open Access Journals (Sweden)

    Stefania Marcheggiani

    2015-12-01

    Full Text Available This issue presents the conclusive results of two European Commission funded Projects, namely Universal Microarrays for the Evaluation of Fresh-water Quality Based on Detection of Pathogens and their Toxins (MicroAQUA and Rationally Designed Aquatic Receptors (RADAR. These projects focused their activities on the quality of drinking water as an extremely important factor for public health of humans and animals. The MicroAQUA Project aimed at developing a universal microarray chip for the detection of various pathogens (cyanobacteria, bacteria, viruses and parasitic protozoa and their toxins in waters. In addition, the project included the detection of select species of diatoms, which represent reliable bio-indicators to assess overall water quality. Large numbers of compounds are released into the environment; some of these are toxins such as endocrine disrupting compounds (EDCs and can affect the endocrine, immune and nervous systems of a wide range of animals causing alterations such as reproductive disorders and cancer. Detection of these contaminants in water systems is important to protect sensitive environmental sites and reduce the risk of toxins entering the food chain. A modular platform for monitoring toxins in water and food production facilities, using biosensors derived from aquatic organisms, was the main goal of RADAR Project.

  1. Radioactive waste packages stored at the Aube facility for low-intermediate activity wastes. A selective and controlled storage

    International Nuclear Information System (INIS)

    2005-01-01

    The waste package is the first barrier designed to protect the man and the environment from the radioactivity contained in wastes. Its design is thus particularly stringent and controlled. This brochure describes the different types of packages for low to intermediate activity wastes like those received and stored at the Aube facility, and also the system implemented by the ANDRA (the French national agency of radioactive wastes) and by waste producers to safely control each step of the design and fabrication of these packages. (J.S.)

  2. Selection of the reference concept for the surface examination stations in the fuels and materials examination facility

    International Nuclear Information System (INIS)

    Frandsen, G.B.; Nash, C.R.

    1978-01-01

    The prototype surface examination station for the Fuels and Materials Examination Facility (FMEF) will use closed circuit television (CCTV) for routine modes of operation along with a nuclear periscope for special examination needs. The CCTV and the nuclear periscope were evaluated against prescribed station requirements and compared in a side-by-side demonstration. A quantitative evaluation of their outputs showed that both systems were capable of meeting surface anomaly detection requirements. The CCTV system was superior in its ability to collect, suppress and present data into a more useful form for the experimenters

  3. Radioactive cDNA microarray (II): Gene expression profiling of antidepressant treatment by human cDNA microarray

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ji Hye; Kang, Rhee Hun; Ham, Byung Joo; Lee, Min Su; Shin, Kyung Ho; Choe, Jae Gol; Kim, Meyoung Kon [College of Medicine, Univ. of Korea, Seoul (Korea, Republic of)

    2003-07-01

    Major depressive disorder is a prevalent psychiatric disorder in primary care, associated with impaired patient functioning and well-being. Fluoxetine is a selective serotonin-reuptake inhibitors (SSRIs) and is a commonly prescribed antidepressant compound. Its action is primarily attributed to selective inhibition of the reuptake of serotonin (5-hydroxytryptamine) in the central nervous system. Objectives ; the aims of this study were two-fold: (1) to determine the usefulness for investigation of the transcription profiles in depression patients, and (2) to assess the differences in gene expression profiles between positive response group and negative response groups by fluoxetine treatment. This study included 53 patients with major depression (26 in positive response group with antidepressant treatment, 27 in negative response group with antidepressant treatment), and 53 healthy controls. To examine the difference of gene expression profile in depression patients, radioactive complementary DNA microarrays were used to evaluate changes in the expression of 1,152 genes in total. Using 33p-labeled probes, this method provided highly sensitive gene expression profiles including brain receptors, drug metabolism, and cellular signaling. Gene transcription profiles were classified into several categories in accordance with the antidepressant gene-regulation. The gene profiles were significantly up-(22 genes) and down-(16 genes) regulated in the positive response group when compared to the control group. Also, in the negative response group, 35 genes were up-regulated and 8 genes were down-regulated when compared to the control group. Consequently, we demonstrated that radioactive human cDNA microarray is highly likely to be an efficient technology for evaluating the gene regulation of antidepressants, such as selective serotonin-reuptake inhibitors (SSRIs), by using high-throughput biotechnology.

  4. Radioactive cDNA microarray (II): Gene expression profiling of antidepressant treatment by human cDNA microarray

    International Nuclear Information System (INIS)

    Lee, Ji Hye; Kang, Rhee Hun; Ham, Byung Joo; Lee, Min Su; Shin, Kyung Ho; Choe, Jae Gol; Kim, Meyoung Kon

    2003-01-01

    Major depressive disorder is a prevalent psychiatric disorder in primary care, associated with impaired patient functioning and well-being. Fluoxetine is a selective serotonin-reuptake inhibitors (SSRIs) and is a commonly prescribed antidepressant compound. Its action is primarily attributed to selective inhibition of the reuptake of serotonin (5-hydroxytryptamine) in the central nervous system. Objectives ; the aims of this study were two-fold: (1) to determine the usefulness for investigation of the transcription profiles in depression patients, and (2) to assess the differences in gene expression profiles between positive response group and negative response groups by fluoxetine treatment. This study included 53 patients with major depression (26 in positive response group with antidepressant treatment, 27 in negative response group with antidepressant treatment), and 53 healthy controls. To examine the difference of gene expression profile in depression patients, radioactive complementary DNA microarrays were used to evaluate changes in the expression of 1,152 genes in total. Using 33p-labeled probes, this method provided highly sensitive gene expression profiles including brain receptors, drug metabolism, and cellular signaling. Gene transcription profiles were classified into several categories in accordance with the antidepressant gene-regulation. The gene profiles were significantly up-(22 genes) and down-(16 genes) regulated in the positive response group when compared to the control group. Also, in the negative response group, 35 genes were up-regulated and 8 genes were down-regulated when compared to the control group. Consequently, we demonstrated that radioactive human cDNA microarray is highly likely to be an efficient technology for evaluating the gene regulation of antidepressants, such as selective serotonin-reuptake inhibitors (SSRIs), by using high-throughput biotechnology

  5. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 13: Part 1, Main text. Environmental Restoration Program

    Energy Technology Data Exchange (ETDEWEB)

    Goins, L.F.; Webb, J.R.; Cravens, C.D.; Mallory, P.K.

    1992-09-01

    This publication contains 1035 abstracted references on environmental restoration, nuclear facility decommissioning, uranium mill tailings management, and site remedial actions. These citations constitute the thirteenth in a series of reports prepared annually for the US Department of Energy (DOE) Environmental Restoration programs. Citations to foreign and domestic literature of all types. There are 13 major sections of the publication, including: (1) DOE Decontamination and Decommissioning Program; (2) Nuclear Facilities Decommissioning; (3) DOE Formerly Utilized Sites Remedial Action Program; (4) DOE Uranium Mill Tailings Remedial Action Project; (5) Uranium Mill Tailings Management; (6) DOE Environmental Restoration Program; (7) DOE Site-Specific Remedial Actions; (8) Contaminated Site Restoration; (9) Remediation of Contaminated Soil and Groundwater; (10) Environmental Data Measurements, Management, and Evaluation; (11) Remedial Action Assessment and Decision-Making; (12) Technology Development and Evaluation; and (13) Environmental and Waste Management Issues. Bibliographic references are arranged in nine subject categories by geographic location and then alphabetically by first author, corporate affiliation, or publication title. Indexes are provided for author, corporate affiliation, title word, publication description, geographic location, subject category, and key word.

  6. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam

    2016-10-09

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  7. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam; Subudhi, Amit; Middha, Sheetal; Acharya, Jyoti; Mugasimangalam, Raja Chinnadurai; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Das, Ashis

    2016-01-01

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  8. Effects of increased nurses’ workload on quality documentation of patient information at selected Primary Health Care facilities in Vhembe District, Limpopo Province

    Directory of Open Access Journals (Sweden)

    Rhulani C. Shihundla

    2016-05-01

    nature. The population consisted of all nurses who work at PHC facilities in Vhembe District. Purposive sampling was used to select nurses and three professional nurses were sampled from each PHC facility. An in-depth face-to-face interview was used to collect data using an interview guide. Results: PHC facilities encountered several effects due to increased nurses’ workload where incomplete patient information is documented. Unavailability of patient information was observed, whilst some documented information was found to be illegible, inaccurate and incomplete. Conclusion: Documentation of information at PHC facilities is an evidence of effective communication amongst professional nurses. There should always be active follow-up and mentoring of the nurses’ documentation to ensure that information is accurately and fully documented in their respective facilities. Nurses find it difficult to cope with the increased workload associated with documenting patient information on the multiple records that are utilized at PHC facilities, leading to incomplete information. The number of nurses at facilities should be increased to reduce the increased workload. Keywords: Effects; increased; professional nurses’; work-load; quality nursing documentation; patient information

  9. Effects of increased nurses' workload on quality documentation of patient information at selected Primary Health Care facilities in Vhembe District, Limpopo Province.

    Science.gov (United States)

    Shihundla, Rhulani C; Lebese, Rachel T; Maputle, Maria S

    2016-05-13

    work at PHC facilities in Vhembe District. Purposive sampling was used to select nurses and three professional nurses were sampled from each PHC facility. An in-depth face-to-face interview was used to collect data using an interview guide. PHC facilities encountered several effects due to increased nurses' workload where incomplete patient information is documented. Unavailability of patient information was observed, whilst some documented information was found to be illegible, inaccurate and incomplete. Documentation of information at PHC facilities is an evidence of effective communication amongst professional nurses. There should always be active follow-up and mentoring of the nurses' documentation to ensure that information is accurately and fully documented in their respective facilities. Nurses find it difficult to cope with the increased workload associated with documenting patient information on the multiple records that are utilized at PHC facilities, leading to incomplete information. The number of nurses at facilities should be increased to reduce the increased workload.

  10. Reverse phase protein microarray technology in traumatic brain injury.

    Science.gov (United States)

    Gyorgy, Andrea B; Walker, John; Wingo, Dan; Eidelman, Ofer; Pollard, Harvey B; Molnar, Andras; Agoston, Denes V

    2010-09-30

    Antibody based, high throughput proteomics technology represents an exciting new approach in understanding the pathobiologies of complex disorders such as cancer, stroke and traumatic brain injury. Reverse phase protein microarray (RPPA) can complement the classical methods based on mass spectrometry as a high throughput validation and quantification method. RPPA technology can address problematic issues, such as sample complexity, sensitivity, quantification, reproducibility and throughput, which are currently associated with mass spectrometry-based approaches. However, there are technical challenges, predominantly associated with the selection and use of antibodies, preparation and representation of samples and with analyzing and quantifying primary RPPA data. Here we present ways to identify and overcome some of the current issues associated with RPPA. We believe that using stringent quality controls, improved bioinformatics analysis and interpretation of primary RPPA data, this method will significantly contribute in generating new level of understanding about complex disorders at the level of systems biology. Published by Elsevier B.V.

  11. Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray

    Directory of Open Access Journals (Sweden)

    Nobumasa Hitoshi

    2007-04-01

    Full Text Available Abstract Background Mycotoxins are fungal secondary metabolites commonly present in feed and food, and are widely regarded as hazardous contaminants. Citrinin, one of the very well known mycotoxins that was first isolated from Penicillium citrinum, is produced by more than 10 kinds of fungi, and is possibly spread all over the world. However, the information on the action mechanism of the toxin is limited. Thus, we investigated the citrinin-induced genomic response for evaluating its toxicity. Results Citrinin inhibited growth of yeast cells at a concentration higher than 100 ppm. We monitored the citrinin-induced mRNA expression profiles in yeast using the ORF DNA microarray and Oligo DNA microarray, and the expression profiles were compared with those of the other stress-inducing agents. Results obtained from both microarray experiments clustered together, but were different from those of the mycotoxin patulin. The oxidative stress response genes – AADs, FLR1, OYE3, GRE2, and MET17 – were significantly induced. In the functional category, expression of genes involved in "metabolism", "cell rescue, defense and virulence", and "energy" were significantly activated. In the category of "metabolism", genes involved in the glutathione synthesis pathway were activated, and in the category of "cell rescue, defense and virulence", the ABC transporter genes were induced. To alleviate the induced stress, these cells might pump out the citrinin after modification with glutathione. While, the citrinin treatment did not induce the genes involved in the DNA repair. Conclusion Results from both microarray studies suggest that citrinin treatment induced oxidative stress in yeast cells. The genotoxicity was less severe than the patulin, suggesting that citrinin is less toxic than patulin. The reproducibility of the expression profiles was much better with the Oligo DNA microarray. However, the Oligo DNA microarray did not completely overcome cross

  12. The role of the fire dampers in the event of fire in a nuclear facility. Selection criteria for devices

    International Nuclear Information System (INIS)

    Savornin, J.; Laborde, J.C.

    1989-10-01

    In nuclear facilities, where unacceptable quantities of radioactive aerosols could be spread in the event of a fire, the ventilation system must be designed so that an underpressure is maintained under such circumstances. This is the reason why the extracting ventilation of the room in which the fire has broken out has generally to be kept going as long as possible. This prevents smoke and radioactive aerosols from spreading to accessways and adjacent rooms. Consequently, the various devices of the ventilation network need to have high fire resistance. Fire dampers can be applied to exhaust air to delay the heat build-up of a major fire. Specialized qualification testing is required for these dampers. The criteria we have used as a basis for specifying the required qualities of installations are defined. The tests that have been performed, or are now in progress, are described. The results obtained so far are given. Devices and arrangements are suggested

  13. Selection of a Site for a Near-Surface Disposal Facility: A Joint Report on Characterization of Sites

    International Nuclear Information System (INIS)

    Motiejunas, S.; Cernakauskas, P.

    2005-01-01

    Report describes general and safety-relevant environmental conditions of investigated sites and provides an overview of information concerning wastes to be disposed of. Safety relevant design aspects are given in the Project Report on Reference Design for a Near-Surface Disposal Facility for Low-and Intermediate-Level Short-Lived Radioactive Waste in Lithuania. This Report summarizes results of investigations performed during 2003-2005 by a number of researchers and evaluated by RATA. The work was performed by the Institute of Geology and Geography, the Lithuanian Energy Institute, Vilnius University, the Institute of Chemistry, UAB Grota, the Lithuanian Geological Survey, Swedish consultants from Geodevelopment, SKB and SKI-ICP, and generalized by RATA

  14. Transfrontier problems in connection with the site selection of power stations and energy facilities with environmental impact

    International Nuclear Information System (INIS)

    Manz, P.; Kanton Basel-Landschaft, Liestal

    1977-01-01

    This contribution deals with the subjects politics and environmental protection, site selection procedures and their consequences, and tasks of international commissions, and concludes that cooperation, research and agreement are essential for environmental and energy policies which are to be beneficial to all. (RW) [de

  15. Imagery Data Base Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Imagery Data Base Facility supports AFRL and other government organizations by providing imagery interpretation and analysis to users for data selection, imagery...

  16. Normalization for triple-target microarray experiments

    Directory of Open Access Journals (Sweden)

    Magniette Frederic

    2008-04-01

    Full Text Available Abstract Background Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis allow hybridization up to four samples simultaneously. The two additional dyes are Alexa488 and Alexa494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data. Results We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize p differently labelled targets co-hybridized on a same array, for any value of p greater than 2. Conclusion The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.

  17. Selective N-alkylation of amines using nitriles under hydrogenation conditions: facile synthesis of secondary and tertiary amines.

    Science.gov (United States)

    Ikawa, Takashi; Fujita, Yuki; Mizusaki, Tomoteru; Betsuin, Sae; Takamatsu, Haruki; Maegawa, Tomohiro; Monguchi, Yasunari; Sajiki, Hironao

    2012-01-14

    Nitriles were found to be highly effective alkylating reagents for the selective N-alkylation of amines under catalytic hydrogenation conditions. For the aromatic primary amines, the corresponding secondary amines were selectively obtained under Pd/C-catalyzed hydrogenation conditions. Although the use of electron poor aromatic amines or bulky nitriles showed a lower reactivity toward the reductive alkylation, the addition of NH(4)OAc enhanced the reactivity to give secondary aromatic amines in good to excellent yields. Under the same reaction conditions, aromatic nitro compounds instead of the aromatic primary amines could be directly transformed into secondary amines via a domino reaction involving the one-pot hydrogenation of the nitro group and the reductive alkylation of the amines. While aliphatic amines were effectively converted to the corresponding tertiary amines under Pd/C-catalyzed conditions, Rh/C was a highly effective catalyst for the N-monoalkylation of aliphatic primary amines without over-alkylation to the tertiary amines. Furthermore, the combination of the Rh/C-catalyzed N-monoalkylation of the aliphatic primary amines and additional Pd/C-catalyzed alkylation of the resulting secondary aliphatic amines could selectively prepare aliphatic tertiary amines possessing three different alkyl groups. According to the mechanistic studies, it seems reasonable to conclude that nitriles were reduced to aldimines before the nucleophilic attack of the amine during the first step of the reaction.

  18. Extended -Regular Sequence for Automated Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jin Hee-Jeong

    2006-01-01

    Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

  19. Linking probe thermodynamics to microarray quantification

    International Nuclear Information System (INIS)

    Li, Shuzhao; Pozhitkov, Alexander; Brouwer, Marius

    2010-01-01

    Understanding the difference in probe properties holds the key to absolute quantification of DNA microarrays. So far, Langmuir-like models have failed to link sequence-specific properties to hybridization signals in the presence of a complex hybridization background. Data from washing experiments indicate that the post-hybridization washing has no major effect on the specifically bound targets, which give the final signals. Thus, the amount of specific targets bound to probes is likely determined before washing, by the competition against nonspecific binding. Our competitive hybridization model is a viable alternative to Langmuir-like models. (comment)

  20. The effectiveness of introducing Group Prenatal Care (GPC) in selected health facilities in a district of Bangladesh: study protocol.

    Science.gov (United States)

    Sultana, Marufa; Mahumud, Rashidul Alam; Ali, Nausad; Ahmed, Sayem; Islam, Ziaul; Khan, Jahangir A M; Sarker, Abdur Razzaque

    2017-01-31

    Despite high rates of antenatal care and relatively good access to health facilities, maternal and neonatal mortality remain high in Bangladesh. There is an immediate need for implementation of evidence-based, cost-effective interventions to improve maternal and neonatal health outcomes. The aim of the study is to assess the effect of the intervention namely Group Prenatal Care (GPC) on utilization of standard number of antenatal care, post natal care including skilled birth attendance and institutional deliveries instead of usual care. The study is quasi-experimental in design. We aim to recruit 576 pregnant women (288 interventions and 288 comparisons) less than 20 weeks of gestational age. The intervention will be delivered over around 6 months. The outcome measure is the difference in maternal service coverage including ANC and PNC coverage, skilled birth attendance and institutional deliveries between the intervention and comparison group. Findings from the research will contribute to improve maternal and newborn outcome in our existing health system. Findings of the research can be used for planning a new strategy and improving the health outcome for Bangladeshi women. Finally addressing the maternal health goal, this study is able to contribute to strengthening health system.

  1. Assessment of the structural shielding integrity of some selected computed tomography facilities in the Greater Accra Region of Ghana

    International Nuclear Information System (INIS)

    Nkansah, A.

    2010-01-01

    The structural shielding integrity was assessed for four of the CT facilities at Trust Hospital, Korle-Bu Teaching Hospital, the 37 Military Hospital and Medical Imaging Ghana Ltd. in the Greater Accra Region of Ghana. From the shielding calculations, the concrete wall thickness computed are 120, 145, 140 and 155mm, for Medical Imaging Ghana Ltd. 37 Military, Trust Hospital and Korle-Bu Teaching Hospital respectively using Default DLP values. The wall thickness using Derived DLP values are 110, 110, 120 and 168mm for Medical Imaging Ghana Ltd, 37 Military Hospital, Trust Hospital and Korle-Bu Teaching Hospital respectively. These values are within the accepted standard concrete thickness of 102- 152mm prescribed by the National Council of Radiological Protection and measurement. The ultrasonic pulse testing indicated that all the sandcrete walls are of good quality and free of voids since pulse velocities estimated were approximately equal to 3.45km/s. an average dose rate measurement for supervised areas is 3.4 μSv/wk and controlled areas is 18.0 μSv/wk. These dose rates were below the acceptable levels of 100 μSv per week for the occupationally exposed and 20 μSv per week for members of the public provided by the ICRU. The results mean that the structural shielding thickness are adequate to protect members of the public and occupationally exposed workers (au).

  2. Radiation damage evaluation on concrete within a facility for Selective Production of Exotic Species (SPES Project), Italy.

