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Sample records for accurate svm-based gene

  1. Multi-class clustering of cancer subtypes through SVM based ensemble of pareto-optimal solutions for gene marker identification.

    Anirban Mukhopadhyay

    Full Text Available With the advancement of microarray technology, it is now possible to study the expression profiles of thousands of genes across different experimental conditions or tissue samples simultaneously. Microarray cancer datasets, organized as samples versus genes fashion, are being used for classification of tissue samples into benign and malignant or their subtypes. They are also useful for identifying potential gene markers for each cancer subtype, which helps in successful diagnosis of particular cancer types. In this article, we have presented an unsupervised cancer classification technique based on multiobjective genetic clustering of the tissue samples. In this regard, a real-coded encoding of the cluster centers is used and cluster compactness and separation are simultaneously optimized. The resultant set of near-Pareto-optimal solutions contains a number of non-dominated solutions. A novel approach to combine the clustering information possessed by the non-dominated solutions through Support Vector Machine (SVM classifier has been proposed. Final clustering is obtained by consensus among the clusterings yielded by different kernel functions. The performance of the proposed multiobjective clustering method has been compared with that of several other microarray clustering algorithms for three publicly available benchmark cancer datasets. Moreover, statistical significance tests have been conducted to establish the statistical superiority of the proposed clustering method. Furthermore, relevant gene markers have been identified using the clustering result produced by the proposed clustering method and demonstrated visually. Biological relationships among the gene markers are also studied based on gene ontology. The results obtained are found to be promising and can possibly have important impact in the area of unsupervised cancer classification as well as gene marker identification for multiple cancer subtypes.

  2. Protein submitochondrial localization from integrated sequence representation and SVM-based backward feature extraction.

    Li, Liqi; Yu, Sanjiu; Xiao, Weidong; Li, Yongsheng; Hu, Wenjuan; Huang, Lan; Zheng, Xiaoqi; Zhou, Shiwen; Yang, Hua

    2015-01-01

    Mitochondrion, a tiny energy factory, plays an important role in various biological processes of most eukaryotic cells. Mitochondrial defection is associated with a series of human diseases. Knowledge of the submitochondrial locations of proteins can help to reveal the biological functions of novel proteins, and understand the mechanisms underlying various biological processes occurring in the mitochondrion. However, experimental methods to determine protein submitochondrial locations are costly and time consuming. Thus it is essential to develop a fast and reliable computational method to predict protein submitochondrial locations. Here, we proposed a support vector machine (SVM) based approach for predicting protein submitochondrial locations. Information from the position-specific score matrix (PSSM), gene ontology (GO) and the protein feature (PROFEAT) was integrated into the principal features of this model. Then a recursive feature selection scheme was employed to select the optimal features. Finally, an SVM module was used to predict protein submitochondrial locations based on the optimal features. Through the jackknife cross-validation test, our method achieved an accuracy of 99.37% on benchmark dataset M317, and 100% on the other two datasets, M1105 and T86. These results indicate that our method is economic and effective for accurate prediction of the protein submitochondrial location.

  3. Power quality events recognition using a SVM-based method

    Cerqueira, Augusto Santiago; Ferreira, Danton Diego; Ribeiro, Moises Vidal; Duque, Carlos Augusto [Department of Electrical Circuits, Federal University of Juiz de Fora, Campus Universitario, 36036 900, Juiz de Fora MG (Brazil)

    2008-09-15

    In this paper, a novel SVM-based method for power quality event classification is proposed. A simple approach for feature extraction is introduced, based on the subtraction of the fundamental component from the acquired voltage signal. The resulting signal is presented to a support vector machine for event classification. Results from simulation are presented and compared with two other methods, the OTFR and the LCEC. The proposed method shown an improved performance followed by a reasonable computational cost. (author)

  4. Generalized SMO algorithm for SVM-based multitask learning.

    Cai, Feng; Cherkassky, Vladimir

    2012-06-01

    Exploiting additional information to improve traditional inductive learning is an active research area in machine learning. In many supervised-learning applications, training data can be naturally separated into several groups, and incorporating this group information into learning may improve generalization. Recently, Vapnik proposed a general approach to formalizing such problems, known as "learning with structured data" and its support vector machine (SVM) based optimization formulation called SVM+. Liang and Cherkassky showed the connection between SVM+ and multitask learning (MTL) approaches in machine learning, and proposed an SVM-based formulation for MTL called SVM+MTL for classification. Training the SVM+MTL classifier requires the solution of a large quadratic programming optimization problem which scales as O(n(3)) with sample size n. So there is a need to develop computationally efficient algorithms for implementing SVM+MTL. This brief generalizes Platt's sequential minimal optimization (SMO) algorithm to the SVM+MTL setting. Empirical results show that, for typical SVM+MTL problems, the proposed generalized SMO achieves over 100 times speed-up, in comparison with general-purpose optimization routines.