    Science.gov (United States)

    Pomaro, B; Salomoni, V A; Gramegna, F; Prete, G; Majorana, C E

    2011-10-30

    Concrete is commonly used as a biological shield against nuclear radiation. As long as, in the design of nuclear facilities, its load carrying capacity is required together with its shielding properties, changes in the mechanical properties due to nuclear radiation are of particular significance and may have to be taken into account in such circumstances. The study presented here allows for reaching first evidences on the behavior of concrete when exposed to nuclear radiation in order to evaluate the consequent effect on the mechanical field, by means of a proper definition of the radiation damage, strictly connected with the strength properties of the building material. Experimental evidences on the decay of the mechanical modulus of concrete have allowed for implementing the required damage law within a 3D F.E. research code which accounts for the coupling among moisture, heat transfer and the mechanical field in concrete treated as a fully coupled porous medium. The development of the damage front in a concrete shielding wall is analyzed under neutron radiation and results within the wall thickness are reported for long-term radiation spans and several concrete mixtures in order to discuss the resulting shielding properties. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Safety assesment necessary in selecting the technologies for partial decommissioning of nuclear facilities. Application to research reactors

    International Nuclear Information System (INIS)

    Niculae, O.; Stan, C.; Vladescu, G.

    2005-01-01

    The main goal of this work is identification and evaluation of safety indicators - quantities used in monitoring the safety assurance during decommissioning processes in nuclear facilities identification of safety indicators is made on basis of qualitative and quantitative analysis, effected for both normal decommissioning, as well as in case of foreseen event occurrence. The safety indicators form an integrated system which can be represented by a pyramidal structural with the following levels (in increasing complexity order): specific indicators, strategic indicators, overall indicators, safety closure. This work suggests that evaluation of safety assurance level during the conduct of a decommissioning process to be based on the overall analysis of the set of indicators emphasizing not only the evaluation of individual safety indicators but also the interdependencies between them. The evaluation method is based on the 'step-by-step' principle. The evaluation was carried-out either directly or by means of dedicated evaluation forms which cover both quantitative and qualitative aspects of the analysis. At the some time identified are the adequate protection measures for the personnel implied in decommissioning, as well as for population and environment. The paper present also technologies adequate in the decommissioning. (authors)

  4. Hepatitis B vaccination coverage and the determinants of vaccination among health care workers in selected health facilities in Lusaka district, Zambia: an exploratory study.

    Science.gov (United States)

    Mungandi, Namwaka; Makasa, Mpundu; Musonda, Patrick

    2017-01-01

    Hepatitis B is a viral infection of the liver and causes both acute and chronic disease. It is transmitted through contact with an infected person's bodily fluids. It is an occupational hazard for healthcare workers and can be prevented by the administration of a vaccine. It is recommended that healthcare workers be vaccinated against vaccine preventable diseases including hepatitis B. The study objective was to determine the prevalence and determinants of hepatitis B vaccination among healthcare workers in selected health facilities in Lusaka. The study took place in seven health facilities across Lusaka district in Zambia. A total sample size of 331 healthcare workers was selected of which; 90 were nurses, 88 were doctors, 86 were laboratory personnel and 67 were general workers. A self-administered structured questionnaire was given to a total of 331 healthcare workers. Investigator led stepwise approach was used to select the best predictor variables in a multiple logistic regression model and all analyses were performed using STATA software, version 12.1 SE (Stata Corporation, College Station, TX, USA). Only 64(19.3%) of the healthcare workers were vaccinated against hepatitis B, with 35 (54.7%) of these being fully vaccinated and 29 (45.3%) partially vaccinated. Analysis showed that; age of the healthcare worker, sharp injuries per year and training in infection control were the variables that were statistically significant in predicting a healthcare worker's vaccination status. It is reassuring to learn that healthcare workers have knowledge regarding hepatitis B and the vaccine and are willing to be vaccinated against it. Health institutions should bear the cost for vaccinating staff and efforts should be made for appropriate health education regarding hepatitis B infection and its prevention. Establishment of policies on compulsory hepatitis B vaccination for healthcare workers in Zambia is recommended.

  5. Observation of hohlraum-wall motion with spectrally selective x-ray imaging at the National Ignition Facility

    Energy Technology Data Exchange (ETDEWEB)

    Izumi, N., E-mail: izumi2@llnl.gov; Meezan, N. B.; Divol, L.; Hall, G. N.; Barrios, M. A.; Jones, O.; Landen, O. L.; Kroll, J. J.; Vonhof, S. A.; Nikroo, A.; Bailey, C. G.; Hardy, C. M.; Ehrlich, R. B.; Town, R. P. J.; Bradley, D. K.; Hinkel, D. E.; Moody, J. D. [Lawrence Livermore National Laboratory, Livermore, California 94551 (United States); Jaquez, J. [General Atomics, San Diego, California 9212 (United States)

    2016-11-15

    The high fuel capsule compression required for indirect drive inertial confinement fusion requires careful control of the X-ray drive symmetry throughout the laser pulse. When the outer cone beams strike the hohlraum wall, the plasma ablated off the hohlraum wall expands into the hohlraum and can alter both the outer and inner cone beam propagations and hence the X-ray drive symmetry especially at the final stage of the drive pulse. To quantitatively understand the wall motion, we developed a new experimental technique which visualizes the expansion and stagnation of the hohlraum wall plasma. Details of the experiment and the technique of spectrally selective x-ray imaging are discussed.

  6. Design of an Enterobacteriaceae Pan-genome Microarray Chip

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Ussery, David

    2010-01-01

    -density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability...... to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination...

  7. Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray.

    Science.gov (United States)

    Fenart, Stéphane; Ndong, Yves-Placide Assoumou; Duarte, Jorge; Rivière, Nathalie; Wilmer, Jeroen; van Wuytswinkel, Olivier; Lucau, Anca; Cariou, Emmanuelle; Neutelings, Godfrey; Gutierrez, Laurent; Chabbert, Brigitte; Guillot, Xavier; Tavernier, Reynald; Hawkins, Simon; Thomasset, Brigitte

    2010-10-21

    Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted flax varieties

  8. Development and validation of a flax (Linum usitatissimum L. gene expression oligo microarray

    Directory of Open Access Journals (Sweden)

    Gutierrez Laurent

    2010-10-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars and its cellulose-rich fibres (fibre-flax cultivars used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Results Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples. A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well

  9. Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies

    Directory of Open Access Journals (Sweden)

    Guillermo Lay-Son

    2015-04-01

    Full Text Available OBJECTIVES: Clinical use of microarray-based techniques for the analysis of many developmental disorders has emerged during the last decade. Thus, chromosomal microarray has been positioned as a first-tier test. This study reports the first experience in a Chilean cohort. METHODS: Chilean patients with developmental disabilities and congenital anomalies were studied with a high-density microarray (CytoScan(tm HD Array, Affymetrix, Inc., Santa Clara, CA, USA. Patients had previous cytogenetic studies with either a normal result or a poorly characterized anomaly. RESULTS: This study tested 40 patients selected by two or more criteria, including: major congenital anomalies, facial dysmorphism, developmental delay, and intellectual disability. Copy number variants (CNVs were found in 72.5% of patients, while a pathogenic CNV was found in 25% of patients and a CNV of uncertain clinical significance was found in 2.5% of patients. CONCLUSION: Chromosomal microarray analysis is a useful and powerful tool for diagnosis of developmental diseases, by allowing accurate diagnosis, improving the diagnosis rate, and discovering new etiologies. The higher cost is a limitation for widespread use in this setting.

  10. Clustering approaches to identifying gene expression patterns from DNA microarray data.

    Science.gov (United States)

    Do, Jin Hwan; Choi, Dong-Kug

    2008-04-30

    The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

  11. A Cercla-Based Decision Model to Support Remedy Selection for an Uncertain Volume of Contaminants at a DOE Facility

    Energy Technology Data Exchange (ETDEWEB)

    Christine E. Kerschus

    1999-03-31

    The Paducah Gaseous Diffusion Plant (PGDP) operated by the Department of Energy is challenged with selecting the appropriate remediation technology to cleanup contaminants at Waste Area Group (WAG) 6. This research utilizes value-focused thinking and multiattribute preference theory concepts to produce a decision analysis model designed to aid the decision makers in their selection process. The model is based on CERCLA's five primary balancing criteria, tailored specifically to WAG 6 and the contaminants of concern, utilizes expert opinion and the best available engineering, cost, and performance data, and accounts for uncertainty in contaminant volume. The model ranks 23 remediation technologies (trains) in their ability to achieve the CERCLA criteria at various contaminant volumes. A sensitivity analysis is performed to examine the effects of changes in expert opinion and uncertainty in volume. Further analysis reveals how volume uncertainty is expected to affect technology cost, time and ability to meet the CERCLA criteria. The model provides the decision makers with a CERCLA-based decision analysis methodology that is objective, traceable, and robust to support the WAG 6 Feasibility Study. In addition, the model can be adjusted to address other DOE contaminated sites.

  12. A Cercla-Based Decision Model to Support Remedy Selection for an Uncertain Volume of Contaminants at a DOE Facility

    International Nuclear Information System (INIS)

    Christine E. Kerschus

    1999-01-01

    The Paducah Gaseous Diffusion Plant (PGDP) operated by the Department of Energy is challenged with selecting the appropriate remediation technology to cleanup contaminants at Waste Area Group (WAG) 6. This research utilizes value-focused thinking and multiattribute preference theory concepts to produce a decision analysis model designed to aid the decision makers in their selection process. The model is based on CERCLA's five primary balancing criteria, tailored specifically to WAG 6 and the contaminants of concern, utilizes expert opinion and the best available engineering, cost, and performance data, and accounts for uncertainty in contaminant volume. The model ranks 23 remediation technologies (trains) in their ability to achieve the CERCLA criteria at various contaminant volumes. A sensitivity analysis is performed to examine the effects of changes in expert opinion and uncertainty in volume. Further analysis reveals how volume uncertainty is expected to affect technology cost, time and ability to meet the CERCLA criteria. The model provides the decision makers with a CERCLA-based decision analysis methodology that is objective, traceable, and robust to support the WAG 6 Feasibility Study. In addition, the model can be adjusted to address other DOE contaminated sites

  13. Radiation damage evaluation on concrete within a facility for Selective Production of Exotic Species (SPES Project), Italy

    International Nuclear Information System (INIS)

    Pomaro, B.; Salomoni, V.A.; Gramegna, F.; Prete, G.; Majorana, C.E.

    2011-01-01

    Highlights: → We present the effect of radiation on concrete as shielding material. → The coupling between hydro-thermal-mechanical fields and radiation damage is shown. → Attention is focused on numerical modelling of concrete in 3D domains. → A new estimate of the radiation damage parameter is given. → A risk assessment of concrete-radiation interactions is developed. - Abstract: Concrete is commonly used as a biological shield against nuclear radiation. As long as, in the design of nuclear facilities, its load carrying capacity is required together with its shielding properties, changes in the mechanical properties due to nuclear radiation are of particular significance and may have to be taken into account in such circumstances. The study presented here allows for reaching first evidences on the behavior of concrete when exposed to nuclear radiation in order to evaluate the consequent effect on the mechanical field, by means of a proper definition of the radiation damage, strictly connected with the strength properties of the building material. Experimental evidences on the decay of the mechanical modulus of concrete have allowed for implementing the required damage law within a 3D F.E. research code which accounts for the coupling among moisture, heat transfer and the mechanical field in concrete treated as a fully coupled porous medium. The development of the damage front in a concrete shielding wall is analyzed under neutron radiation and results within the wall thickness are reported for long-term radiation spans and several concrete mixtures in order to discuss the resulting shielding properties.

  14. Microarray analysis of thioacetamide-treated type 1 diabetic rats

    International Nuclear Information System (INIS)

    Devi, Sachin S.; Mehendale, Harihara M.

    2006-01-01

    It is well known that diabetes imparts high sensitivity to numerous hepatotoxicants. Previously, we have shown that a normally non-lethal dose of thioacetamide (TA, 300 mg/kg) causes 90% mortality in type 1 diabetic (DB) rats due to inhibited tissue repair allowing progression of liver injury. On the other hand, DB rats exposed to 30 mg TA/kg exhibit delayed tissue repair and delayed recovery from injury. The objective of this study was to investigate the mechanism of impaired tissue repair and progression of liver injury in TA-treated DB rats by using cDNA microarray. Gene expression pattern was examined at 0, 6, and 12 h after TA challenge, and selected mechanistic leads from microarray experiments were confirmed by real-time RT-PCR and further investigated at protein level over the time course of 0 to 36 h after TA treatment. Diabetic condition itself increased gene expression of proteases and decreased gene expression of protease inhibitors. Administration of 300 mg TA/kg to DB rats further elevated gene expression of proteases and suppressed gene expression of protease inhibitors, explaining progression of liver injury in DB rats after TA treatment. Inhibited expression of genes involved in cell division cycle (cyclin D1, IGFBP-1, ras, E2F) was observed after exposure of DB rats to 300 mg TA/kg, explaining inhibited tissue repair in these rats. On the other hand, DB rats receiving 30 mg TA/kg exhibit delayed expression of genes involved in cell division cycle, explaining delayed tissue repair in these rats. In conclusion, impaired cyclin D1 signaling along with increased proteases and decreased protease inhibitors may explain impaired tissue repair that leads to progression of liver injury initiated by TA in DB rats

  15. An Efficient Ensemble Learning Method for Gene Microarray Classification

    Directory of Open Access Journals (Sweden)

    Alireza Osareh

    2013-01-01

    Full Text Available The gene microarray analysis and classification have demonstrated an effective way for the effective diagnosis of diseases and cancers. However, it has been also revealed that the basic classification techniques have intrinsic drawbacks in achieving accurate gene classification and cancer diagnosis. On the other hand, classifier ensembles have received increasing attention in various applications. Here, we address the gene classification issue using RotBoost ensemble methodology. This method is a combination of Rotation Forest and AdaBoost techniques which in turn preserve both desirable features of an ensemble architecture, that is, accuracy and diversity. To select a concise subset of informative genes, 5 different feature selection algorithms are considered. To assess the efficiency of the RotBoost, other nonensemble/ensemble techniques including Decision Trees, Support Vector Machines, Rotation Forest, AdaBoost, and Bagging are also deployed. Experimental results have revealed that the combination of the fast correlation-based feature selection method with ICA-based RotBoost ensemble is highly effective for gene classification. In fact, the proposed method can create ensemble classifiers which outperform not only the classifiers produced by the conventional machine learning but also the classifiers generated by two widely used conventional ensemble learning methods, that is, Bagging and AdaBoost.

  16. Image microarrays derived from tissue microarrays (IMA-TMA: New resource for computer-aided diagnostic algorithm development

    Directory of Open Access Journals (Sweden)

    Jennifer A Hipp

    2012-01-01

    Full Text Available Background: Conventional tissue microarrays (TMAs consist of cores of tissue inserted into a recipient paraffin block such that a tissue section on a single glass slide can contain numerous patient samples in a spatially structured pattern. Scanning TMAs into digital slides for subsequent analysis by computer-aided diagnostic (CAD algorithms all offers the possibility of evaluating candidate algorithms against a near-complete repertoire of variable disease morphologies. This parallel interrogation approach simplifies the evaluation, validation, and comparison of such candidate algorithms. A recently developed digital tool, digital core (dCORE, and image microarray maker (iMAM enables the capture of uniformly sized and resolution-matched images, with these representing key morphologic features and fields of view, aggregated into a single monolithic digital image file in an array format, which we define as an image microarray (IMA. We further define the TMA-IMA construct as IMA-based images derived from whole slide images of TMAs themselves. Methods: Here we describe the first combined use of the previously described dCORE and iMAM tools, toward the goal of generating a higher-order image construct, with multiple TMA cores from multiple distinct conventional TMAs assembled as a single digital image montage. This image construct served as the basis of the carrying out of a massively parallel image analysis exercise, based on the use of the previously described spatially invariant vector quantization (SIVQ algorithm. Results: Multicase, multifield TMA-IMAs of follicular lymphoma and follicular hyperplasia were separately rendered, using the aforementioned tools. Each of these two IMAs contained a distinct spectrum of morphologic heterogeneity with respect to both tingible body macrophage (TBM appearance and apoptotic body morphology. SIVQ-based pattern matching, with ring vectors selected to screen for either tingible body macrophages or apoptotic

  17. 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia.

    Science.gov (United States)

    Schönmann, Susan; Loy, Alexander; Wimmersberger, Céline; Sobek, Jens; Aquino, Catharine; Vandamme, Peter; Frey, Beat; Rehrauer, Hubert; Eberl, Leo

    2009-04-01

    For cultivation-independent and highly parallel analysis of members of the genus Burkholderia, an oligonucleotide microarray (phylochip) consisting of 131 hierarchically nested 16S rRNA gene-targeted oligonucleotide probes was developed. A novel primer pair was designed for selective amplification of a 1.3 kb 16S rRNA gene fragment of Burkholderia species prior to microarray analysis. The diagnostic performance of the microarray for identification and differentiation of Burkholderia species was tested with 44 reference strains of the genera Burkholderia, Pandoraea, Ralstonia and Limnobacter. Hybridization patterns based on presence/absence of probe signals were interpreted semi-automatically using the novel likelihood-based strategy of the web-tool Phylo- Detect. Eighty-eight per cent of the reference strains were correctly identified at the species level. The evaluated microarray was applied to investigate shifts in the Burkholderia community structure in acidic forest soil upon addition of cadmium, a condition that selected for Burkholderia species. The microarray results were in agreement with those obtained from phylogenetic analysis of Burkholderia 16S rRNA gene sequences recovered from the same cadmiumcontaminated soil, demonstrating the value of the Burkholderia phylochip for determinative and environmental studies.

  18. Microarray glycan profiling reveals algal fucoidan epitopes in diverse marine metazoans

    DEFF Research Database (Denmark)

    Asunción Salmeán, Armando; Hervé, Cécile; Jørgensen, Bodil

    2017-01-01

    Despite the biological importance and pharmacological potential of glycans from marine organisms, there are many unanswered questions regarding their distribution, function, and evolution. Here we describe microarray-based glycan profiling of a diverse selection of marine animals using antibodies...... raised against fucoidan isolated from a brown alga. We demonstrate the presence of two fucoidan epitopes in six animals belonging to three phyla including Porifera, Molusca, and Chordata. We studied the spatial distribution of these epitopes in Cliona celata ("boring sponge") and identified...

  19. Adaptive algorithm of selecting optimal variant of errors detection system for digital means of automation facility of oil and gas complex

    Science.gov (United States)

    Poluyan, A. Y.; Fugarov, D. D.; Purchina, O. A.; Nesterchuk, V. V.; Smirnova, O. V.; Petrenkova, S. B.

    2018-05-01

    To date, the problems associated with the detection of errors in digital equipment (DE) systems for the automation of explosive objects of the oil and gas complex are extremely actual. Especially this problem is actual for facilities where a violation of the accuracy of the DE will inevitably lead to man-made disasters and essential material damage, at such facilities, the diagnostics of the accuracy of the DE operation is one of the main elements of the industrial safety management system. In the work, the solution of the problem of selecting the optimal variant of the errors detection system of errors detection by a validation criterion. Known methods for solving these problems have an exponential valuation of labor intensity. Thus, with a view to reduce time for solving the problem, a validation criterion is compiled as an adaptive bionic algorithm. Bionic algorithms (BA) have proven effective in solving optimization problems. The advantages of bionic search include adaptability, learning ability, parallelism, the ability to build hybrid systems based on combining. [1].

  20. Perception of quality of maternal healthcare services among women utilising antenatal services in selected primary health facilities in Anambra State, Southeast Nigeria

    Science.gov (United States)

    Emelumadu, Obiageli F.; Onyeonoro, Ugochukwu Uchenna; Ukegbu, Andrew Ugwunna; Ezeama, Nkiru N.; Ifeadike, Chigozie Ozoemena; Okezie, Obasi Kanu

    2014-01-01

    Background: This is a cross-sectional descriptive study aimed at assessing antenatal care service attendees’ perception of quality of maternal healthcare (MHC) services in Anambra State, southeast Nigeria. Materials and Methods: A total of 310 pregnant women utilising antenatal care (ANC) services in three purposively selected primary health centres (PHCs) in rural communities in Anambra State were studied. Reponses were elicited from the participants selected consecutively over a 4-month period, using a pre-tested, semi-structured interviewer-administered questionnaire on socio-demographic characteristics, utilisation and perception of MHC services. Data collected were analysed using SPSS version 17. Results: Findings showed that utilisation of facility for both antenatal (97.0%; 95% CI, 94.4–98.4%) and natal services (92.7%; 95% CI 89.2–95.2%) were quite high. Generally, most of the women were satisfied with MHC services (89.7%). Most of them were satisfied with the staff attitude (85.1%), waiting time (84.1%) and cost of services (79.5%). Being ≥30 years (X2 = 4.61, P = 0.032), married (X2 = 9.70, P = 0.008) and multiparous (X2 = 9.14, P = 0.028), as well as utilisation of formal health facility for antenatal (X2 = 26.94, P = 0.000) and natal (X2 = 33.42, P = 0.000) services were associated with satisfaction with maternal health services. Conclusions: The study showed high level of satisfaction with quality of maternal health services among antenatal attendees and highlights the need to strengthen interventions that increase uptake of formal MHC services. PMID:24791050

  1. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

    Directory of Open Access Journals (Sweden)

    Reinders Marcel JT

    2009-11-01

    Full Text Available Abstract Background Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear. Results We have performed a comprehensive sensitivity analysis of microarray breast cancer classification under the two types of feature variability mentioned above. We used data from six state of the art preprocessing methods, using a compendium consisting of eight diferent datasets, involving 1131 hybridizations, containing data from both one and two-color array technology. For a wide range of classifiers, we performed a joint study on performance, concordance and stability. In the stability analysis we explicitly tested classifiers for their noise tolerance by using perturbed expression profiles that are based on uncertainty information directly related to the preprocessing methods. Our results indicate that signature composition is strongly influenced by feature variability, even if the array platform and the stratification of patient samples are identical. In addition, we show that there is often a high level of discordance between individual class assignments for signatures constructed on data coming from different preprocessing schemes, even if the actual signature composition is identical

  2. Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB.