  5. SVM-based glioma grading: Optimization by feature reduction analysis.

    Zöllner, Frank G; Emblem, Kyrre E; Schad, Lothar R

    2012-09-01

    We investigated the predictive power of feature reduction analysis approaches in support vector machine (SVM)-based classification of glioma grade. In 101 untreated glioma patients, three analytic approaches were evaluated to derive an optimal reduction in features; (i) Pearson's correlation coefficients (PCC), (ii) principal component analysis (PCA) and (iii) independent component analysis (ICA). Tumor grading was performed using a previously reported SVM approach including whole-tumor cerebral blood volume (CBV) histograms and patient age. Best classification accuracy was found using PCA at 85% (sensitivity=89%, specificity=84%) when reducing the feature vector from 101 (100-bins rCBV histogram+age) to 3 principal components. In comparison, classification accuracy by PCC was 82% (89%, 77%, 2 dimensions) and 79% by ICA (87%, 75%, 9 dimensions). For improved speed (up to 30%) and simplicity, feature reduction by all three methods provided similar classification accuracy to literature values (∼87%) while reducing the number of features by up to 98%.

  6. Efficient SVM-based Recognition of Chinese Personal Names

    Yu Ying(宇缨); Wang Xiaolong; Liu Bingquan; Wang Hui

    2004-01-01

    This paper provides a flexible and efficient method to identify Chinese personal names based on SVM (Support Vector Machines). In its approach, forming rules of personal name is employed to select candidate set, then SVM based identification strategies is used to recognize real personal name in the candidate set. Basic semanteme of word in context and frequency information of word inside candidate are selected as features in its methodology, which reduce the feature space scale dramatically and calculate more efficiently. Results of open testing achieved F-measure 90.59% in 2 million words news and F-measure 86.67% in 16.17 million words news based on this project.

  7. SVM-based prediction of caspase substrate cleavage sites

    Ranganathan Shoba

    2006-12-01

    Full Text Available Abstract Background Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of such cleavage sites will complement structural and functional studies on substrates cleavage as well as discovery of new substrates. Recently, different computational methods have been developed to predict the cleavage sites of caspase substrates with varying degrees of success. As the support vector machines (SVM algorithm has been shown to be useful in several biological classification problems, we have implemented an SVM-based method to investigate its applicability to this domain. Results A set of unique caspase substrates cleavage sites were obtained from literature and used for evaluating the SVM method. Datasets containing (i the tetrapeptide cleavage sites, (ii the tetrapeptide cleavage sites, augmented by two adjacent residues, P1' and P2' amino acids and (iii the tetrapeptide cleavage sites with ten additional upstream and downstream flanking sequences (where available were tested. The SVM method achieved an accuracy ranging from 81.25% to 97.92% on independent test sets. The SVM method successfully predicted the cleavage of a novel caspase substrate and its mutants. Conclusion This study presents an SVM approach for predicting caspase substrate cleavage sites based on the cleavage sites and the downstream and upstream flanking sequences. The method shows an improvement over existing methods and may be useful for predicting hitherto undiscovered cleavage sites.

  8. SVM-based glioma grading. Optimization by feature reduction analysis

    Zoellner, Frank G.; Schad, Lothar R. [University Medical Center Mannheim, Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Emblem, Kyrre E. [Massachusetts General Hospital, Charlestown, A.A. Martinos Center for Biomedical Imaging, Boston MA (United States). Dept. of Radiology; Harvard Medical School, Boston, MA (United States); Oslo Univ. Hospital (Norway). The Intervention Center