    Science.gov (United States)

    Chatziioannou, Aristotelis; Moulos, Panagiotis; Kolisis, Fragiskos N

    2009-10-27

    The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods. We describe here Gene ARMADA (Automated Robust MicroArray Data Analysis), a MATLAB implemented platform with a Graphical User Interface. This suite integrates all steps of microarray data analysis including automated data import, noise correction and filtering, normalization, statistical selection of differentially expressed genes, clustering, classification and annotation. In its current version, Gene ARMADA fully supports 2 coloured cDNA and Affymetrix oligonucleotide arrays, plus custom arrays for which experimental details are given in tabular form (Excel spreadsheet, comma separated values, tab-delimited text formats). It also supports the analysis of already processed results through its versatile import editor. Besides being fully automated, Gene ARMADA incorporates numerous functionalities of the Statistics and Bioinformatics Toolboxes of MATLAB. In addition, it provides numerous visualization and exploration tools plus customizable export data formats for seamless integration by other analysis tools or MATLAB, for further processing. Gene ARMADA requires MATLAB 7.4 (R2007a) or higher and is also distributed as a stand-alone application with MATLAB Component Runtime. Gene ARMADA provides a

  3. Shared probe design and existing microarray reanalysis using PICKY

    Directory of Open Access Journals (Sweden)

    Chou Hui-Hsien

    2010-04-01

    Full Text Available Abstract Background Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations. Results PICKY 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. PICKY 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, PICKY does not sacrifice the quality of shared probes when choosing them. The latest PICKY 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making PICKY 2.1 more versatile to microarray users. Conclusions Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations.

  4. A Critical Perspective On Microarray Breast Cancer Gene Expression Profiling

    NARCIS (Netherlands)

    Sontrop, H.M.J.

    2015-01-01

    Microarrays offer biologists an exciting tool that allows the simultaneous assessment of gene expression levels for thousands of genes at once. At the time of their inception, microarrays were hailed as the new dawn in cancer biology and oncology practice with the hope that within a decade diseases

  5. The Importance of Normalization on Large and Heterogeneous Microarray Datasets

    Science.gov (United States)

    DNA microarray technology is a powerful functional genomics tool increasingly used for investigating global gene expression in environmental studies. Microarrays can also be used in identifying biological networks, as they give insight on the complex gene-to-gene interactions, ne...

  6. 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.

  7. Uses of Dendrimers for DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Jean-Pierre Majoral

    2006-08-01

    Full Text Available Biosensors such as DNA microarrays and microchips are gaining an increasingimportance in medicinal, forensic, and environmental analyses. Such devices are based onthe detection of supramolecular interactions called hybridizations that occur betweencomplementary oligonucleotides, one linked to a solid surface (the probe, and the other oneto be analyzed (the target. This paper focuses on the improvements that hyperbranched andperfectly defined nanomolecules called dendrimers can provide to this methodology. Twomain uses of dendrimers for such purpose have been described up to now; either thedendrimer is used as linker between the solid surface and the probe oligonucleotide, or thedendrimer is used as a multilabeled entity linked to the target oligonucleotide. In the firstcase the dendrimer generally induces a higher loading of probes and an easier hybridization,due to moving away the solid phase. In the second case the high number of localized labels(generally fluorescent induces an increased sensitivity, allowing the detection of smallquantities of biological entities.

  8. External quality assessment of AFB smear microscopy performances and its associated factors in selected private health facilities in Addis Ababa, Ethiopia.

    Science.gov (United States)

    Mosissa, Lemi; Kebede, Abebaw; Mindaye, Tedla; Getahun, Muluwork; Tulu, Sisay; Desta, Kassu

    2016-01-01

    Tuberculosis (TB) is still a public health problem in sub Saharan African countries. In resource-limited settings, TB diagnosis relies on sputum smear microscopy, with low and variable sensitivities, especially in paucibacillary pediatric and HIV-associated TB patients. Tuberculosis microscopy centers have several weaknesses like overworking, insufficiently trained personnel, inconsistent reagent supplies, and poorly maintained equipments; thus, there is a critical need for investments in laboratory infrastructure, capacity building, and quality assurance schemes. The performance of TB microscopy centers in the private health facilities in Addis Ababa is not known so far. The main objective of the study was to assess laboratory performance of acid fast bacilli (AFB) smear microscopy and its associated factors in selected private health facilities in Addis Ababa, Ethiopia. A cross-sectional study was conducted in 33 selected private health facilities of Addis Ababa, Ethiopia comprising 7 hospitals, 2 NGO health centers, 23 higher clinics and 1 diagnostic laboratory that provide AFB smear microscopy services. The study was conducted from January to April 2014. A total of 283 stained sputum smears were randomly collected from participant laboratories for blinded rechecking, 320 panel slides were sent to 32 microscopy centers to evaluate their performance on AFB reading, staining and reporting. Checklists were used to assess quality issues of laboratories. Data were captured, cleaned, and analyzed using SPSS version 16.0; χ(2) tests, kappa statistics were used for comparison purpose. P value laboratories, 2-scored 100%, 15 scored 80-95% & the remaining 15 scored 50-75% for overall proficiency test performance. There were 10 (3.15%) major errors and 121 (37.8%) minor errors. The sensitivity, specificity, PPV and NPV of panel reading by microscopy centers were 89%, 96%, 96%, and 90% respectively. Out of 283 randomly selected slides for blind rechecking, 11 (3.9%) slides

  9. Challenges faced by caregivers of children on antiretroviral therapy at Mutale Municipality selected healthcare facilities, Vhembe District, Limpopo Province.

    Science.gov (United States)

    Mafune, Rhudzani V; Lebese, Rachel T; Nemathaga, Livhuwani H

    2017-08-28

    Children depend solely on caregivers who can be either parents or guardians for drug administration to enhance adherence to antiretroviral treatment (ART), which might pose any number of challenges. The purpose of this study was to explore and describe the challenges faced by caregivers of children on ART at Mutale Municipality, Vhembe District, Limpopo Province. The research design was qualitative, explorative, descriptive and contextual in nature. The population consisted of 16 caregivers who were 18 years of age and above, and mentally capable, irrespective of educational qualifications, caring for children aged between 0 and 15 years who were on ART between April 2013 and October 2014. Non-probability, purposive sampling was used to select the 16 caregivers. Required permission, approval and ethical clearance were obtained from the University of Venda Higher Degree Committee, Limpopo Provincial Health Department and relevant institutions. An in-depth, individual, unstructured interview method was used to collect data. One central question was asked: 'What are the challenges you experience when caring for a child on antiretroviral treatment?' Subsequent questions were based on the participants' responses to the central question. Qualitative data were analysed by means of Tesch's open-coding method. The findings of this study revealed that participants, that is, caregivers of children on ART, experienced financial burdens because of transport costs needed to comply with follow-up dates and insufficient of money for food, clothing the child in need of care, pocket money for lunch boxes during school hours and time lost while waiting for consultations. Participants reported some level of stigmatisation against children on ART by family members, especially the husbands or in-laws of the secondary caregivers. Many primary and secondary caregivers seemed to have given up seeking support from government and community structures. The conclusions drawn from this research

  10. Bystander effect: Biological endpoints and microarray analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chaudhry, M. Ahmad [Department of Medical Laboratory and Radiation Sciences, College of Nursing and Health Sciences, University of Vermont, 302 Rowell Building, Burlington, VT 05405 (United States) and DNA Microarray Facility, University of Vermont, Burlington, VT 05405 (United States)]. E-mail: mchaudhr@uvm.edu

    2006-05-11

    In cell populations exposed to ionizing radiation, the biological effects occur in a much larger proportion of cells than are estimated to be traversed by radiation. It has been suggested that irradiated cells are capable of providing signals to the neighboring unirradiated cells resulting in damage to these cells. This phenomenon is termed the bystander effect. The bystander effect induces persistent, long-term, transmissible changes that result in delayed death and neoplastic transformation. Because the bystander effect is relevant to carcinogenesis, it could have significant implications for risk estimation for radiation exposure. The nature of the bystander effect signal and how it impacts the unirradiated cells remains to be elucidated. Examination of the changes in gene expression could provide clues to understanding the bystander effect and could define the signaling pathways involved in sustaining damage to these cells. The microarray technology serves as a tool to gain insight into the molecular pathways leading to bystander effect. Using medium from irradiated normal human diploid lung fibroblasts as a model system we examined gene expression alterations in bystander cells. The microarray data revealed that the radiation-induced gene expression profile in irradiated cells is different from unirradiated bystander cells suggesting that the pathways leading to biological effects in the bystander cells are different from the directly irradiated cells. The genes known to be responsive to ionizing radiation were observed in irradiated cells. Several genes were upregulated in cells receiving media from irradiated cells. Surprisingly no genes were found to be downregulated in these cells. A number of genes belonging to extracellular signaling, growth factors and several receptors were identified in bystander cells. Interestingly 15 genes involved in the cell communication processes were found to be upregulated. The induction of receptors and the cell

  11. Bystander effect: Biological endpoints and microarray analysis

    International Nuclear Information System (INIS)

    Chaudhry, M. Ahmad

    2006-01-01

    In cell populations exposed to ionizing radiation, the biological effects occur in a much larger proportion of cells than are estimated to be traversed by radiation. It has been suggested that irradiated cells are capable of providing signals to the neighboring unirradiated cells resulting in damage to these cells. This phenomenon is termed the bystander effect. The bystander effect induces persistent, long-term, transmissible changes that result in delayed death and neoplastic transformation. Because the bystander effect is relevant to carcinogenesis, it could have significant implications for risk estimation for radiation exposure. The nature of the bystander effect signal and how it impacts the unirradiated cells remains to be elucidated. Examination of the changes in gene expression could provide clues to understanding the bystander effect and could define the signaling pathways involved in sustaining damage to these cells. The microarray technology serves as a tool to gain insight into the molecular pathways leading to bystander effect. Using medium from irradiated normal human diploid lung fibroblasts as a model system we examined gene expression alterations in bystander cells. The microarray data revealed that the radiation-induced gene expression profile in irradiated cells is different from unirradiated bystander cells suggesting that the pathways leading to biological effects in the bystander cells are different from the directly irradiated cells. The genes known to be responsive to ionizing radiation were observed in irradiated cells. Several genes were upregulated in cells receiving media from irradiated cells. Surprisingly no genes were found to be downregulated in these cells. A number of genes belonging to extracellular signaling, growth factors and several receptors were identified in bystander cells. Interestingly 15 genes involved in the cell communication processes were found to be upregulated. The induction of receptors and the cell

  12. cDNA microarray screening in food safety

    International Nuclear Information System (INIS)

    Roy, Sashwati; Sen, Chandan K.

    2006-01-01

    The cDNA microarray technology and related bioinformatics tools presents a wide range of novel application opportunities. The technology may be productively applied to address food safety. In this mini-review article, we present an update highlighting the late breaking discoveries that demonstrate the vitality of cDNA microarray technology as a tool to analyze food safety with reference to microbial pathogens and genetically modified foods. In order to bring the microarray technology to mainstream food safety, it is important to develop robust user-friendly tools that may be applied in a field setting. In addition, there needs to be a standardized process for regulatory agencies to interpret and act upon microarray-based data. The cDNA microarray approach is an emergent technology in diagnostics. Its values lie in being able to provide complimentary molecular insight when employed in addition to traditional tests for food safety, as part of a more comprehensive battery of tests

  13. Versatile High Resolution Oligosaccharide Microarrays for Plant Glycobiology and Cell Wall Research

    DEFF Research Database (Denmark)

    Pedersen, Henriette Lodberg; Fangel, Jonatan Ulrik; McCleary, Barry

    2012-01-01

    Microarrays are powerful tools for high throughput analysis, and hundreds or thousands of molecular interactions can be assessed simultaneously using very small amounts of analytes. Nucleotide microarrays are well established in plant research, but carbohydrate microarrays are much less establish...

  14. Kaiser Engineers Hanford internal position paper -- Project W-236A, Multi-function Waste Tank Facility -- Peer reviews of selected activities

    International Nuclear Information System (INIS)

    Stine, M.D.

    1995-01-01

    The purpose of this paper is to develop and document a proposed position on the performance of independent peer reviews on selected design and analysis components of the Title 1 [Preliminary] and Title 2 [Final] design phases of the Multi-Function Waste Tank Facility [MWTF] project. An independent, third-party peer review is defined as a documented critical review of documents, data, designs, design inputs, tests, calculations, or related materials. The peer review should be conducted by persons independent of those who performed the work, but who are technically qualified to perform the original work. The peer review is used to assess the validity of assumptions and functional requirements, to assess the appropriateness and logic of selected methodologies and design inputs, and to verify calculations, analyses and computer software. The peer review can be conducted at the end of the design activity, at specific stages of the design process, or continuously and concurrently with the design activity. This latter method is often referred to as ''Continuous Peer Review.''

  15. Quality of Sulfadoxine-Pyrimethamine Given as Antimalarial Prophylaxis in Pregnant Women in Selected Health Facilities in Central Region of Ghana

    Directory of Open Access Journals (Sweden)

    Danny F. Yeboah

    2016-01-01

    Full Text Available The use of sulfadoxine-pyrimethamine (SP as an intermittent preventive treatment (IPT against malaria during pregnancy has become a policy in most sub-Sahara African countries and crucially depends on the efficacy of SP. This study sets out to evaluate the effectiveness of the SP given to the pregnant women in some selected health facilities in the Central Region of Ghana to prevent maternal malaria in pregnant women. A total of 543 pregnant women recruited from 7 selected health centres in Central Region of Ghana participated in the study. Parasite density of Plasmodium falciparum was determined from peripheral blood of the pregnant women using microscopy. High performance liquid chromatography (HPLC and dissolution tester were used to determine the quality of the SP. Malaria infection was recorded in 11.2% of pregnant women who had a history of SP consumption. SP failed the dissolution test. Pregnant women who did not receive IPT-SP were 44%. Low haemoglobin level was recorded in 73.5% of the pregnant women. The results indicated that SP was substandard. IPT-SP is ineffective in preventing malaria infection.

  16. A cell spot microarray method for production of high density siRNA transfection microarrays

    Directory of Open Access Journals (Sweden)

    Mpindi John-Patrick

    2011-03-01

    Full Text Available Abstract Background High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible. Results Here, we describe the optimization of a miniaturized cell spot microarray (CSMA method, which facilitates utilization of the transfection microarray technique for disparate RNAi analyses. To promote rapid adaptation of the method, the concept has been tested with a panel of 92 adherent cell types, including primary human cells. We demonstrate the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells. Conclusions The CSMA method facilitates reproducible preparation of highly parallel cell microarrays for large-scale gene knockdown analyses. This will be critical towards expanding the cell based functional genetic screens to include more RNAi constructs, allow combinatorial RNAi analyses, multi-parametric phenotypic readouts or comparative analysis of many different cell types.

  17. A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

    Directory of Open Access Journals (Sweden)

    Wang Lily

    2008-07-01

    Full Text Available Abstract Background Cancer diagnosis and clinical outcome prediction are among the most important emerging applications of gene expression microarray technology with several molecular signatures on their way toward clinical deployment. Use of the most accurate classification algorithms available for microarray gene expression data is a critical ingredient in order to develop the best possible molecular signatures for patient care. As suggested by a large body of literature to date, support vector machines can be considered "best of class" algorithms for classification of such data. Recent work, however, suggests that random forest classifiers may outperform support vector machines in this domain. Results In the present paper we identify methodological biases of prior work comparing random forests and support vector machines and conduct a new rigorous evaluation of the two algorithms that corrects these limitations. Our experiments use 22 diagnostic and prognostic datasets and show that support vector machines outperform random forests, often by a large margin. Our data also underlines the importance of sound research design in benchmarking and comparison of bioinformatics algorithms. Conclusion We found that both on average and in the majority of microarray datasets, random forests are outperformed by support vector machines both in the settings when no gene selection is performed and when several popular gene selection methods are used.

  18. Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks

    Directory of Open Access Journals (Sweden)

    Ji Wei

    2010-10-01

    Full Text Available Abstract Background Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discretization has been conducted, in the context of gene regulatory network inference from time series gene expression data. Results In this study, we propose a new discretization method "bikmeans", and compare its performance with four other widely-used discretization methods using different datasets, modeling algorithms and number of intervals. Sensitivities, specificities and total accuracies were calculated and statistical analysis was carried out. Bikmeans method always gave high total accuracies. Conclusions Our results indicate that proper discretization methods can consistently improve gene regulatory network inference independent of network modeling algorithms and datasets. Our new method, bikmeans, resulted in significant better total accuracies than other methods.

  19. Site selection process for radioactive waste repository (radioactive facility) in Cuba as a fundamental safety criteria; Proceso de seleccion de emplazamiento como criterio fundamental de la seguridad para el repositorio de desechos radiactivos (instalacion radiactiva) en Cuba

    Energy Technology Data Exchange (ETDEWEB)

    Vital, Jose Luis Peralta; Castillo, Reinaldo Gil; Chales Suarez, Gustavo; Rodriguez Reyes, Aymee [Centro de Tecnologia Nuclear, La Habana (Cuba)

    1999-11-01

    The paper show the process of search carried out for the selection of the safest site in the National territory, in order to sitting the Facility (Repository) that will disposal the low and intermediate level radioactive wastes, as well as the possible Storage Facility for nuclear spent Fuel (radioactive wastes of high activity). We summarize the obtained Methodology and the Criterions of exclusion adopted for the development of the Process of site selection, as well as the current condition of the researches that will permit the obtaining of the nominative objectives. (author) 18 refs., 1 fig., 1 tab.

  20. Microintaglio Printing for Soft Lithography-Based in Situ Microarrays

    Directory of Open Access Journals (Sweden)

    Manish Biyani

    2015-07-01

    Full Text Available Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called “microintaglio printing technology”, for large-scale bio-microarray fabrication using a microreactor array (µRA-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density, ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era.

  1. 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.

  2. Tissue Microarray TechnologyA Brief Review

    Directory of Open Access Journals (Sweden)

    Ramya S Vokuda

    2018-01-01

    Full Text Available In this era of modern revolutionisation in the field of medical laboratory technology, everyone is aiming at taking the innovations from laboratory to bed side. One such technique that is most relevant to the pathologic community is Tissue Microarray (TMA technology. This is becoming quite popular amongst all the members of this family, right from laboratory scientists to clinicians and residents to technologists. The reason for this technique to gain popularity is attributed to its cost effectiveness and time saving protocols. Though, every technique is accompanied by disadvantages, the benefits out number them. This technique is very versatile as many downstream molecular assays such as immunohistochemistry, cytogenetic studies, Fluorescent In situ-Hybridisation (FISH etc., can be carried out on a single slide with multiple numbers of samples. It is a very practical approach that aids effectively to identify novel biomarkers in cancer diagnostics and therapeutics. It helps in assessing the molecular markers on a large scale very quickly. Also, the quality assurance protocols in pathological laboratory has exploited TMA to a great extent. However, the application of TMA technology is beyond oncology. This review shall focus on the different aspects of this technology such as construction of TMA, instrumentation, types, advantages and disadvantages and utilisation of the technique in various disease conditions.

  3. 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.

  4. Transcriptome analysis of zebrafish embryogenesis using microarrays.

    Directory of Open Access Journals (Sweden)

    Sinnakaruppan Mathavan

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  5. 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.

  6. Application of microarray analysis on computer cluster and cloud platforms.

    Science.gov (United States)

    Bernau, C; Boulesteix, A-L; Knaus, J

    2013-01-01

    Analysis of recent high-dimensional biological data tends to be computationally intensive as many common approaches such as resampling or permutation tests require the basic statistical analysis to be repeated many times. A crucial advantage of these methods is that they can be easily parallelized due to the computational independence of the resampling or permutation iterations, which has induced many statistics departments to establish their own computer clusters. An alternative is to rent computing resources in the cloud, e.g. at Amazon Web Services. In this article we analyze whether a selection of statistical projects, recently implemented at our department, can be efficiently realized on these cloud resources. Moreover, we illustrate an opportunity to combine computer cluster and cloud resources. In order to compare the efficiency of computer cluster and cloud implementations and their respective parallelizations we use microarray analysis procedures and compare their runtimes on the different platforms. Amazon Web Services provide various instance types which meet the particular needs of the different statistical projects we analyzed in this paper. Moreover, the network capacity is sufficient and the parallelization is comparable in efficiency to standard computer cluster implementations. Our results suggest that many statistical projects can be efficiently realized on cloud resources. It is important to mention, however, that workflows can change substantially as a result of a shift from computer cluster to cloud computing.

  7. Application of four dyes in gene expression analyses by microarrays

    Directory of Open Access Journals (Sweden)

    van Schooten Frederik J

    2005-07-01

    Full Text Available Abstract Background DNA microarrays are widely used in gene expression analyses. To increase throughput and minimize costs without reducing gene expression data obtained, we investigated whether four mRNA samples can be analyzed simultaneously by applying four different fluorescent dyes. Results Following tests for cross-talk of fluorescence signals, Alexa 488, Alexa 594, Cyanine 3 and Cyanine 5 were selected for hybridizations. For self-hybridizations, a single RNA sample was labelled with all dyes and hybridized on commercial cDNA arrays or on in-house spotted oligonucleotide arrays. Correlation coefficients for all combinations of dyes were above 0.9 on the cDNA array. On the oligonucleotide array they were above 0.8, except combinations with Alexa 488, which were approximately 0.5. Standard deviation of expression differences for replicate spots were similar on the cDNA array for all dye combinations, but on the oligonucleotide array combinations with Alexa 488 showed a higher variation. Conclusion In conclusion, the four dyes can be used simultaneously for gene expression experiments on the tested cDNA array, but only three dyes can be used on the tested oligonucleotide array. This was confirmed by hybridizations of control with test samples, as all combinations returned similar numbers of differentially expressed genes with comparable effects on gene expression.

  8. A facile and selective approach for enrichment of l-cysteine in human plasma sample based on zinc organic polymer: Optimization by response surface methodology.

    Science.gov (United States)

    Bahrani, Sonia; Ghaedi, Mehrorang; Ostovan, Abbas; Javadian, Hamedreza; Mansoorkhani, Mohammad Javad Khoshnood; Taghipour, Tahere

    2018-02-05

    In this research, a facile and selective method was described to extract l-cysteine (l-Cys), an essential α-amino acid for anti-ageing playing an important role in human health, from human blood plasma sample. The importance of this research was the mild and time-consuming synthesis of zinc organic polymer (Zn-MOP) as an adsorbent and evaluation of its ability for efficient enrichment of l-Cys by ultrasound-assisted dispersive micro solid-phase extraction (UA-DMSPE) method. The structure of Zn-MOP was investigated by FT-IR, XRD and SEM. Analysis of variance (ANOVA) was applied for the experimental data to reach the best optimum conditions. The quantification of l-Cys was carried out by high performance liquid chromatography with UV detection set at λ=230nm. The calibration graph showed reasonable linear responses towards l-Cys concentrations in the range of 4.0-1000μg/L (r 2 =0.999) with low limit of detection (0.76μg/L, S/N=3) and RSD≤2.18 (n=3). The results revealed the applicability and high performance of this novel strategy in detecting trace l-Cys by Zn-MOP in complicated matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Cell-Based Microarrays for In Vitro Toxicology

    Science.gov (United States)

    Wegener, Joachim

    2015-07-01

    DNA/RNA and protein microarrays have proven their outstanding bioanalytical performance throughout the past decades, given the unprecedented level of parallelization by which molecular recognition assays can be performed and analyzed. Cell microarrays (CMAs) make use of similar construction principles. They are applied to profile a given cell population with respect to the expression of specific molecular markers and also to measure functional cell responses to drugs and chemicals. This review focuses on the use of cell-based microarrays for assessing the cytotoxicity of drugs, toxins, or chemicals in general. It also summarizes CMA construction principles with respect to the cell types that are used for such microarrays, the readout parameters to assess toxicity, and the various formats that have been established and applied. The review ends with a critical comparison of CMAs and well-established microtiter plate (MTP) approaches.

  10. High throughput screening of starch structures using carbohydrate microarrays

    DEFF Research Database (Denmark)

    Tanackovic, Vanja; Rydahl, Maja Gro; Pedersen, Henriette Lodberg

    2016-01-01

    In this study we introduce the starch-recognising carbohydrate binding module family 20 (CBM20) from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated...

  11. Microarray of DNA probes on carboxylate functional beads surface

    Institute of Scientific and Technical Information of China (English)

    黄承志; 李原芳; 黄新华; 范美坤

    2000-01-01

    The microarray of DNA probes with 5’ -NH2 and 5’ -Tex/3’ -NH2 modified terminus on 10 um carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) is characterized in the preseni paper. it was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentra-tion of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.

  12. Microarray of DNA probes on carboxylate functional beads surface

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The microarray of DNA probes with 5′-NH2 and 5′-Tex/3′-NH2 modified terminus on 10 m m carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)- carbodiimide (EDC) is characterized in the present paper. It was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentration of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.

  13. Rapid Diagnosis of Bacterial Meningitis Using a Microarray

    Directory of Open Access Journals (Sweden)

    Ren-Jy Ben

    2008-06-01

    Conclusion: The microarray method provides a more accurate and rapid diagnostic tool for bacterial meningitis compared to traditional culture methods. Clinical application of this new technique may reduce the potential risk of delay in treatment.

  14. Variance estimation in the analysis of microarray data

    KAUST Repository

    Wang, Yuedong; Ma, Yanyuan; Carroll, Raymond J.

    2009-01-01

    Microarrays are one of the most widely used high throughput technologies. One of the main problems in the area is that conventional estimates of the variances that are required in the t-statistic and other statistics are unreliable owing

  15. Novel Protein Microarray Technology to Examine Men with Prostate Cancer

    National Research Council Canada - National Science Library

    Lilja, Hans

    2005-01-01

    The authors developed a novel macro and nanoporous silicon surface for protein microarrays to facilitate high-throughput biomarker discovery, and high-density protein-chip array analyses of complex biological samples...

  16. Universal Reference RNA as a standard for microarray experiments

    Directory of Open Access Journals (Sweden)

    Fero Michael

    2004-03-01

    Full Text Available Abstract Background Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR, developed with the goal of providing hybridization signal at each microarray probe location (spot. Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment. Results Human, mouse and rat URR (UHRR, UMRR and URRR, respectively were prepared from pools of RNA derived from individual cell lines representing different tissues. A variety of microarrays were used to determine percentage of spots hybridizing with URR and producing signal above a user defined threshold (microarray coverage. Microarray coverage was consistently greater than 80% for all arrays tested. We confirmed that individual cell lines contribute their own unique set of genes to URR, arguing for a pool of RNA from several cell lines as a better configuration for URR as opposed to a single cell line source for URR. Microarray coverage comparing two separately prepared batches each of UHRR, UMRR and URRR were highly correlated (Pearson's correlation coefficients of 0.97. Conclusion Results of this study demonstrate that large quantities of pooled RNA from individual cell lines are reproducibly prepared and possess diverse gene representation. This type of reference provides a standard for reducing variation in microarray experiments and allows more reliable comparison of gene expression data within and between experiments and

  17. Addressable droplet microarrays for single cell protein analysis.

    Science.gov (United States)

    Salehi-Reyhani, Ali; Burgin, Edward; Ces, Oscar; Willison, Keith R; Klug, David R

    2014-11-07

    Addressable droplet microarrays are potentially attractive as a way to achieve miniaturised, reduced volume, high sensitivity analyses without the need to fabricate microfluidic devices or small volume chambers. We report a practical method for producing oil-encapsulated addressable droplet microarrays which can be used for such analyses. To demonstrate their utility, we undertake a series of single cell analyses, to determine the variation in copy number of p53 proteins in cells of a human cancer cell line.

  18. Microarrays for Universal Detection and Identification of Phytoplasmas

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Nyskjold, Henriette; Bertaccini, Assunta

    2013-01-01

    Detection and identification of phytoplasmas is a laborious process often involving nested PCR followed by restriction enzyme analysis and fine-resolution gel electrophoresis. To improve throughput, other methods are needed. Microarray technology offers a generic assay that can potentially detect...... and differentiate all types of phytoplasmas in one assay. The present protocol describes a microarray-based method for identification of phytoplasmas to 16Sr group level....

  19. Plant-pathogen interactions: what microarray tells about it?

    Science.gov (United States)

    Lodha, T D; Basak, J

    2012-01-01

    Plant defense responses are mediated by elementary regulatory proteins that affect expression of thousands of genes. Over the last decade, microarray technology has played a key role in deciphering the underlying networks of gene regulation in plants that lead to a wide variety of defence responses. Microarray is an important tool to quantify and profile the expression of thousands of genes simultaneously, with two main aims: (1) gene discovery and (2) global expression profiling. Several microarray technologies are currently in use; most include a glass slide platform with spotted cDNA or oligonucleotides. Till date, microarray technology has been used in the identification of regulatory genes, end-point defence genes, to understand the signal transduction processes underlying disease resistance and its intimate links to other physiological pathways. Microarray technology can be used for in-depth, simultaneous profiling of host/pathogen genes as the disease progresses from infection to resistance/susceptibility at different developmental stages of the host, which can be done in different environments, for clearer understanding of the processes involved. A thorough knowledge of plant disease resistance using successful combination of microarray and other high throughput techniques, as well as biochemical, genetic, and cell biological experiments is needed for practical application to secure and stabilize yield of many crop plants. This review starts with a brief introduction to microarray technology, followed by the basics of plant-pathogen interaction, the use of DNA microarrays over the last decade to unravel the mysteries of plant-pathogen interaction, and ends with the future prospects of this technology.

  20. Gene targeting associated with the radiation sensitivity in squamous cell carcinoma by using microarray analysis

    International Nuclear Information System (INIS)

    Nimura, Yoshinori; Kumagai, Ken; Kouzu, Yoshinao; Higo, Morihiro; Kato, Yoshikuni; Seki, Naohiko; Yamada, Shigeru

    2005-01-01

    In order to identify a set of genes related to radiation sensitivity of squamous cell carcinoma (SCC) and establish a predictive method, we compared expression profiles of radio-sensitive/radio-resistant SCC cell lines, using the in-house cDNA microarray consisting of 2,201 human genes derived from full-length enriched SCC cDNA libraries and the Human oligo chip 30 K (Hitachi Software Engineering). Surviving fractions (SF) after irradiation of heavy iron were calculated by colony formation assay. Three pairs (TE2-TE13, YES5-YES6, and HSC3-HSC2), sensitive (SF1 0.6), were selected for the microarray analysis. The results of cDNA microarray analysis showed that 20 genes in resistant cell lines and 5 genes in sensitive cell lines were up regulated more than 1.5-fold compared with sensitive and resistant cell lines respectively. Fourteen out of 25 genes were confirmed the gene expression profiles by real-time polymerase chain reaction (PCR). Twenty-seven genes identified by Human oligo chip 30 K are candidate for the markers to distinguish radio-sensitive from radio-resistant. These results suggest that the isolated 27 genes are the candidates that might be used as specific molecular markers to predict radiation sensitivity. (author)

  1. Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.

    Directory of Open Access Journals (Sweden)

    Michael A Cook

    Full Text Available BACKGROUND: Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM, we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. CONCLUSIONS/SIGNIFICANCE: These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.

  2. Microarray Meta-Analysis of RNA-Binding Protein Functions in Alternative Polyadenylation

    Science.gov (United States)

    Hu, Wenchao; Liu, Yuting; Yan, Jun

    2014-01-01

    Alternative polyadenylation (APA) is a post-transcriptional mechanism to generate diverse mRNA transcripts with different 3′UTRs from the same gene. In this study, we systematically searched for the APA events with differential expression in public mouse microarray data. Hundreds of genes with over-represented differential APA events and the corresponding experiments were identified. We further revealed that global APA differential expression occurred prevalently in tissues such as brain comparing to peripheral tissues, and biological processes such as development, differentiation and immune responses. Interestingly, we also observed widespread differential APA events in RNA-binding protein (RBP) genes such as Rbm3, Eif4e2 and Elavl1. Given the fact that RBPs are considered as the main regulators of differential APA expression, we constructed a co-expression network between APAs and RBPs using the microarray data. Further incorporation of CLIP-seq data of selected RBPs showed that Nova2 represses and Mbnl1 promotes the polyadenylation of closest poly(A) sites respectively. Altogether, our study is the first microarray meta-analysis in a mammal on the regulation of APA by RBPs that integrated massive mRNA expression data under a wide-range of biological conditions. Finally, we present our results as a comprehensive resource in an online website for the research community. PMID:24622240

  3. Cross-species hybridization of woodchuck hepatitis virus-induced hepatocellular carcinoma using human oligonucleotide microarrays

    Institute of Scientific and Technical Information of China (English)

    Paul W Anderson; Bud C Tennant; Zhenghong Lee

    2006-01-01

    AIM: To demonstrate the feasibility of using woodchuck samples on human microarrays, to provide insight into pathways involving positron emission tomography (PET) imaging tracers and to identify genes that could be potential molecular imaging targets for woodchuck hepatocellular carcinoma.METHODS: Labeled cRNA from woodchuck tissue samples were hybridized to Affymetrix U133 plus 2.0 GeneChips(R). Ten genes were selected for validation using quantitative RT-PCR and literature review was made.RESULTS: Testis enhanced gene transcript (BAX Inhibitor 1), alpha-fetoprotein, isocitrate dehydrogenase 3 (NAD+) beta, acetyl-CoA synthetase 2, carnitine palmitoyltransferase 2, and N-myc2 were up-regulated and spermidine/spermine N1-acetyltransferase was down-regulated in the woodchuck HCC. We also found previously published results supporting 8 of the 10 most up-regulated genes and all 10 of the 10 most downregulated genes.CONCLUSION: Many of our microarray results were validated using RT-PCR or literature search. Hence, we believe that woodchuck HCC and non-cancerous liver samples can be used on human microarrays to yield meaningful results.

  4. GEPAS, a web-based tool for microarray data analysis and interpretation

    Science.gov (United States)

    Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Huerta-Cepas, Jaime; Minguez, Pablo; Alloza, Eva; Al-Shahrour, Fátima; Vegas-Azcárate, Susana; Goetz, Stefan; Escobar, Pablo; Garcia-Garcia, Francisco; Conesa, Ana; Montaner, David; Dopazo, Joaquín

    2008-01-01

    Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org. PMID:18508806

  5. ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

    Directory of Open Access Journals (Sweden)

    Krasnogor Natalio

    2009-10-01

    Full Text Available Abstract Background Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

  6. Protein microarray: sensitive and effective immunodetection for drug residues

    Directory of Open Access Journals (Sweden)

    Zer Cindy

    2010-02-01

    Full Text Available Abstract Background Veterinary drugs such as clenbuterol (CL and sulfamethazine (SM2 are low molecular weight ( Results The artificial antigens were spotted on microarray slides. Standard concentrations of the compounds were added to compete with the spotted antigens for binding to the antisera to determine the IC50. Our microarray assay showed the IC50 were 39.6 ng/ml for CL and 48.8 ng/ml for SM2, while the traditional competitive indirect-ELISA (ci-ELISA showed the IC50 were 190.7 ng/ml for CL and 156.7 ng/ml for SM2. We further validated the two methods with CL fortified chicken muscle tissues, and the protein microarray assay showed 90% recovery while the ci-ELISA had 76% recovery rate. When tested with CL-fed chicken muscle tissues, the protein microarray assay had higher sensitivity (0.9 ng/g than the ci-ELISA (0.1 ng/g for detection of CL residues. Conclusions The protein microarrays showed 4.5 and 3.5 times lower IC50 than the ci-ELISA detection for CL and SM2, respectively, suggesting that immunodetection of small molecules with protein microarray is a better approach than the traditional ELISA technique.

  7. A comparative analysis of DNA barcode microarray feature size

    Directory of Open Access Journals (Sweden)

    Smith Andrew M

    2009-10-01

    Full Text Available Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density, but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO collection used for screens of pooled yeast (Saccharomyces cerevisiae deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.

  8. Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

    Directory of Open Access Journals (Sweden)

    Andrea Flannery

    2015-12-01

    Full Text Available Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i conventional carbohydrate or glycan microarrays; (ii whole mucin microarrays; and (iii microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments.

  9. Calling Biomarkers in Milk Using a Protein Microarray on Your Smartphone

    Science.gov (United States)

    Ludwig, Susann K. J.; Tokarski, Christian; Lang, Stefan N.; van Ginkel, Leendert A.; Zhu, Hongying; Ozcan, Aydogan; Nielen, Michel W. F.

    2015-01-01

    Here we present the concept of a protein microarray-based fluorescence immunoassay for multiple biomarker detection in milk extracts by an ordinary smartphone. A multiplex immunoassay was designed on a microarray chip, having built-in positive and negative quality controls. After the immunoassay procedure, the 48 microspots were labelled with Quantum Dots (QD) depending on the protein biomarker levels in the sample. QD-fluorescence was subsequently detected by the smartphone camera under UV light excitation from LEDs embedded in a simple 3D-printed opto-mechanical smartphone attachment. The somewhat aberrant images obtained under such conditions, were corrected by newly developed Android-based software on the same smartphone, and protein biomarker profiles were calculated. The indirect detection of recombinant bovine somatotropin (rbST) in milk extracts based on altered biomarker profile of anti-rbST antibodies was selected as a real-life challenge. RbST-treated and untreated cows clearly showed reproducible treatment-dependent biomarker profiles in milk, in excellent agreement with results from a flow cytometer reference method. In a pilot experiment, anti-rbST antibody detection was multiplexed with the detection of another rbST-dependent biomarker, insulin-like growth factor 1 (IGF-1). Milk extract IGF-1 levels were found to be increased after rbST treatment and correlated with the results obtained from the reference method. These data clearly demonstrate the potential of the portable protein microarray concept towards simultaneous detection of multiple biomarkers. We envisage broad application of this ‘protein microarray on a smartphone’-concept for on-site testing, e.g., in food safety, environment and health monitoring. PMID:26308444

  10. Calling Biomarkers in Milk Using a Protein Microarray on Your Smartphone.

    Directory of Open Access Journals (Sweden)

    Susann K J Ludwig

    Full Text Available Here we present the concept of a protein microarray-based fluorescence immunoassay for multiple biomarker detection in milk extracts by an ordinary smartphone. A multiplex immunoassay was designed on a microarray chip, having built-in positive and negative quality controls. After the immunoassay procedure, the 48 microspots were labelled with Quantum Dots (QD depending on the protein biomarker levels in the sample. QD-fluorescence was subsequently detected by the smartphone camera under UV light excitation from LEDs embedded in a simple 3D-printed opto-mechanical smartphone attachment. The somewhat aberrant images obtained under such conditions, were corrected by newly developed Android-based software on the same smartphone, and protein biomarker profiles were calculated. The indirect detection of recombinant bovine somatotropin (rbST in milk extracts based on altered biomarker profile of anti-rbST antibodies was selected as a real-life challenge. RbST-treated and untreated cows clearly showed reproducible treatment-dependent biomarker profiles in milk, in excellent agreement with results from a flow cytometer reference method. In a pilot experiment, anti-rbST antibody detection was multiplexed with the detection of another rbST-dependent biomarker, insulin-like growth factor 1 (IGF-1. Milk extract IGF-1 levels were found to be increased after rbST treatment and correlated with the results obtained from the reference method. These data clearly demonstrate the potential of the portable protein microarray concept towards simultaneous detection of multiple biomarkers. We envisage broad application of this 'protein microarray on a smartphone'-concept for on-site testing, e.g., in food safety, environment and health monitoring.

  11. Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton

    Science.gov (United States)

    Muller, Jean; Mehlen, André; Vetter, Guillaume; Yatskou, Mikalai; Muller, Arnaud; Chalmel, Frédéric; Poch, Olivier; Friederich, Evelyne; Vallar, Laurent

    2007-01-01

    Background The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expression of the set of actin cytoskeleton genes are integrated to control actin dynamics and organisation is currently a challenge and should provide insights in identifying potential targets for drug discovery. Here we report the development of a dedicated microarray, the Actichip, containing 60-mer oligonucleotide probes for 327 genes selected for transcriptome analysis of the human actin cytoskeleton. Results Genomic data and sequence analysis features were retrieved from GenBank and stored in an integrative database called Actinome. From these data, probes were designed using a home-made program (CADO4MI) allowing sequence refinement and improved probe specificity by combining the complementary information recovered from the UniGene and RefSeq databases. Actichip performance was analysed by hybridisation with RNAs extracted from epithelial MCF-7 cells and human skeletal muscle. Using thoroughly standardised procedures, we obtained microarray images with excellent quality resulting in high data reproducibility. Actichip displayed a large dynamic range extending over three logs with a limit of sensitivity between one and ten copies of transcript per cell. The array allowed accurate detection of small changes in gene expression and reliable classification of samples based on the expression profiles of tissue-specific genes. When compared to two other oligonucleotide microarray platforms, Actichip showed similar sensitivity and concordant expression ratios. Moreover, Actichip was able to discriminate the highly similar actin isoforms whereas the two other platforms did not. Conclusion Our data demonstrate that

  12. Can subtle changes in gene expression be consistently detected with different microarray platforms?

    Directory of Open Access Journals (Sweden)

    Kuiper Rowan

    2008-03-01

    Full Text Available Abstract Background The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Results Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms. Conclusion The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to

  13. Facilities & Leadership

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    Department of Veterans Affairs — The facilities web service provides VA facility information. The VA facilities locator is a feature that is available across the enterprise, on any webpage, for the...