    2012-11-01

    We investigated the predictive power of feature reduction analysis approaches in support vector machine (SVM)-based classification of glioma grade. In 101 untreated glioma patients, three analytic approaches were evaluated to derive an optimal reduction in features; (i) Pearson's correlation coefficients (PCC), (ii) principal component analysis (PCA) and (iii) independent component analysis (ICA). Tumor grading was performed using a previously reported SVM approach including whole-tumor cerebral blood volume (CBV) histograms and patient age. Best classification accuracy was found using PCA at 85% (sensitivity = 89%, specificity = 84%) when reducing the feature vector from 101 (100-bins rCBV histogram + age) to 3 principal components. In comparison, classification accuracy by PCC was 82% (89%, 77%, 2 dimensions) and 79% by ICA (87%, 75%, 9 dimensions). For improved speed (up to 30%) and simplicity, feature reduction by all three methods provided similar classification accuracy to literature values ({proportional_to}87%) while reducing the number of features by up to 98%. (orig.)

  9. SVM based layout retargeting for fast and regularized inverse lithography

    Kai-sheng LUO; Zheng SHI; Xiao-lang YAN; Zhen GENG

    2014-01-01

    Inverse lithography technology (ILT), also known as pixel-based optical proximity correction (PB-OPC), has shown promising capability in pushing the current 193 nm lithography to its limit. By treating the mask optimization process as an inverse problem in lithography, ILT provides a more complete exploration of the solution space and better pattern fidelity than the tradi-tional edge-based OPC. However, the existing methods of ILT are extremely time-consuming due to the slow convergence of the optimization process. To address this issue, in this paper we propose a support vector machine (SVM) based layout retargeting method for ILT, which is designed to generate a good initial input mask for the optimization process and promote the convergence speed. Supervised by optimized masks of training layouts generated by conventional ILT, SVM models are learned and used to predict the initial pixel values in the‘undefined areas’ of the new layout. By this process, an initial input mask close to the final optimized mask of the new layout is generated, which reduces iterations needed in the following optimization process. Manu-facturability is another critical issue in ILT;however, the mask generated by our layout retargeting method is quite irregular due to the prediction inaccuracy of the SVM models. To compensate for this drawback, a spatial filter is employed to regularize the retargeted mask for complexity reduction. We implemented our layout retargeting method with a regularized level-set based ILT (LSB-ILT) algorithm under partially coherent illumination conditions. Experimental results show that with an initial input mask generated by our layout retargeting method, the number of iterations needed in the optimization process and runtime of the whole process in ILT are reduced by 70.8%and 69.0%, respectively.

  10. SVM-Based Spectral Analysis for Heart Rate from Multi-Channel WPPG Sensor Signals

    Xiong, Jiping; Cai, Lisang; Wang, Fei; He, Xiaowei

    2017-01-01

    Although wrist-type photoplethysmographic (hereafter referred to as WPPG) sensor signals can measure heart rate quite conveniently, the subjects’ hand movements can cause strong motion artifacts, and then the motion artifacts will heavily contaminate WPPG signals. Hence, it is challenging for us to accurately estimate heart rate from WPPG signals during intense physical activities. The WWPG method has attracted more attention thanks to the popularity of wrist-worn wearable devices. In this paper, a mixed approach called Mix-SVM is proposed, it can use multi-channel WPPG sensor signals and simultaneous acceleration signals to measurement heart rate. Firstly, we combine the principle component analysis and adaptive filter to remove a part of the motion artifacts. Due to the strong relativity between motion artifacts and acceleration signals, the further denoising problem is regarded as a sparse signals reconstruction problem. Then, we use a spectrum subtraction method to eliminate motion artifacts effectively. Finally, the spectral peak corresponding to heart rate is sought by an SVM-based spectral analysis method. Through the public PPG database in the 2015 IEEE Signal Processing Cup, we acquire the experimental results, i.e., the average absolute error was 1.01 beat per minute, and the Pearson correlation was 0.9972. These results also confirm that the proposed Mix-SVM approach has potential for multi-channel WPPG-based heart rate estimation in the presence of intense physical exercise. PMID:28273818