  14. A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina.

    Science.gov (United States)

    Bidard, Frédérique; Imbeaud, Sandrine; Reymond, Nancie; Lespinet, Olivier; Silar, Philippe; Clavé, Corinne; Delacroix, Hervé; Berteaux-Lecellier, Véronique; Debuchy, Robert

    2010-06-18

    The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.

  15. A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

    Directory of Open Access Journals (Sweden)

    Bidard Frédérique

    2010-06-01

    Full Text Available Abstract Background The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. Findings We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS, we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. Conclusions A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.

  16. Facile preparation of an alternating copolymer-based high molecular shape-selective organic phase for reversed-phase liquid chromatography.

    Science.gov (United States)

    Mallik, Abul K; Noguchi, Hiroki; Rahman, Mohammed Mizanur; Takafuji, Makoto; Ihara, Hirotaka

    2018-06-22

    The synthesis of a new alternating copolymer-grafted silica phase is described for the separation of shape-constrained isomers of polycyclic aromatic hydrocarbons (PAHs) and tocopherols in reversed-phase high-performance liquid chromatography (RP-HPLC). Telomerization of the monomers (octadecyl acrylate and N-methylmaleimide) was carried out with a silane coupling agent; 3-mercaptopropyltrimethoxysilane (MPS), and the telomer (T) was grafted onto porous silica surface to prepare the alternating copolymer-grafted silica phase (Sil-alt-T). The new hybrid material was characterized by elemental analyses, diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, and solid-state 13 C and 29 Si cross-polarization magic-angle spinning (CP/MAS) NMR spectroscopy. The results of 13 C CP/MAS NMR demonstrated that the alkyl chains of the grafted polymers in Sil-alt-T remained disordered, amorphous, and mobile represented by gauche conformational form. Separation abilities and molecular-shape selectivities of the prepared organic phase were evaluated by the separation of PAHs isomers and Standard Reference Material 869b, Column Selectivity Test Mixture for Liquid Chromatography, respectively and compared with commercially available octadecylsilylated silica (ODS) and C 30 columns as well as previously reported alternating copolymer-based column. The effectiveness of this phase is also demonstrated by the separation of tocopherol isomers. Oriented functional groups along the polymer main chains and cavity formations are investigated to be the driving force for better separation with multiple-interactions with the solutes. One of the advantages of the Sil-alt-T phase to that of the previously reported phase is the synthesis of the telomer first and then immobilized onto silica surface. In this case, the telomer was characterized easily with simple spectroscopic techniques and the molecular mass and polydispersity index of the telomer were determined by size exclusion

  17. Which Members of the Microbial Communities Are Active? Microarrays

    Science.gov (United States)

    Morris, Brandon E. L.

    only at the early stages of understanding the microbial processes that occur in petroliferous formations and the surrounding subterranean environment. Important first steps in characterising the microbiology of oilfield systems involve identifying the microbial community structure and determining how population diversity changes are affected by the overall geochemical and biological parameters of the system. This is relatively easy to do today by using general 16S rRNA primers for PCR and building clone libraries. For example, previous studies using molecular methods characterised many dominant prokaryotes in petroleum reservoirs (Orphan et al., 2000) and in two Alaskan North Slope oil facilities (Duncan et al., 2009; Pham et al., 2009). However, the problem is that more traditional molecular biology approaches, such as 16S clone libraries, fail to detect large portions of the community perhaps missing up to half of the biodiversity (see Hong et al., 2009) and require significant laboratory time to construct large libraries necessary to increase the probability of detecting the majority of even bacterial biodiversity. In the energy sector, the overarching desire would be to quickly assess the extent of in situ hydrocarbon biodegradation or to disrupt detrimental processes such as biofouling, and in these cases it may not be necessary to identify specific microbial species. Rather, it would be more critical to evaluate metabolic processes or monitor gene products that are implicated in the specific activity of interest. Research goals such as these are well suited for a tailored application of microarray technology.

  18. Biochemistry Facility

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    Federal Laboratory Consortium — The Biochemistry Facility provides expert services and consultation in biochemical enzyme assays and protein purification. The facility currently features 1) Liquid...

  19. Prevalence of pregnancy-related complications and course of labour of surviving women who gave birth in selected health facilities in Rwanda: a health facility-based, cross-sectional study.

    Science.gov (United States)

    Semasaka Sengoma, Jean Paul; Krantz, Gunilla; Nzayirambaho, Manasse; Munyanshongore, Cyprien; Edvardsson, Kristina; Mogren, Ingrid

    2017-07-09

    This study estimated health facility-based prevalence for pre-eclampsia/eclampsia, postpartum haemorrhage and caesarean section (CS) due to prolonged labour/dystocia. The background characteristics of Rwandan pregnant women, the course of labour and the level of healthcare were investigated in relation to pregnancy and delivery outcomes. This is health facility-based study and data were collected in 2014-2015 through structured interviews and medical records (n=817) in Kigali and Northern Province, Rwanda. Frequencies and prevalence were used to describe participants' background factors, labour and delivery-related characteristics. Bivariable and multivariable logistic regression models were performed for different background factors and pregnancy/delivery outcomes. Pre-eclampsia/eclampsia, postpartum haemorrhage and CS due to prolonged labour/dystocia represented 1%, 2.7% and 5.4% of all participants, respectively. In total, 56.4% of the participants were transferred from facilities with low levels to those with higher levels of healthcare, and the majority were transferred from health centres to district hospitals, with CS as the main reason for transfer. Participants who arrived at the health facility with cervical dilation grade of ≤3 cm spent more hours in maternity ward than those who arrived with cervical dilatation grade of ≥4 cm. Risk factors for CS due to prolonged labour or dystocia were poor households, nulliparity and residence far from health facility. The estimated health facility-based prevalence of pregnancy-related complications was relatively low in this sample from Rwanda. CS was the main reason for the transfer of pregnant women from health centres to district hospitals. Upgrading the capacity of health centres in the management of pregnant women in Rwanda may improve maternal and fetal health. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is

  20. The impact of two Department of Energy orders on the design and cost of select plutonium facilities at Los Alamos National Laboratory

    International Nuclear Information System (INIS)

    Rey, V.C.

    1999-01-01

    The Los Alamos National Laboratory (LANL) is a research and development facility in northern New Mexico, owned by the federal government and operated for the US Department of Energy (DOE) by the University of California (UC). LANL conducts research and experiments in many arenas including plutonium. Its plutonium facilities are required to meet the facility design and safety criteria of applicable DOE orders as specified in the UC contract. Although DOE 420.1, Facility Safety, superseded DOE 6430.1A, General Design Criteria, the UC contract requires LANL to adhere to DOE 6430.1A, Division 13 in its special nuclear facilities. A comparison of costs and savings relative to installation of double-wall piping at two LANL plutonium facilities is demonstrated. DOE 6430.1A is prescriptive in its design criteria whereas DOE 420.1 is a performance-based directive. The differences in these orders impact time and design costs in nuclear construction projects. LANL's approach to integrated quality and conduct of operations for design, needs to be re-evaluated. In conclusion, there is a need for highly-technical, knowledgeable people and an integrated, quality/conduct of operations-based approach to assure that nuclear facilities are designed and constructed in a safe and cost-effective manner

  1. Combination of Small Molecule Microarray and Confocal Microscopy Techniques for Live Cell Staining Fluorescent Dye Discovery

    Directory of Open Access Journals (Sweden)

    Attila Bokros

    2013-08-01

    Full Text Available Discovering new fluorochromes is significantly advanced by high-throughput screening (HTS methods. In the present study a combination of small molecule microarray (SMM prescreening and confocal laser scanning microscopy (CLSM was developed in order to discover novel cell staining fluorescent dyes. Compounds with high native fluorescence were selected from a 14,585-member library and further tested on living cells under the microscope. Eleven compartment-specific, cell-permeable (or plasma membrane-targeted fluorochromes were identified. Their cytotoxicity was tested and found that between 1–10 micromolar range, they were non-toxic even during long-term incubations.

  2. Identification of a radiosensitivity signature using integrative metaanalysis of published microarray data for NCI-60 cancer cells

    Directory of Open Access Journals (Sweden)

    Kim Han

    2012-07-01

    Full Text Available Abstract Background In the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathways, four different microarray experiments were reanalyzed before radiotherapy. Results Radiosensitivity profiling data using clonogenic assay and gene expression profiling data from four published microarray platforms applied to NCI-60 cancer cell panel were used. The survival fraction at 2 Gy (SF2, range from 0 to 1 was calculated as a measure of radiosensitivity and a linear regression model was applied to identify genes or a gene set with a correlation between expression and radiosensitivity (SF2. Radiosensitivity signature genes were identified using significant analysis of microarrays (SAM and gene set analysis was performed using a global test using linear regression model. Using the radiation-related signaling pathway and identified genes, a genetic network was generated. According to SAM, 31 genes were identified as common to all the microarray platforms and therefore a common radiosensitivity signature. In gene set analysis, functions in the cell cycle, DNA replication, and cell junction, including adherence and gap junctions were related to radiosensitivity. The integrin, VEGF, MAPK, p53, JAK-STAT and Wnt signaling pathways were overrepresented in radiosensitivity. Significant genes including ACTN1, CCND1, HCLS1, ITGB5, PFN2, PTPRC, RAB13, and WAS, which are adhesion-related molecules that were identified by both SAM and gene set analysis, and showed interaction in the genetic network with the integrin signaling pathway. Conclusions Integration of four different microarray experiments and gene selection using gene set analysis discovered possible target genes and pathways relevant to radiosensitivity. Our results suggested that the identified genes are candidates for radiosensitivity biomarkers and that

  3. Integration of Multiplexed Microfluidic Electrokinetic Concentrators with a Morpholino Microarray via Reversible Surface Bonding for Enhanced DNA Hybridization.

    Science.gov (United States)

    Martins, Diogo; Wei, Xi; Levicky, Rastislav; Song, Yong-Ak

    2016-04-05

    We describe a microfluidic concentration device to accelerate the surface hybridization reaction between DNA and morpholinos (MOs) for enhanced detection. The microfluidic concentrator comprises a single polydimethylsiloxane (PDMS) microchannel onto which an ion-selective layer of conductive polymer poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) ( PSS) was directly printed and then reversibly surface bonded onto a morpholino microarray for hybridization. Using this electrokinetic trapping concentrator, we could achieve a maximum concentration factor of ∼800 for DNA and a limit of detection of 10 nM within 15 min. In terms of the detection speed, it enabled faster hybridization by around 10-fold when compared to conventional diffusion-based hybridization. A significant advantage of our approach is that the fabrication of the microfluidic concentrator is completely decoupled from the microarray; by eliminating the need to deposit an ion-selective layer on the microarray surface prior to device integration, interfacing between both modules, the PDMS chip for electrokinetic concentration and the substrate for DNA sensing are easier and applicable to any microarray platform. Furthermore, this fabrication strategy facilitates a multiplexing of concentrators. We have demonstrated the proof-of-concept for multiplexing by building a device with 5 parallel concentrators connected to a single inlet/outlet and applying it to parallel concentration and hybridization. Such device yielded similar concentration and hybridization efficiency compared to that of a single-channel device without adding any complexity to the fabrication and setup. These results demonstrate that our concentrator concept can be applied to the development of a highly multiplexed concentrator-enhanced microarray detection system for either genetic analysis or other diagnostic assays.

  4. Significance analysis of lexical bias in microarray data

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    Falkow Stanley

    2003-04-01

    Full Text Available Abstract Background Genes that are determined to be significantly differentially regulated in microarray analyses often appear to have functional commonalities, such as being components of the same biochemical pathway. This results in certain words being under- or overrepresented in the list of genes. Distinguishing between biologically meaningful trends and artifacts of annotation and analysis procedures is of the utmost importance, as only true biological trends are of interest for further experimentation. A number of sophisticated methods for identification of significant lexical trends are currently available, but these methods are generally too cumbersome for practical use by most microarray users. Results We have developed a tool, LACK, for calculating the statistical significance of apparent lexical bias in microarray datasets. The frequency of a user-specified list of search terms in a list of genes which are differentially regulated is assessed for statistical significance by comparison to randomly generated datasets. The simplicity of the input files and user interface targets the average microarray user who wishes to have a statistical measure of apparent lexical trends in analyzed datasets without the need for bioinformatics skills. The software is available as Perl source or a Windows executable. Conclusion We have used LACK in our laboratory to generate biological hypotheses based on our microarray data. We demonstrate the program's utility using an example in which we confirm significant upregulation of SPI-2 pathogenicity island of Salmonella enterica serovar Typhimurium by the cation chelator dipyridyl.

  5. A Fisheye Viewer for microarray-based gene expression data.

    Science.gov (United States)

    Wu, Min; Thao, Cheng; Mu, Xiangming; Munson, Ethan V

    2006-10-13

    Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of raw microarray-based gene expression data. This paper presents one such interface--an electronic table (E-table) that uses fisheye distortion technology. The Fisheye Viewer for microarray-based gene expression data has been successfully developed to view MIAME data stored in the MAGE-ML format. The viewer can be downloaded from the project web site http://polaris.imt.uwm.edu:7777/fisheye/. The fisheye viewer was implemented in Java so that it could run on multiple platforms. We implemented the E-table by adapting JTable, a default table implementation in the Java Swing user interface library. Fisheye views use variable magnification to balance magnification for easy viewing and compression for maximizing the amount of data on the screen. This Fisheye Viewer is a lightweight but useful tool for biologists to quickly overview the raw microarray-based gene expression data in an E-table.

  6. A fisheye viewer for microarray-based gene expression data

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    Munson Ethan V

    2006-10-01

    Full Text Available Abstract Background Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of raw microarray-based gene expression data. This paper presents one such interface – an electronic table (E-table that uses fisheye distortion technology. Results The Fisheye Viewer for microarray-based gene expression data has been successfully developed to view MIAME data stored in the MAGE-ML format. The viewer can be downloaded from the project web site http://polaris.imt.uwm.edu:7777/fisheye/. The fisheye viewer was implemented in Java so that it could run on multiple platforms. We implemented the E-table by adapting JTable, a default table implementation in the Java Swing user interface library. Fisheye views use variable magnification to balance magnification for easy viewing and compression for maximizing the amount of data on the screen. Conclusion This Fisheye Viewer is a lightweight but useful tool for biologists to quickly overview the raw microarray-based gene expression data in an E-table.

  7. AN IMPROVED FUZZY CLUSTERING ALGORITHM FOR MICROARRAY IMAGE SPOTS SEGMENTATION

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    V.G. Biju

    2015-11-01

    Full Text Available An automatic cDNA microarray image processing using an improved fuzzy clustering algorithm is presented in this paper. The spot segmentation algorithm proposed uses the gridding technique developed by the authors earlier, for finding the co-ordinates of each spot in an image. Automatic cropping of spots from microarray image is done using these co-ordinates. The present paper proposes an improved fuzzy clustering algorithm Possibility fuzzy local information c means (PFLICM to segment the spot foreground (FG from background (BG. The PFLICM improves fuzzy local information c means (FLICM algorithm by incorporating typicality of a pixel along with gray level information and local spatial information. The performance of the algorithm is validated using a set of simulated cDNA microarray images added with different levels of AWGN noise. The strength of the algorithm is tested by computing the parameters such as the Segmentation matching factor (SMF, Probability of error (pe, Discrepancy distance (D and Normal mean square error (NMSE. SMF value obtained for PFLICM algorithm shows an improvement of 0.9 % and 0.7 % for high noise and low noise microarray images respectively compared to FLICM algorithm. The PFLICM algorithm is also applied on real microarray images and gene expression values are computed.

  8. Advanced Data Mining of Leukemia Cells Micro-Arrays

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    Richard S. Segall

    2009-12-01

    Full Text Available This paper provides continuation and extensions of previous research by Segall and Pierce (2009a that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM. As Segall and Pierce (2009a and Segall and Pierce (2009b the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is provided on the work of others pertaining to the applications of data mining to micro-array databases of Leukemia cells and micro-array databases in general. As noted in predecessor article by Segall and Pierce (2009a, micro-array databases are one of the most popular functional genomics tools in use today. This research in this paper is intended to use advanced data mining technologies for better interpretations and knowledge discovery as generated by the patterns of gene expressions of HL60, Jurkat, NB4 and U937 Leukemia cells. The advanced data mining performed entailed using other data mining tools such as cubic clustering criterion, variable importance rankings, decision trees, and more detailed examinations of data mining statistics and study of other self-organized maps (SOM clustering regions of workspace as generated by SAS Enterprise Miner version 4. Conclusions and future directions of the research are also presented.

  9. Spot detection and image segmentation in DNA microarray data.

    Science.gov (United States)

    Qin, Li; Rueda, Luis; Ali, Adnan; Ngom, Alioune

    2005-01-01

    Following the invention of microarrays in 1994, the development and applications of this technology have grown exponentially. The numerous applications of microarray technology include clinical diagnosis and treatment, drug design and discovery, tumour detection, and environmental health research. One of the key issues in the experimental approaches utilising microarrays is to extract quantitative information from the spots, which represent genes in a given experiment. For this process, the initial stages are important and they influence future steps in the analysis. Identifying the spots and separating the background from the foreground is a fundamental problem in DNA microarray data analysis. In this review, we present an overview of state-of-the-art methods for microarray image segmentation. We discuss the foundations of the circle-shaped approach, adaptive shape segmentation, histogram-based methods and the recently introduced clustering-based techniques. We analytically show that clustering-based techniques are equivalent to the one-dimensional, standard k-means clustering algorithm that utilises the Euclidean distance.

  10. Microarray-based screening of heat shock protein inhibitors.

    Science.gov (United States)

    Schax, Emilia; Walter, Johanna-Gabriela; Märzhäuser, Helene; Stahl, Frank; Scheper, Thomas; Agard, David A; Eichner, Simone; Kirschning, Andreas; Zeilinger, Carsten

    2014-06-20

    Based on the importance of heat shock proteins (HSPs) in diseases such as cancer, Alzheimer's disease or malaria, inhibitors of these chaperons are needed. Today's state-of-the-art techniques to identify HSP inhibitors are performed in microplate format, requiring large amounts of proteins and potential inhibitors. In contrast, we have developed a miniaturized protein microarray-based assay to identify novel inhibitors, allowing analysis with 300 pmol of protein. The assay is based on competitive binding of fluorescence-labeled ATP and potential inhibitors to the ATP-binding site of HSP. Therefore, the developed microarray enables the parallel analysis of different ATP-binding proteins on a single microarray. We have demonstrated the possibility of multiplexing by immobilizing full-length human HSP90α and HtpG of Helicobacter pylori on microarrays. Fluorescence-labeled ATP was competed by novel geldanamycin/reblastatin derivatives with IC50 values in the range of 0.5 nM to 4 μM and Z(*)-factors between 0.60 and 0.96. Our results demonstrate the potential of a target-oriented multiplexed protein microarray to identify novel inhibitors for different members of the HSP90 family. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. A High-Throughput Antibody-Based Microarray Typing Platform

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    Ashan Perera

    2013-05-01

    Full Text Available Many rapid methods have been developed for screening foods for the presence of pathogenic microorganisms. Rapid methods that have the additional ability to identify microorganisms via multiplexed immunological recognition have the potential for classification or typing of microbial contaminants thus facilitating epidemiological investigations that aim to identify outbreaks and trace back the contamination to its source. This manuscript introduces a novel, high throughput typing platform that employs microarrayed multiwell plate substrates and laser-induced fluorescence of the nucleic acid intercalating dye/stain SYBR Gold for detection of antibody-captured bacteria. The aim of this study was to use this platform for comparison of different sets of antibodies raised against the same pathogens as well as demonstrate its potential effectiveness for serotyping. To that end, two sets of antibodies raised against each of the “Big Six” non-O157 Shiga toxin-producing E. coli (STEC as well as E. coli O157:H7 were array-printed into microtiter plates, and serial dilutions of the bacteria were added and subsequently detected. Though antibody specificity was not sufficient for the development of an STEC serotyping method, the STEC antibody sets performed reasonably well exhibiting that specificity increased at lower capture antibody concentrations or, conversely, at lower bacterial target concentrations. The favorable results indicated that with sufficiently selective and ideally concentrated sets of biorecognition elements (e.g., antibodies or aptamers, this high-throughput platform can be used to rapidly type microbial isolates derived from food samples within ca. 80 min of total assay time. It can also potentially be used to detect the pathogens from food enrichments and at least serve as a platform for testing antibodies.

  12. Dance Facilities.

    Science.gov (United States)

    Ashton, Dudley, Ed.; Irey, Charlotte, Ed.

    This booklet represents an effort to assist teachers and administrators in the professional planning of dance facilities and equipment. Three chapters present the history of dance facilities, provide recommended dance facilities and equipment, and offer some adaptations of dance facilities and equipment, for elementary, secondary and college level…

  13. Factorial microarray analysis of zebra mussel (Dreissena polymorpha: Dreissenidae, Bivalvia adhesion

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    Faisal Mohamed

    2010-05-01

    Full Text Available Abstract Background The zebra mussel (Dreissena polymorpha has been well known for its expertise in attaching to substances under the water. Studies in past decades on this underwater adhesion focused on the adhesive protein isolated from the byssogenesis apparatus of the zebra mussel. However, the mechanism of the initiation, maintenance, and determination of the attachment process remains largely unknown. Results In this study, we used a zebra mussel cDNA microarray previously developed in our lab and a factorial analysis to identify the genes that were involved in response to the changes of four factors: temperature (Factor A, current velocity (Factor B, dissolved oxygen (Factor C, and byssogenesis status (Factor D. Twenty probes in the microarray were found to be modified by one of the factors. The transcription products of four selected genes, DPFP-BG20_A01, EGP-BG97/192_B06, EGP-BG13_G05, and NH-BG17_C09 were unique to the zebra mussel foot based on the results of quantitative reverse transcription PCR (qRT-PCR. The expression profiles of these four genes under the attachment and non-attachment were also confirmed by qRT-PCR and the result is accordant to that from microarray assay. The in situ hybridization with the RNA probes of two identified genes DPFP-BG20_A01 and EGP-BG97/192_B06 indicated that both of them were expressed by a type of exocrine gland cell located in the middle part of the zebra mussel foot. Conclusions The results of this study suggested that the changes of D. polymorpha byssogenesis status and the environmental factors can dramatically affect the expression profiles of the genes unique to the foot. It turns out that the factorial design and analysis of the microarray experiment is a reliable method to identify the influence of multiple factors on the expression profiles of the probesets in the microarray; therein it provides a powerful tool to reveal the mechanism of zebra mussel underwater attachment.

  14. Development of a novel multiplex DNA microarray for Fusarium graminearum and analysis of azole fungicide responses

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    Deising Holger B

    2011-01-01

    Full Text Available Abstract Background The toxigenic fungal plant pathogen Fusarium graminearum compromises wheat production worldwide. Azole fungicides play a prominent role in controlling this pathogen. Sequencing of its genome stimulated the development of high-throughput technologies to study mechanisms of coping with fungicide stress and adaptation to fungicides at a previously unprecedented precision. DNA-microarrays have been used to analyze genome-wide gene expression patterns and uncovered complex transcriptional responses. A recently developed one-color multiplex array format allowed flexible, effective, and parallel examinations of eight RNA samples. Results We took advantage of the 8 × 15 k Agilent format to design, evaluate, and apply a novel microarray covering the whole F. graminearum genome to analyze transcriptional responses to azole fungicide treatment. Comparative statistical analysis of expression profiles uncovered 1058 genes that were significantly differentially expressed after azole-treatment. Quantitative RT-PCR analysis for 31 selected genes indicated high conformity to results from the microarray hybridization. Among the 596 genes with significantly increased transcript levels, analyses using GeneOntology and FunCat annotations detected the ergosterol-biosynthesis pathway genes as the category most significantly responding, confirming the mode-of-action of azole fungicides. Cyp51A, which is one of the three F. graminearum paralogs of Cyp51 encoding the target of azoles, was the most consistently differentially expressed gene of the entire study. A molecular phylogeny analyzing the relationships of the three CYP51 proteins in the context of 38 fungal genomes belonging to the Pezizomycotina indicated that CYP51C (FGSG_11024 groups with a new clade of CYP51 proteins. The transcriptional profiles for genes encoding ABC transporters and transcription factors suggested several involved in mechanisms alleviating the impact of the fungicide

  15. Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays

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    Kreil David P

    2008-08-01

    Full Text Available Abstract Background DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely dependent on conclusions drawn from analogies to Saccharomyces cerevisiae. To close this gap for a yeast species employed for its high capacity to produce heterologous proteins, we developed full genome DNA microarrays for P. pastoris and analyzed the unfolded protein response (UPR in this yeast species, as compared to S. cerevisiae. Results By combining the partially annotated gene list of P. pastoris with de novo gene finding a list of putative open reading frames was generated for which an oligonucleotide probe set was designed using the probe design tool TherMODO (a thermodynamic model-based oligoset design optimizer. To evaluate the performance of the novel array design, microarrays carrying the oligo set were hybridized with samples from treatments with dithiothreitol (DTT or a strain overexpressing the UPR transcription factor HAC1, both compared with a wild type strain in normal medium as untreated control. DTT treatment was compared with literature data for S. cerevisiae, and revealed similarities, but also important differences between the two yeast species. Overexpression of HAC1, the most direct control for UPR genes, resulted in significant new understanding of this important regulatory pathway in P. pastoris, and generally in yeasts. Conclusion The differences observed between P. pastoris and S. cerevisiae underline the importance of DNA microarrays for industrial production strains. P. pastoris reacts to DTT treatment mainly by the regulation of genes related to chemical stimulus, electron transport and respiration, while the overexpression of HAC1 induced many genes

  16. Factorial microarray analysis of zebra mussel (Dreissena polymorpha: Dreissenidae, Bivalvia) adhesion.

    Science.gov (United States)

    Xu, Wei; Faisal, Mohamed

    2010-05-28

    The zebra mussel (Dreissena polymorpha) has been well known for its expertise in attaching to substances under the water. Studies in past decades on this underwater adhesion focused on the adhesive protein isolated from the byssogenesis apparatus of the zebra mussel. However, the mechanism of the initiation, maintenance, and determination of the attachment process remains largely unknown. In this study, we used a zebra mussel cDNA microarray previously developed in our lab and a factorial analysis to identify the genes that were involved in response to the changes of four factors: temperature (Factor A), current velocity (Factor B), dissolved oxygen (Factor C), and byssogenesis status (Factor D). Twenty probes in the microarray were found to be modified by one of the factors. The transcription products of four selected genes, DPFP-BG20_A01, EGP-BG97/192_B06, EGP-BG13_G05, and NH-BG17_C09 were unique to the zebra mussel foot based on the results of quantitative reverse transcription PCR (qRT-PCR). The expression profiles of these four genes under the attachment and non-attachment were also confirmed by qRT-PCR and the result is accordant to that from microarray assay. The in situ hybridization with the RNA probes of two identified genes DPFP-BG20_A01 and EGP-BG97/192_B06 indicated that both of them were expressed by a type of exocrine gland cell located in the middle part of the zebra mussel foot. The results of this study suggested that the changes of D. polymorpha byssogenesis status and the environmental factors can dramatically affect the expression profiles of the genes unique to the foot. It turns out that the factorial design and analysis of the microarray experiment is a reliable method to identify the influence of multiple factors on the expression profiles of the probesets in the microarray; therein it provides a powerful tool to reveal the mechanism of zebra mussel underwater attachment.

  17. Acceptability of lifelong treatment among HIV-positive pregnant and breastfeeding women (Option B+) in selected health facilities in Zimbabwe: a qualitative study.

    Science.gov (United States)

    Chadambuka, Addmore; Katirayi, Leila; Muchedzi, Auxilia; Tumbare, Esther; Musarandega, Reuben; Mahomva, Agnes I; Woelk, Godfrey

    2017-07-25

    Zimbabwe's Ministry of Health and Child Care (MOHCC) adopted 2013 World Health Organization (WHO) prevention of mother-to-child HIV transmission (PMTCT) guidelines recommending initiation of HIV-positive pregnant and breastfeeding women (PPBW) on lifelong antiretroviral treatment (ART) irrespective of clinical stage (Option B+). Option B+ was officially launched in Zimbabwe in November 2013; however the acceptability of life-long ART and its potential uptake among women was not known. A qualitative study was conducted at selected sites in Harare (urban) and Zvimba (rural) to explore Option B+ acceptability; barriers, and facilitators to ART adherence and service uptake. In-depth interviews (IDIs), focus group discussions (FGDs) and key informant interviews (KIIs) were conducted with PPBW, healthcare providers, and community members. All interviews were audio-recorded, transcribed, and translated; data were coded and analyzed in MaxQDA v10. Forty-three IDIs, 22 FGDs, and five KIIs were conducted. The majority of women accepted lifelong ART. There was however, a fear of commitment to taking lifelong medication because they were afraid of defaulting, especially after cessation of breastfeeding. There was confusion around dosage; and fear of side effects, not having enough food to take drugs, and the lack of opportunities to ask questions in counseling. Participants reported the need for strengthening community sensitization for Option B+. Facilitators included receiving a simplified pill regimen; ability to continue breastfeeding beyond 6 months like HIV-negative women; and partner, community and health worker support. Barriers included distance of health facility, non-disclosure of HIV status, poor male partner support and knowing someone who had negative experience on ART. This study found that Option B+ is generally accepted among PPBW as a means to strengthen their health and protect their babies. Consistent with previous literature, this study demonstrated the

  18. Acceptability of lifelong treatment among HIV-positive pregnant and breastfeeding women (Option B+ in selected health facilities in Zimbabwe: a qualitative study

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    Addmore Chadambuka

    2017-07-01

    Full Text Available Abstract Background Zimbabwe’s Ministry of Health and Child Care (MOHCC adopted 2013 World Health Organization (WHO prevention of mother-to-child HIV transmission (PMTCT guidelines recommending initiation of HIV-positive pregnant and breastfeeding women (PPBW on lifelong antiretroviral treatment (ART irrespective of clinical stage (Option B+. Option B+ was officially launched in Zimbabwe in November 2013; however the acceptability of life-long ART and its potential uptake among women was not known. Methods A qualitative study was conducted at selected sites in Harare (urban and Zvimba (rural to explore Option B+ acceptability; barriers, and facilitators to ART adherence and service uptake. In-depth interviews (IDIs, focus group discussions (FGDs and key informant interviews (KIIs were conducted with PPBW, healthcare providers, and community members. All interviews were audio-recorded, transcribed, and translated; data were coded and analyzed in MaxQDA v10. Results Forty-three IDIs, 22 FGDs, and five KIIs were conducted. The majority of women accepted lifelong ART. There was however, a fear of commitment to taking lifelong medication because they were afraid of defaulting, especially after cessation of breastfeeding. There was confusion around dosage; and fear of side effects, not having enough food to take drugs, and the lack of opportunities to ask questions in counseling. Participants reported the need for strengthening community sensitization for Option B+. Facilitators included receiving a simplified pill regimen; ability to continue breastfeeding beyond 6 months like HIV-negative women; and partner, community and health worker support. Barriers included distance of health facility, non-disclosure of HIV status, poor male partner support and knowing someone who had negative experience on ART. Conclusions This study found that Option B+ is generally accepted among PPBW as a means to strengthen their health and protect their babies

  19. DNA microarray data and contextual analysis of correlation graphs

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    Hingamp Pascal

    2003-04-01

    Full Text Available Abstract Background DNA microarrays are used to produce large sets of expression measurements from which specific biological information is sought. Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation. Results We study networks of co-expressed genes obtained from DNA microarray experiments. The mathematical concept of curvature on graphs is used to group genes or samples into clusters to which relevant gene or sample annotations are automatically assigned. Application to publicly available yeast and human lymphoma data demonstrates the reliability of the method in spite of its simplicity, especially with respect to the small number of parameters involved. Conclusions We provide a method for automatically determining relevant gene clusters among the many genes monitored with microarrays. The automatic annotations and the graphical interface improve the readability of the data. A C++ implementation, called Trixy, is available from http://tagc.univ-mrs.fr/bioinformatics/trixy.html.

  20. MICROARRAY IMAGE GRIDDING USING GRID LINE REFINEMENT TECHNIQUE

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    V.G. Biju

    2015-05-01

    Full Text Available An important stage in microarray image analysis is gridding. Microarray image gridding is done to locate sub arrays in a microarray image and find co-ordinates of spots within each sub array. For accurate identification of spots, most of the proposed gridding methods require human intervention. In this paper a fully automatic gridding method which enhances spot intensity in the preprocessing step as per a histogram based threshold method is used. The gridding step finds co-ordinates of spots from horizontal and vertical profile of the image. To correct errors due to the grid line placement, a grid line refinement technique is proposed. The algorithm is applied on different image databases and results are compared based on spot detection accuracy and time. An average spot detection accuracy of 95.06% depicts the proposed method’s flexibility and accuracy in finding the spot co-ordinates for different database images.

  1. A Versatile Microarray Platform for Capturing Rare Cells

    Science.gov (United States)

    Brinkmann, Falko; Hirtz, Michael; Haller, Anna; Gorges, Tobias M.; Vellekoop, Michael J.; Riethdorf, Sabine; Müller, Volkmar; Pantel, Klaus; Fuchs, Harald

    2015-10-01

    Analyses of rare events occurring at extremely low frequencies in body fluids are still challenging. We established a versatile microarray-based platform able to capture single target cells from large background populations. As use case we chose the challenging application of detecting circulating tumor cells (CTCs) - about one cell in a billion normal blood cells. After incubation with an antibody cocktail, targeted cells are extracted on a microarray in a microfluidic chip. The accessibility of our platform allows for subsequent recovery of targets for further analysis. The microarray facilitates exclusion of false positive capture events by co-localization allowing for detection without fluorescent labelling. Analyzing blood samples from cancer patients with our platform reached and partly outreached gold standard performance, demonstrating feasibility for clinical application. Clinical researchers free choice of antibody cocktail without need for altered chip manufacturing or incubation protocol, allows virtual arbitrary targeting of capture species and therefore wide spread applications in biomedical sciences.

  2. Normalization and gene p-value estimation: issues in microarray data processing.

    Science.gov (United States)

    Fundel, Katrin; Küffner, Robert; Aigner, Thomas; Zimmer, Ralf

    2008-05-28

    Numerous methods exist for basic processing, e.g. normalization, of microarray gene expression data. These methods have an important effect on the final analysis outcome. Therefore, it is crucial to select methods appropriate for a given dataset in order to assure the validity and reliability of expression data analysis. Furthermore, biological interpretation requires expression values for genes, which are often represented by several spots or probe sets on a microarray. How to best integrate spot/probe set values into gene values has so far been a somewhat neglected problem. We present a case study comparing different between-array normalization methods with respect to the identification of differentially expressed genes. Our results show that it is feasible and necessary to use prior knowledge on gene expression measurements to select an adequate normalization method for the given data. Furthermore, we provide evidence that combining spot/probe set p-values into gene p-values for detecting differentially expressed genes has advantages compared to combining expression values for spots/probe sets into gene expression values. The comparison of different methods suggests to use Stouffer's method for this purpose. The study has been conducted on gene expression experiments investigating human joint cartilage samples of osteoarthritis related groups: a cDNA microarray (83 samples, four groups) and an Affymetrix (26 samples, two groups) data set. The apparently straight forward steps of gene expression data analysis, e.g. between-array normalization and detection of differentially regulated genes, can be accomplished by numerous different methods. We analyzed multiple methods and the possible effects and thereby demonstrate the importance of the single decisions taken during data processing. We give guidelines for evaluating normalization outcomes. An overview of these effects via appropriate measures and plots compared to prior knowledge is essential for the biological

  3. Label and Label-Free Detection Techniques for Protein Microarrays

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    Amir Syahir

    2015-04-01

    Full Text Available Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano‑biological events.

  4. Advanced Data Mining of Leukemia Cells Micro-Arrays

    OpenAIRE

    Richard S. Segall; Ryan M. Pierce

    2009-01-01

    This paper provides continuation and extensions of previous research by Segall and Pierce (2009a) that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM). As Segall and Pierce (2009a) and Segall and Pierce (2009b) the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is pro...

  5. Fabrication of Biomolecule Microarrays for Cell Immobilization Using Automated Microcontact Printing.

    Science.gov (United States)

    Foncy, Julie; Estève, Aurore; Degache, Amélie; Colin, Camille; Cau, Jean Christophe; Malaquin, Laurent; Vieu, Christophe; Trévisiol, Emmanuelle

    2018-01-01

    Biomolecule microarrays are generally produced by conventional microarrayer, i.e., by contact or inkjet printing. Microcontact printing represents an alternative way of deposition of biomolecules on solid supports but even if various biomolecules have been successfully microcontact printed, the production of biomolecule microarrays in routine by microcontact printing remains a challenging task and needs an effective, fast, robust, and low-cost automation process. Here, we describe the production of biomolecule microarrays composed of extracellular matrix protein for the fabrication of cell microarrays by using an automated microcontact printing device. Large scale cell microarrays can be reproducibly obtained by this method.

  6. Detection of genomic deletions in rice using oligonucleotide microarrays

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    Bordeos Alicia

    2009-03-01

    Full Text Available Abstract Background The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL. However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. Results We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/. Conclusion We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a

  7. Evaluation of a quality improvement intervention for obstetric and neonatal care in selected public health facilities across six states of India.

    Science.gov (United States)

    Sarin, Enisha; Kole, Subir K; Patel, Rachana; Sooden, Ankur; Kharwal, Sanchit; Singh, Rashmi; Rahimzai, Mirwais; Livesley, Nigel

    2017-05-02

    While increase in the number of women delivering in health facilities has been rapid, the quality of obstetric and neonatal care continues to be poor in India, contributing to high maternal and neonatal mortality. The USAID ASSIST Project supported health workers in 125 public health facilities (delivering approximately 180,000 babies per year) across six states to use quality improvement (QI) approaches to provide better care to women and babies before, during and immediately after delivery. As part of this intervention, each month, health workers recorded data related to nine elements of routine care alongside data on perinatal mortality. We aggregated facility level data and conducted segmented regression to analyse the effect of the intervention over time. Care improved to 90-99% significantly (p improving provision of routine care, yet these approaches are underused in the Indian health system. We discuss the implications of this for policy makers.

  8. 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.

  9. [Preparation of the cDNA microarray on the differential expressed cDNA of senescence-accelerated mouse's hippocampus].

    Science.gov (United States)

    Cheng, Xiao-Rui; Zhou, Wen-Xia; Zhang, Yong-Xiang

    2006-05-01

    Alzheimer' s disease (AD) is the most common form of dementia in the elderly. AD is an invariably fatal neurodegenerative disorder with no effective treatment. Senescence-accelerated mouse prone 8 (SAMP8) is a model for studying age-related cognitive impairments and also is a good model to study brain aging and one of mouse model of AD. The technique of cDNA microarray can monitor the expression levels of thousands of genes simultaneously and can be used to study AD with the character of multi-mechanism, multi-targets and multi-pathway. In order to disclose the mechanism of AD and find the drug targets of AD, cDNA microarray containing 3136 cDNAs amplified from the suppression subtracted cDNA library of hippocampus of SAMP8 and SAMR1 was prepared with 16 blocks and 14 x 14 pins, the housekeeping gene beta-actin and G3PDH as inner conference. The background of this microarray was low and unanimous, and dots divided evenly. The conditions of hybridization and washing were optimized during the hybridization of probe and target molecule. After the data of hybridization analysis, the differential expressed cDNAs were sequenced and analyzed by the bioinformatics, and some of genes were quantified by the real time RT-PCR and the reliability of this cDNA microarray were validated. This cDNA microarray may be the good means to select the differential expressed genes and disclose the molecular mechanism of SAMP8's brain aging and AD.

  10. Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE

    Directory of Open Access Journals (Sweden)

    Ile Kristina E

    2003-07-01

    Full Text Available Abstract Background The ADGE technique is a method designed to magnify the ratios of gene expression before detection. It improves the detection sensitivity to small change of gene expression and requires small amount of starting material. However, the throughput of ADGE is low. We integrated ADGE with DNA microarray (ADGE microarray and compared it with regular microarray. Results When ADGE was integrated with DNA microarray, a quantitative relationship of a power function between detected and input ratios was found. Because of ratio magnification, ADGE microarray was better able to detect small changes in gene expression in a drug resistant model cell line system. The PCR amplification of templates and efficient labeling reduced the requirement of starting material to as little as 125 ng of total RNA for one slide hybridization and enhanced the signal intensity. Integration of ratio magnification, template amplification and efficient labeling in ADGE microarray reduced artifacts in microarray data and improved detection fidelity. The results of ADGE microarray were less variable and more reproducible than those of regular microarray. A gene expression profile generated with ADGE microarray characterized the drug resistant phenotype, particularly with reference to glutathione, proliferation and kinase pathways. Conclusion ADGE microarray magnified the ratios of differential gene expression in a power function, improved the detection sensitivity and fidelity and reduced the requirement for starting material while maintaining high throughput. ADGE microarray generated a more informative expression pattern than regular microarray.

  11. A Discrete Wavelet Based Feature Extraction and Hybrid Classification Technique for Microarray Data Analysis

    Directory of Open Access Journals (Sweden)

    Jaison Bennet

    2014-01-01

    Full Text Available Cancer classification by doctors and radiologists was based on morphological and clinical features and had limited diagnostic ability in olden days. The recent arrival of DNA microarray technology has led to the concurrent monitoring of thousands of gene expressions in a single chip which stimulates the progress in cancer classification. In this paper, we have proposed a hybrid approach for microarray data classification based on nearest neighbor (KNN, naive Bayes, and support vector machine (SVM. Feature selection prior to classification plays a vital role and a feature selection technique which combines discrete wavelet transform (DWT and moving window technique (MWT is used. The performance of the proposed method is compared with the conventional classifiers like support vector machine, nearest neighbor, and naive Bayes. Experiments have been conducted on both real and benchmark datasets and the results indicate that the ensemble approach produces higher classification accuracy than conventional classifiers. This paper serves as an automated system for the classification of cancer and can be applied by doctors in real cases which serve as a boon to the medical community. This work further reduces the misclassification of cancers which is highly not allowed in cancer detection.

  12. Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review.

    Science.gov (United States)

    Raddatz, Barbara B; Spitzbarth, Ingo; Matheis, Katja A; Kalkuhl, Arno; Deschl, Ulrich; Baumgärtner, Wolfgang; Ulrich, Reiner

    2017-09-01

    High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms. The scientific literature concerning high-throughput data-mining techniques usually addresses mathematicians or computer scientists as the target audience. In contrast, the present review provides the reader with a clear and systematic basis from a veterinary pathologist's perspective. Therefore, the aims are (1) to introduce the reader to the necessary methodological background; (2) to introduce the sequential steps commonly performed in a microarray analysis including quality control, annotation, normalization, selection of differentially expressed genes, clustering, gene ontology and pathway analysis, analysis of manually selected genes, and biomarker discovery; and (3) to provide references to publically available and user-friendly software suites. In summary, the data analysis methods presented within this review will enable veterinary pathologists to analyze high-throughput transcriptome data obtained from their own experiments, supplemental data that accompany scientific publications, or public repositories in order to obtain a more in-depth insight into underlying disease mechanisms.

  13. Single-cell multiple gene expression analysis based on single-molecule-detection microarray assay for multi-DNA determination

    Energy Technology Data Exchange (ETDEWEB)

    Li, Lu [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Wang, Xianwei [School of Life Sciences, Shandong University, Jinan 250100 (China); Zhang, Xiaoli [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Wang, Jinxing [School of Life Sciences, Shandong University, Jinan 250100 (China); Jin, Wenrui, E-mail: jwr@sdu.edu.cn [School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China)

    2015-01-07

    Highlights: • A single-molecule-detection (SMD) microarray for 10 samples is fabricated. • The based-SMD microarray assay (SMA) can determine 8 DNAs for each sample. • The limit of detection of SMA is as low as 1.3 × 10{sup −16} mol L{sup −1}. • The SMA can be applied in single-cell multiple gene expression analysis. - Abstract: We report a novel ultra-sensitive and high-selective single-molecule-detection microarray assay (SMA) for multiple DNA determination. In the SMA, a capture DNA (DNAc) microarray consisting of 10 subarrays with 9 spots for each subarray is fabricated on a silanized glass coverslip as the substrate. On the subarrays, the spot-to-spot spacing is 500 μm and each spot has a diameter of ∼300 μm. The sequence of the DNAcs on the 9 spots of a subarray is different, to determine 8 types of target DNAs (DNAts). Thus, 8 types of DNAts are captured to their complementary DNAcs at 8 spots of a subarray, respectively, and then labeled with quantum dots (QDs) attached to 8 types of detection DNAs (DNAds) with different sequences. The ninth spot is used to detect the blank value. In order to determine the same 8 types of DNAts in 10 samples, the 10 DNAc-modified subarrays on the microarray are identical. Fluorescence single-molecule images of the QD-labeled DNAts on each spot of the subarray are acquired using a home-made single-molecule microarray reader. The amounts of the DNAts are quantified by counting the bright dots from the QDs. For a microarray, 8 types of DNAts in 10 samples can be quantified in parallel. The limit of detection of the SMA for DNA determination is as low as 1.3 × 10{sup −16} mol L{sup −1}. The SMA for multi-DNA determination can also be applied in single-cell multiple gene expression analysis through quantification of complementary DNAs (cDNAs) corresponding to multiple messenger RNAs (mRNAs) in single cells. To do so, total RNA in single cells is extracted and reversely transcribed into their cDNAs. Three

  14. Flexible hemispheric microarrays of highly pressure-sensitive sensors based on breath figure method.

    Science.gov (United States)

    Wang, Zhihui; Zhang, Ling; Liu, Jin; Jiang, Hao; Li, Chunzhong

    2018-05-30

    Recently, flexible pressure sensors featuring high sensitivity, broad sensing range and real-time detection have aroused great attention owing to their crucial role in the development of artificial intelligent devices and healthcare systems. Herein, highly sensitive pressure sensors based on hemisphere-microarray flexible substrates are fabricated via inversely templating honeycomb structures deriving from a facile and static breath figure process. The interlocked and subtle microstructures greatly improve the sensing characteristics and compressibility of the as-prepared pressure sensor, endowing it a sensitivity as high as 196 kPa-1 and a wide pressure sensing range (0-100 kPa), as well as other superior performance, including a lower detection limit of 0.5 Pa, fast response time (10 000 cycles). Based on the outstanding sensing performance, the potential capability of our pressure sensor in capturing physiological information and recognizing speech signals has been demonstrated, indicating promising application in wearable and intelligent electronics.

  15. A step by step selection method for the location and the size of a waste-to-energy facility targeting the maximum output energy and minimization of gate fee.

    Science.gov (United States)

    Kyriakis, Efstathios; Psomopoulos, Constantinos; Kokkotis, Panagiotis; Bourtsalas, Athanasios; Themelis, Nikolaos

    2017-06-23

    This study attempts the development of an algorithm in order to present a step by step selection method for the location and the size of a waste-to-energy facility targeting the maximum output energy, also considering the basic obstacle which is in many cases, the gate fee. Various parameters identified and evaluated in order to formulate the proposed decision making method in the form of an algorithm. The principle simulation input is the amount of municipal solid wastes (MSW) available for incineration and along with its net calorific value are the most important factors for the feasibility of the plant. Moreover, the research is focused both on the parameters that could increase the energy production and those that affect the R1 energy efficiency factor. Estimation of the final gate fee is achieved through the economic analysis of the entire project by investigating both expenses and revenues which are expected according to the selected site and outputs of the facility. In this point, a number of commonly revenue methods were included in the algorithm. The developed algorithm has been validated using three case studies in Greece-Athens, Thessaloniki, and Central Greece, where the cities of Larisa and Volos have been selected for the application of the proposed decision making tool. These case studies were selected based on a previous publication made by two of the authors, in which these areas where examined. Results reveal that the development of a «solid» methodological approach in selecting the site and the size of waste-to-energy (WtE) facility can be feasible. However, the maximization of the energy efficiency factor R1 requires high utilization factors while the minimization of the final gate fee requires high R1 and high metals recovery from the bottom ash as well as economic exploitation of recovered raw materials if any.

  16. The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data

    Directory of Open Access Journals (Sweden)

    Hyunseok P Kang

    2010-01-01

    Full Text Available Background: Tissue microarrays (TMAs are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF provides a flexible method to represent knowledge in triples, which take the form Subject- Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs, which are global in scope. We present an OWL (Web Ontology Language schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration. Methods: A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format. Results: We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES to OWL. Conclusion: By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.

  17. Waste Facilities

    Data.gov (United States)

    Vermont Center for Geographic Information — This dataset was developed from the Vermont DEC's list of certified solid waste facilities. It includes facility name, contact information, and the materials...

  18. Health Facilities

    Science.gov (United States)

    Health facilities are places that provide health care. They include hospitals, clinics, outpatient care centers, and specialized care centers, ... psychiatric care centers. When you choose a health facility, you might want to consider How close it ...

  19. Fabrication Facilities

    Data.gov (United States)

    Federal Laboratory Consortium — The Fabrication Facilities are a direct result of years of testing support. Through years of experience, the three fabrication facilities (Fort Hood, Fort Lewis, and...

  20. 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.

  1. Kernel Based Nonlinear Dimensionality Reduction and Classification for Genomic Microarray

    Directory of Open Access Journals (Sweden)

    Lan Shu

    2008-07-01

    Full Text Available Genomic microarrays are powerful research tools in bioinformatics and modern medicinal research because they enable massively-parallel assays and simultaneous monitoring of thousands of gene expression of biological samples. However, a simple microarray experiment often leads to very high-dimensional data and a huge amount of information, the vast amount of data challenges researchers into extracting the important features and reducing the high dimensionality. In this paper, a nonlinear dimensionality reduction kernel method based locally linear embedding(LLE is proposed, and fuzzy K-nearest neighbors algorithm which denoises datasets will be introduced as a replacement to the classical LLE’s KNN algorithm. In addition, kernel method based support vector machine (SVM will be used to classify genomic microarray data sets in this paper. We demonstrate the application of the techniques to two published DNA microarray data sets. The experimental results confirm the superiority and high success rates of the presented method.

  2. The microarray detecting six fruit-tree viruses

    Czech Academy of Sciences Publication Activity Database

    Lenz, Ondřej; Petrzik, Karel; Špak, Josef

    2009-01-01

    Roč. 148, July (2009), s. 27 ISSN 1866-590X. [International Conference on Virus and other Graft Transmissible Diseases of Fruit Crops /21./. 05.07.2009-10.07.2009, Neustadt] R&D Projects: GA MŠk OC 853.001 Institutional research plan: CEZ:AV0Z50510513 Keywords : microarray * detection * virus Subject RIV: EE - Microbiology, Virology

  3. A Customized DNA Microarray for Microbial Source Tracking ...

    Science.gov (United States)

    It is estimated that more than 160, 000 miles of rivers and streams in the United States are impaired due to the presence of waterborne pathogens. These pathogens typically originate from human and other animal fecal pollution sources; therefore, a rapid microbial source tracking (MST) method is needed to facilitate water quality assessment and impaired water remediation. We report a novel qualitative DNA microarray technology consisting of 453 probes for the detection of general fecal and host-associated bacteria, viruses, antibiotic resistance, and other environmentally relevant genetic indicators. A novel data normalization and reduction approach is also presented to help alleviate false positives often associated with high-density microarray applications. To evaluate the performance of the approach, DNA and cDNA was isolated from swine, cattle, duck, goose and gull fecal reference samples, as well as soiled poultry liter and raw municipal sewage. Based on nonmetric multidimensional scaling analysis of results, findings suggest that the novel microarray approach may be useful for pathogen detection and identification of fecal contamination in recreational waters. The ability to simultaneously detect a large collection of environmentally important genetic indicators in a single test has the potential to provide water quality managers with a wide range of information in a short period of time. Future research is warranted to measure microarray performance i

  4. GenePublisher: automated analysis of DNA microarray data

    DEFF Research Database (Denmark)

    Knudsen, Steen; Workman, Christopher; Sicheritz-Ponten, T.

    2003-01-01

    GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with aspecification of the data. The server performs normalization...

  5. Towards a programmable magnetic bead microarray in a microfluidic channel

    DEFF Research Database (Denmark)

    Smistrup, Kristian; Bruus, Henrik; Hansen, Mikkel Fougt

    2007-01-01

    to use larger currents and obtain forces of longer range than from thin current lines at a given power limit. Guiding of magnetic beads in the hybrid magnetic separator and the construction of a programmable microarray of magnetic beads in the microfluidic channel by hydrodynamic focusing is presented....

  6. CONFIRMING MICROARRAY DATA--IS IT REALLY NECESSARY?

    Science.gov (United States)

    The generation of corroborative data has become a commonly used approach for ensuring the veracity of microarray data. Indeed, the need to conduct corroborative studies has now become official editorial policy for at least two journals, and several more are considering introducin...

  7. Microarrays: Molecular allergology and nanotechnology for personalised medicine (II).

    Science.gov (United States)

    Lucas, J M

    2010-01-01

    Progress in nanotechnology and DNA recombination techniques have produced tools for the diagnosis and investigation of allergy at molecular level. The most advanced examples of such progress are the microarray techniques, which have been expanded not only in research in the field of proteomics but also in application to the clinical setting. Microarrays of allergic components offer results relating to hundreds of allergenic components in a single test, and using a small amount of serum which can be obtained from capillary blood. The availability of new molecules will allow the development of panels including new allergenic components and sources, which will require evaluation for clinical use. Their application opens the door to component-based diagnosis, to the holistic perception of sensitisation as represented by molecular allergy, and to patient-centred medical practice by allowing great diagnostic accuracy and the definition of individualised immunotherapy for each patient. The present article reviews the application of allergenic component microarrays to allergology for diagnosis, management in the form of specific immunotherapy, and epidemiological studies. A review is also made of the use of protein and gene microarray techniques in basic research and in allergological diseases. Lastly, an evaluation is made of the challenges we face in introducing such techniques to clinical practice, and of the future perspectives of this new technology. Copyright 2010 SEICAP. Published by Elsevier Espana. All rights reserved.

  8. Exploiting fluorescence for multiplex immunoassays on protein microarrays

    International Nuclear Information System (INIS)

    Herbáth, Melinda; Balogh, Andrea; Matkó, János; Papp, Krisztián; Prechl, József

    2014-01-01

    Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications. (topical review)

  9. Development of DNA Microarrays for Metabolic Pathway and Bioprocess Monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Gregory Stephanopoulos

    2004-07-31

    Transcriptional profiling experiments utilizing DNA microarrays to study the intracellular accumulation of PHB in Synechocystis has proved difficult in large part because strains that show significant differences in PHB which would justify global analysis of gene expression have not been isolated.

  10. SNP typing on the NanoChip electronic microarray

    DEFF Research Database (Denmark)

    Børsting, Claus; Sanchez Sanchez, Juan Jose; Morling, Niels

    2005-01-01

    We describe a single nucleotide polymorphism (SNP) typing protocol developed for the NanoChip electronic microarray. The NanoChip array consists of 100 electrodes covered by a thin hydrogel layer containing streptavidin. An electric currency can be applied to one, several, or all electrodes...

  11. Application of Microarray technology in research and diagnostics

    DEFF Research Database (Denmark)

    Helweg-Larsen, Rehannah Borup

    The overall purpose of this thesis is to evaluate the use of microarray analysis to investigate the transcriptome of human cancers and human follicular cells and define the correlation between expression of human genes and specific cancer types as well as the developmental competence of the oocyte...

  12. Bacterial identification and subtyping using DNA microarray and DNA sequencing.

    Science.gov (United States)

    Al-Khaldi, Sufian F; Mossoba, Magdi M; Allard, Marc M; Lienau, E Kurt; Brown, Eric D

    2012-01-01

    The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

  13. Exploring Lactobacillus plantarum genome diversity by using microarrays

    NARCIS (Netherlands)

    Molenaar, D.; Bringel, F.; Schuren, F.H.; Vos, de W.M.; Siezen, R.J.; Kleerebezem, M.

    2005-01-01

    Lactobacillus plantarum is a versatile and flexible species that is encountered in a variety of niches and can utilize a broad range of fermentable carbon sources. To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments of L.

  14. See what you eat--broad GMO screening with microarrays.

    Science.gov (United States)

    von Götz, Franz

    2010-03-01

    Despite the controversy of whether genetically modified organisms (GMOs) are beneficial or harmful for humans, animals, and/or ecosystems, the number of cultivated GMOs is increasing every year. Many countries and federations have implemented safety and surveillance systems for GMOs. Potent testing technologies need to be developed and implemented to monitor the increasing number of GMOs. First, these GMO tests need to be comprehensive, i.e., should detect all, or at least the most important, GMOs on the market. This type of GMO screening requires a high degree of parallel tests or multiplexing. To date, DNA microarrays have the highest number of multiplexing capabilities when nucleic acids are analyzed. This trend article focuses on the evolution of DNA microarrays for GMO testing. Over the last 7 years, combinations of multiplex PCR detection and microarray detection have been developed to qualitatively assess the presence of GMOs. One example is the commercially available DualChip GMO (Eppendorf, Germany; http://www.eppendorf-biochip.com), which is the only GMO screening system successfully validated in a multicenter study. With use of innovative amplification techniques, promising steps have recently been taken to make GMO detection with microarrays quantitative.

  15. Microarray-Based Identification of Transcription Factor Target Genes

    NARCIS (Netherlands)

    Gorte, M.; Horstman, A.; Page, R.B.; Heidstra, R.; Stromberg, A.; Boutilier, K.A.

    2011-01-01

    Microarray analysis is widely used to identify transcriptional changes associated with genetic perturbation or signaling events. Here we describe its application in the identification of plant transcription factor target genes with emphasis on the design of suitable DNA constructs for controlling TF

  16. Microarray-based RNA profiling of breast cancer

    DEFF Research Database (Denmark)

    Larsen, Martin J; Thomassen, Mads; Tan, Qihua

    2014-01-01

    analyzed the same 234 breast cancers on two different microarray platforms. One dataset contained known batch-effects associated with the fabrication procedure used. The aim was to assess the significance of correcting for systematic batch-effects when integrating data from different platforms. We here...

  17. Microarray expression profiling of human dental pulp from single subject.

    Science.gov (United States)

    Tete, Stefano; Mastrangelo, Filiberto; Scioletti, Anna Paola; Tranasi, Michelangelo; Raicu, Florina; Paolantonio, Michele; Stuppia, Liborio; Vinci, Raffaele; Gherlone, Enrico; Ciampoli, Cristian; Sberna, Maria Teresa; Conti, Pio

    2008-01-01

    Microarray is a recently developed simultaneous analysis of expression patterns of thousand of genes. The aim of this research was to evaluate the expression profile of human healthy dental pulp in order to find the presence of genes activated and encoding for proteins involved in the physiological process of human dental pulp. We report data obtained by analyzing expression profiles of human tooth pulp from single subjects, using an approach based on the amplification of the total RNA. Experiments were performed on a high-density array able to analyse about 21,000 oligonucleotide sequences of about 70 bases in duplicate, using an approach based on the amplification of the total RNA from the pulp of a single tooth. Obtained data were analyzed using the S.A.M. system (Significance Analysis of Microarray) and genes were merged according to their molecular functions and biological process by the Onto-Express software. The microarray analysis revealed 362 genes with specific pulp expression. Genes showing significant high expression were classified in genes involved in tooth development, protoncogenes, genes of collagen, DNAse, Metallopeptidases and Growth factors. We report a microarray analysis, carried out by extraction of total RNA from specimens of healthy human dental pulp tissue. This approach represents a powerful tool in the study of human normal and pathological pulp, allowing minimization of the genetic variability due to the pooling of samples from different individuals.

  18. 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.

  19. Characterization of stormwater at selected South Carolina Department of Transportation maintenance yard and section shed facilities in Ballentine, Conway, and North Charleston, South Carolina, 2010-2012

    Science.gov (United States)

    Journey, Celeste A.; Conlon, Kevin J.

    2013-01-01

    The South Carolina Department of Transportation operates section shed and maintenance yard facilities throughout the State. The U.S. Geological Survey conducted a cooperative investigation with the South Carolina Department of Transportation to characterize water-quality constituents that are transported in stormwater from representative maintenance yard and section shed facilities in South Carolina. At a section shed in Ballentine, S.C., stormwater discharges to a retention pond outfall (Ballentine). At the Conway maintenance yard, stormwater in the southernmost section discharges to a pipe outfall (Conway1), and stormwater in the remaining area discharges to a grass-lined ditch (Conway2). At the North Charleston maintenance yard, stormwater discharges from the yard to Turkey Creek through a combination of pipes, ditches, and overland flow; therefore, samples were collected from the main channel of Turkey Creek at the upstream (North Charleston1) and downstream (North Charleston2) limits of the North Charleston maintenance yard facility. The storms sampled during this study had a wide range of rainfall amounts, durations, and intensities at each of the facilities and, therefore, were considered to be reasonably representative of the potential for contaminant transport. At all facilities, stormwater discharge was significantly correlated to rainfall amount and intensity. Event-mean unit-area stormwater discharge increased with increasing impervious surface at the Conway and North Charleston maintenance yards. The Ballentine facility with 79 percent impervious surface had a mean unit-area discharge similar to that of the North Charleston maintenance yard (62 percent impervious surface). That similarity may be attributed, in part, to the effects of the retention pond on the stormwater runoff at the Ballentine facility and to the greater rainfall intensities and amounts at the North Charleston facility. Stormwater samples from the facilities were analyzed for multiple

  20. Comparison of gene coverage of mouse oligonucleotide microarray platforms

    Directory of Open Access Journals (Sweden)

    Medrano Juan F

    2006-03-01

    Full Text Available Abstract Background The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. Results A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis: Affymetrix430 2.0 (75.6%, ABI Genome Survey (81.24%, Agilent (79.33%, Codelink (78.09%, Sentrix (90.47%; and four array-ready oligosets: Sigma (47.95%, Operon v.3 (69.89%, Operon v.4 (84.03%, and MEEBO (84.03%. The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. Conclusion The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here

  1. Workflows for microarray data processing in the Kepler environment

    Directory of Open Access Journals (Sweden)

    Stropp Thomas

    2012-05-01

    Full Text Available Abstract Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data and therefore are close to

  2. Workflows for microarray data processing in the Kepler environment.

    Science.gov (United States)

    Stropp, Thomas; McPhillips, Timothy; Ludäscher, Bertram; Bieda, Mark

    2012-05-17

    Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or R

  3. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  4. Workflows for microarray data processing in the Kepler environment

    Science.gov (United States)

    2012-01-01

    Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or

  5. Computational biology of genome expression and regulation--a review of microarray bioinformatics.

    Science.gov (United States)

    Wang, Junbai

    2008-01-01

    Microarray technology is being used widely in various biomedical research areas; the corresponding microarray data analysis is an essential step toward the best utilizing of array technologies. Here we review two components of the microarray data analysis: a low level of microarray data analysis that emphasizes the designing, the quality control, and the preprocessing of microarray experiments, then a high level of microarray data analysis that focuses on the domain-specific microarray applications such as tumor classification, biomarker prediction, analyzing array CGH experiments, and reverse engineering of gene expression networks. Additionally, we will review the recent development of building a predictive model in genome expression and regulation studies. This review may help biologists grasp a basic knowledge of microarray bioinformatics as well as its potential impact on the future evolvement of biomedical research fields.

  6. THE MAQC PROJECT: ESTABLISHING QC METRICS AND THRESHOLDS FOR MICROARRAY QUALITY CONTROL

    Science.gov (United States)

    Microarrays represent a core technology in pharmacogenomics and toxicogenomics; however, before this technology can successfully and reliably be applied in clinical practice and regulatory decision-making, standards and quality measures need to be developed. The Microarray Qualit...

  7. Contingent post-closure plan, hazardous waste management units at selected maintenance facilities, US Army National Training Center, Fort Irwin, California

    International Nuclear Information System (INIS)

    1992-01-01

    The National Training Center (NTC) at Fort Irwin, California, is a US Army training installation that provides tactical experience for battalion/task forces and squadrons in a mid- to high-intensity combat scenario. Through joint exercises with US Air Force and other services, the NTC also provides a data source for improvements of training doctrines, organization, and equipment. To meet the training and operational needs of the NTC, several maintenance facilities provide general and direct support for mechanical devices, equipment, and vehicles. Maintenance products used at these facilities include fuels, petroleum-based oils, lubricating grease, various degreasing solvents, antifreeze (ethylene glycol), transmission fluid, brake fluid, and hydraulic oil. Used or spent petroleum-based products generated at the maintenance facilities are temporarily accumulated in underground storage tanks (USTs), collected by the NTC hazardous waste management contractor (HAZCO), and stored at the Petroleum, Oil, and Lubricant (POL) Storage Facility, Building 630, until shipped off site to be recovered, reused, and/or reclaimed. Spent degreasing solvents and other hazardous wastes are containerized and stored on-base for up to 90 days at the NTC's Hazardous Waste Storage Facility, Building 703. The US Environmental Protection Agency (EPA) performed an inspection and reviewed the hazardous waste management operations of the NTC. Inspections indicated that the NTC had violated one or more requirements of Subtitle C of the Resource Conservation and Recovery Act (RCRA) and as a result of these violations was issued a Notice of Noncompliance, Notice of Necessity for Conference, and Proposed Compliance Schedule (NON) dated October 13, 1989. The following post-closure plan is the compliance-based approach for the NTC to respond to the regulatory violations cited in the NON

  8. Microarray analysis in the archaeon Halobacterium salinarum strain R1.

    Directory of Open Access Journals (Sweden)

    Jens Twellmeyer

    Full Text Available BACKGROUND: Phototrophy of the extremely halophilic archaeon Halobacterium salinarum was explored for decades. The research was mainly focused on the expression of bacteriorhodopsin and its functional properties. In contrast, less is known about genome wide transcriptional changes and their impact on the physiological adaptation to phototrophy. The tool of choice to record transcriptional profiles is the DNA microarray technique. However, the technique is still rarely used for transcriptome analysis in archaea. METHODOLOGY/PRINCIPAL FINDINGS: We developed a whole-genome DNA microarray based on our sequence data of the Hbt. salinarum strain R1 genome. The potential of our tool is exemplified by the comparison of cells growing under aerobic and phototrophic conditions, respectively. We processed the raw fluorescence data by several stringent filtering steps and a subsequent MAANOVA analysis. The study revealed a lot of transcriptional differences between the two cell states. We found that the transcriptional changes were relatively weak, though significant. Finally, the DNA microarray data were independently verified by a real-time PCR analysis. CONCLUSION/SIGNIFICANCE: This is the first DNA microarray analysis of Hbt. salinarum cells that were actually grown under phototrophic conditions. By comparing the transcriptomics data with current knowledge we could show that our DNA microarray tool is well applicable for transcriptome analysis in the extremely halophilic archaeon Hbt. salinarum. The reliability of our tool is based on both the high-quality array of DNA probes and the stringent data handling including MAANOVA analysis. Among the regulated genes more than 50% had unknown functions. This underlines the fact that haloarchaeal phototrophy is still far away from being completely understood. Hence, the data recorded in this study will be subject to future systems biology analysis.

  9. Washing scaling of GeneChip microarray expression

    Directory of Open Access Journals (Sweden)

    Krohn Knut

    2010-05-01

    Full Text Available Abstract Background Post-hybridization washing is an essential part of microarray experiments. Both the quality of the experimental washing protocol and adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities. Results We conducted experiments on GeneChip microarrays with altered protocols for washing, scanning and staining to study the probe-level intensity changes as a function of the number of washing cycles. For calibration and analysis of the intensity data we make use of the 'hook' method which allows intensity contributions due to non-specific and specific hybridization of perfect match (PM and mismatch (MM probes to be disentangled in a sequence specific manner. On average, washing according to the standard protocol removes about 90% of the non-specific background and about 30-50% and less than 10% of the specific targets from the MM and PM, respectively. Analysis of the washing kinetics shows that the signal-to-noise ratio doubles roughly every ten stringent washing cycles. Washing can be characterized by time-dependent rate constants which reflect the heterogeneous character of target binding to microarray probes. We propose an empirical washing function which estimates the survival of probe bound targets. It depends on the intensity contribution due to specific and non-specific hybridization per probe which can be estimated for each probe using existing methods. The washing function allows probe intensities to be calibrated for the effect of washing. On a relative scale, proper calibration for washing markedly increases expression measures, especially in the limit of small and large values. Conclusions Washing is among the factors which potentially distort expression measures. The proposed first-order correction method allows direct implementation in existing calibration algorithms for microarray data. We provide an experimental

  10. DNA microarray-based PCR ribotyping of Clostridium difficile.

    Science.gov (United States)

    Schneeberg, Alexander; Ehricht, Ralf; Slickers, Peter; Baier, Vico; Neubauer, Heinrich; Zimmermann, Stefan; Rabold, Denise; Lübke-Becker, Antina; Seyboldt, Christian

    2015-02-01

    This study presents a DNA microarray-based assay for fast and simple PCR ribotyping of Clostridium difficile strains. Hybridization probes were designed to query the modularly structured intergenic spacer region (ISR), which is also the template for conventional and PCR ribotyping with subsequent capillary gel electrophoresis (seq-PCR) ribotyping. The probes were derived from sequences available in GenBank as well as from theoretical ISR module combinations. A database of reference hybridization patterns was set up from a collection of 142 well-characterized C. difficile isolates representing 48 seq-PCR ribotypes. The reference hybridization patterns calculated by the arithmetic mean were compared using a similarity matrix analysis. The 48 investigated seq-PCR ribotypes revealed 27 array profiles that were clearly distinguishable. The most frequent human-pathogenic ribotypes 001, 014/020, 027, and 078/126 were discriminated by the microarray. C. difficile strains related to 078/126 (033, 045/FLI01, 078, 126, 126/FLI01, 413, 413/FLI01, 598, 620, 652, and 660) and 014/020 (014, 020, and 449) showed similar hybridization patterns, confirming their genetic relatedness, which was previously reported. A panel of 50 C. difficile field isolates was tested by seq-PCR ribotyping and the DNA microarray-based assay in parallel. Taking into account that the current version of the microarray does not discriminate some closely related seq-PCR ribotypes, all isolates were typed correctly. Moreover, seq-PCR ribotypes without reference profiles available in the database (ribotype 009 and 5 new types) were correctly recognized as new ribotypes, confirming the performance and expansion potential of the microarray. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  11. Recommendations for the use of microarrays in prenatal diagnosis.

    Science.gov (United States)

    Suela, Javier; López-Expósito, Isabel; Querejeta, María Eugenia; Martorell, Rosa; Cuatrecasas, Esther; Armengol, Lluis; Antolín, Eugenia; Domínguez Garrido, Elena; Trujillo-Tiebas, María José; Rosell, Jordi; García Planells, Javier; Cigudosa, Juan Cruz

    2017-04-07

    Microarray technology, recently implemented in international prenatal diagnosis systems, has become one of the main techniques in this field in terms of detection rate and objectivity of the results. This guideline attempts to provide background information on this technology, including technical and diagnostic aspects to be considered. Specifically, this guideline defines: the different prenatal sample types to be used, as well as their characteristics (chorionic villi samples, amniotic fluid, fetal cord blood or miscarriage tissue material); variant reporting policies (including variants of uncertain significance) to be considered in informed consents and prenatal microarray reports; microarray limitations inherent to the technique and which must be taken into account when recommending microarray testing for diagnosis; a detailed clinical algorithm recommending the use of microarray testing and its introduction into routine clinical practice within the context of other genetic tests, including pregnancies in families with a genetic history or specific syndrome suspicion, first trimester increased nuchal translucency or second trimester heart malformation and ultrasound findings not related to a known or specific syndrome. This guideline has been coordinated by the Spanish Association for Prenatal Diagnosis (AEDP, «Asociación Española de Diagnóstico Prenatal»), the Spanish Human Genetics Association (AEGH, «Asociación Española de Genética Humana») and the Spanish Society of Clinical Genetics and Dysmorphology (SEGCyD, «Sociedad Española de Genética Clínica y Dismorfología»). Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

  12. Integrated olfactory receptor and microarray gene expression databases

    Directory of Open Access Journals (Sweden)

    Crasto Chiquito J

    2007-06-01

    Full Text Available Abstract Background Gene expression patterns of olfactory receptors (ORs are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB, which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction. Description ORMD is a Web-accessible database that provides a secure data repository for OR microarray experiments. It contains both publicly available and private data; accessing the latter requires authenticated login. The ORMD is designed to allow users to not only deposit gene expression data but also manage their projects/experiments. For example, contributors can choose whether to make their datasets public. For each experiment, users can download the raw data files and view and export the gene expression data. For each OR gene being probed in a microarray experiment, a hyperlink to that gene in ORDB provides access to genomic and proteomic information related to the corresponding olfactory receptor. Individual ORs archived in ORDB are also linked to ORMD, allowing users access to the related microarray gene expression data. Conclusion ORMD serves as a data repository and project management system. It facilitates the study of microarray experiments of gene expression in the olfactory system. In conjunction with ORDB, ORMD integrates gene expression data with the genomic and functional data of ORs, and is thus a useful resource for both olfactory researchers and the public.

  13. Seeded Bayesian Networks: Constructing genetic networks from microarray data

    Directory of Open Access Journals (Sweden)

    Quackenbush John

    2008-07-01

    Full Text Available Abstract Background DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes that underlie cellular metabolism and physiology. The challenge in analyzing large-scale expression data has been to extract biologically meaningful inferences regarding these processes – often represented as networks – in an environment where the datasets are often imperfect and biological noise can obscure the actual signal. Although many techniques have been developed in an attempt to address these issues, to date their ability to extract meaningful and predictive network relationships has been limited. Here we describe a method that draws on prior information about gene-gene interactions to infer biologically relevant pathways from microarray data. Our approach consists of using preliminary networks derived from the literature and/or protein-protein interaction data as seeds for a Bayesian network analysis of microarray results. Results Through a bootstrap analysis of gene expression data derived from a number of leukemia studies, we demonstrate that seeded Bayesian Networks have the ability to identify high-confidence gene-gene interactions which can then be validated by comparison to other sources of pathway data. Conclusion The use of network seeds greatly improves the ability of Bayesian Network analysis to learn gene interaction networks from gene expression data. We demonstrate that the use of seeds derived from the biomedical literature or high-throughput protein-protein interaction data, or the combination, provides improvement over a standard Bayesian Network analysis, allowing networks involving dynamic processes to be deduced from the static snapshots of biological systems that represent the most common source of microarray data. Software implementing these methods has been included in the widely used TM4 microarray analysis package.

  14. Identification of molecular mechanisms of radiation-induced vascular damage in normal tissues using microarray analyses

    International Nuclear Information System (INIS)

    Kruse, J.J.C.M.; Te Poele, J.A.M.; Russell, N.S.; Boersma, L.J.; Stewart, F.A.

    2003-01-01

    Radiation-induced telangiectasia, characterized by thin-walled dilated blood vessels, can be a serious late complication in patients that have been previously treated for cancer. It might cause cosmetic problems when occurring in the skin, and excessive bleeding requiring surgery when occurring in rectal mucosa. The mechanisms underlying the development of radiation-induced telangiectasia are unclear. The aim of the present study is to determine whether microarrays are useful for studying mechanisms of radiation-induced telangiectasia. The second aim is to test the hypotheses that telangiectasia is characterized by a final common pathway in different tissues. Microarray experiments were performed using amplified RNA from (sham)irradiated mouse tissues (kidney, rectum) at different intervals (1-30 weeks) after irradiation. After normalization procedures, the differentially expressed genes were identified. Control/repeat experiments were done to confirm that the observations were not artifacts of the array procedure. The mouse kidney experiments showed significant upregulation of 31 and 42 genes and downregulation of 9 and 4 genes at 10 and 20 weeks after irradiation, respectively. Irradiated mouse rectum has 278 upregulated and 537 downregulated genes at 10 weeks and 86 upregulated and 29 downregulated genes at 20 weeks. During the development of telangiectasia, 19 upregulated genes and 5 downregulated genes were common to both tissues. Upregulation of Jagged-1, known to play a role in angiogenesis, is particularly interesting in the context of radiation-induced telangiectasia. Microarrays are affective discovery tools to identify novel genes of interest, which may be involved in radiation-induced normal tissue injury. Using information from control arrays (particularly straight color, color reverse and self-self experiments) allowed for a more accurate and reproducible identification of differentially expressed genes than the selection of an arbitrary 2-fold change

  15. ArraySolver: an algorithm for colour-coded graphical display and Wilcoxon signed-rank statistics for comparing microarray gene expression data.

    Science.gov (United States)

    Khan, Haseeb Ahmad

    2004-01-01

    The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t-test, analysis of variance, Pearson test and Mann-Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed-rank test, which is an appropriate test for two-groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour-coded graphical display and comparison of gene expression data using the Wilcoxon signed-rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n < or = 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform.

  16. 16S rRNA based microarray analysis of ten periodontal bacteria in patients with different forms of periodontitis.

    Science.gov (United States)

    Topcuoglu, Nursen; Kulekci, Guven

    2015-10-01

    DNA microarray analysis is a computer based technology, that a reverse capture, which targets 10 periodontal bacteria (ParoCheck) is available for rapid semi-quantitative determination. The aim of this three-year retrospective study was to display the microarray analysis results for the subgingival biofilm samples taken from patient cases diagnosed with different forms of periodontitis. A total of 84 patients with generalized aggressive periodontitis (GAP,n:29), generalized chronic periodontitis (GCP, n:25), peri-implantitis (PI,n:14), localized aggressive periodontitis (LAP,n:8) and refractory chronic periodontitis (RP,n:8) were consecutively selected from the archives of the Oral Microbiological Diagnostic Laboratory. The subgingival biofilm samples were analyzed by the microarray-based identification of 10 selected species. All the tested species were detected in the samples. The red complex bacteria were the most prevalent with very high levels in all groups. Fusobacterium nucleatum was detected in all samples at high levels. The green and blue complex bacteria were less prevalent compared with red and orange complex, except Aggregatibacter actinomycetemcomitas was detected in all LAP group. Positive correlations were found within all the red complex bacteria and between red and orange complex bacteria especially in GCP and GAP groups. Parocheck enables to monitoring of periodontal pathogens in all forms of periodontal disease and can be alternative to other guiding and reliable microbiologic tests. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 18. Part 1B: Citations with abstracts, sections 10 through 16

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    This bibliography contains 3,638 citations with abstracts of documents relevant to environmental restoration, nuclear facility decontamination and decommissioning (D and D), uranium mill tailings management, and site remedial actions. The bibliography contains scientific, technical, financial, and regulatory information that pertains to DOE environmental restoration programs. The citations are separated by topic into 16 sections, including (1) DOE Environmental Restoration Program; (2) DOE D and D Program; (3) Nuclear Facilities Decommissioning; (4) DOE Formerly Utilized sites Remedial Action Program; (5) NORM-Contaminated Site Restoration; (6) DOE Uranium Mill Tailings Remedial Action Project; (7) Uranium Mill Tailings Management; (8) DOE Site-Wide Remedial Actions; (9) DOE Onsite Remedial Action Projects; (10) Contaminated Site Remedial Actions; (11) DOE Underground Storage Tank Remediation; (12) DOE Technology Development, Demonstration, and Evaluation; (13) Soil Remediation; (14) Groundwater Remediation; (15) Environmental Measurements, Analysis, and Decision-Making; and (16) Environmental Management Issues.

  18. Nuclear facility decommissioning and site remedial actions: A selected bibliography, Volume 18. Part 1A: Citations with abstracts, sections 1 through 9

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    This bibliography contains 3,638 citations with abstracts of documents relevant to environmental restoration, nuclear facility decontamination and decommissioning (D and D), uranium mill tailings management, and site remedial actions. The bibliography contains scientific, technical, financial, and regulatory information that pertains to DOE environmental restoration programs. The citations are separated by topic into 16 sections, including (1) DOE Environmental Restoration program; (2) DOE D and D Program; (3) Nuclear Facilities Decommissioning; (4) DOE Formerly Utilized Sites Remedial Action Program; (5) NORM-Contaminated Site Restoration; (6) DOE Uranium Mill Tailings Remedial Action Project; (7) Uranium Mill Tailings Management; (8) DOE Site-Wide Remedial Actions; (9) DOE Onsite Remedial Action Projects; (10) Contaminated Site Remedial Actions; (11) DOE Underground Storage Tank Remediation; (12) DOE Technology Development, Demonstration, and Evaluation; (13) Soil Remediation; (14) Groundwater Remediation; (15) Environmental Measurements, Analysis, and Decision-Making; and (16) Environmental Management Issues.

  19. Selection of a Data Acquisition and Controls System Communications and Software Architecture for Johnson Space Center's Space Environment Simulation Laboratory Thermal and Vacuum Test Facilities

    Science.gov (United States)

    Jordan, Eric A.

    2004-01-01

    Upgrade of data acquisition and controls systems software at Johnson Space Center's Space Environment Simulation Laboratory (SESL) involved the definition, evaluation and selection of a system communication architecture and software components. A brief discussion of the background of the SESL and its data acquisition and controls systems provides a context for discussion of the requirements for each selection. Further framework is provided as upgrades to these systems accomplished in the 1990s and in 2003 are compared to demonstrate the role that technological advances have had in their improvement. Both of the selections were similar in their three phases; 1) definition of requirements, 2) identification of candidate products and their evaluation and testing and 3) selection by comparison of requirement fulfillment. The candidates for the communication architecture selection embraced several different methodologies which are explained and contrasted. Requirements for this selection are presented and the selection process is described. Several candidates for the software component of the data acquisition and controls system are identified, requirements for evaluation and selection are presented, and the evaluation process is described.

  20. Effects of increased nurses’ workload on quality documentation of patient information at selected Primary Health Care facilities in Vhembe District, Limpopo Province

    OpenAIRE

    Rhulani C. Shihundla; Rachel T. Lebese; Maria S. Maputle

    2016-01-01

    Background: Recording of information on multiple documents increases professional nurses’ responsibilities and workload during working hours. There are multiple registers and books at Primary Health Care (PHC) facilities in which a patient’s information is to be recorded for different services during a visit to a health professional. Antenatal patients coming for the first visit must be recorded in the following documents: tick register; Prevention of Mother-ToChild Transmission (PMTCT) regis...