  11. SVM-Based Spectral Analysis for Heart Rate from Multi-Channel WPPG Sensor Signals

    Jiping Xiong

    2017-03-01

    Full Text Available Although wrist-type photoplethysmographic (hereafter referred to as WPPG sensor signals can measure heart rate quite conveniently, the subjects’ hand movements can cause strong motion artifacts, and then the motion artifacts will heavily contaminate WPPG signals. Hence, it is challenging for us to accurately estimate heart rate from WPPG signals during intense physical activities. The WWPG method has attracted more attention thanks to the popularity of wrist-worn wearable devices. In this paper, a mixed approach called Mix-SVM is proposed, it can use multi-channel WPPG sensor signals and simultaneous acceleration signals to measurement heart rate. Firstly, we combine the principle component analysis and adaptive filter to remove a part of the motion artifacts. Due to the strong relativity between motion artifacts and acceleration signals, the further denoising problem is regarded as a sparse signals reconstruction problem. Then, we use a spectrum subtraction method to eliminate motion artifacts effectively. Finally, the spectral peak corresponding to heart rate is sought by an SVM-based spectral analysis method. Through the public PPG database in the 2015 IEEE Signal Processing Cup, we acquire the experimental results, i.e., the average absolute error was 1.01 beat per minute, and the Pearson correlation was 0.9972. These results also confirm that the proposed Mix-SVM approach has potential for multi-channel WPPG-based heart rate estimation in the presence of intense physical exercise.

  12. SVM-Based Spectral Analysis for Heart Rate from Multi-Channel WPPG Sensor Signals.

    Xiong, Jiping; Cai, Lisang; Wang, Fei; He, Xiaowei

    2017-03-03

    Although wrist-type photoplethysmographic (hereafter referred to as WPPG) sensor signals can measure heart rate quite conveniently, the subjects' hand movements can cause strong motion artifacts, and then the motion artifacts will heavily contaminate WPPG signals. Hence, it is challenging for us to accurately estimate heart rate from WPPG signals during intense physical activities. The WWPG method has attracted more attention thanks to the popularity of wrist-worn wearable devices. In this paper, a mixed approach called Mix-SVM is proposed, it can use multi-channel WPPG sensor signals and simultaneous acceleration signals to measurement heart rate. Firstly, we combine the principle component analysis and adaptive filter to remove a part of the motion artifacts. Due to the strong relativity between motion artifacts and acceleration signals, the further denoising problem is regarded as a sparse signals reconstruction problem. Then, we use a spectrum subtraction method to eliminate motion artifacts effectively. Finally, the spectral peak corresponding to heart rate is sought by an SVM-based spectral analysis method. Through the public PPG database in the 2015 IEEE Signal Processing Cup, we acquire the experimental results, i.e., the average absolute error was 1.01 beat per minute, and the Pearson correlation was 0.9972. These results also confirm that the proposed Mix-SVM approach has potential for multi-channel WPPG-based heart rate estimation in the presence of intense physical exercise.

  13. Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

    Andersen, Mikael R; Nielsen, Jakob B; Klitgaard, Andreas; Petersen, Lene M; Zachariasen, Mia; Hansen, Tilde J; Blicher, Lene H; Gotfredsen, Charlotte H; Larsen, Thomas O; Nielsen, Kristian F; Mortensen, Uffe H

    2013-01-02

    Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 of 16 known clusters and nearly accurate for the remaining 3 clusters. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (superclusters), and validate this both with legacy data and experimentally by prediction and verification of a supercluster consisting of the synthase AN1242 and the prenyltransferase AN11080, as well as identification of the product compound nidulanin A. We have used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.

  14. Modelling and Simulation of SVM Based DVR System for Voltage Sag Mitigation

    S. Leela

    2013-12-01

    Full Text Available The aim of this study is to design and simulate three phase DVR system using MATLAB simulink. SVM based DVR is proposed to reduce the sag on the transmission line. The SVM based DVR injects voltage into the line to compensate the voltage drop. Sag is created by connecting a heavy load in parallel with the existing system. This sag will be compensated by injecting the inverter output through an injection transformer. The results of simulation are compared with the theoretical results.

  15. Rapid and accurate synthesis of TALE genes from synthetic oligonucleotides.

    Wang, Fenghua; Zhang, Hefei; Gao, Jingxia; Chen, Fengjiao; Chen, Sijie; Zhang, Cuizhen; Peng, Gang

    2016-01-01

    Custom synthesis of transcription activator-like effector (TALE) genes has relied upon plasmid libraries of pre-fabricated TALE-repeat monomers or oligomers. Here we describe a novel synthesis method that directly incorporates annealed synthetic oligonucleotides into the TALE-repeat units. Our approach utilizes iterative sets of oligonucleotides and a translational frame check strategy to ensure the high efficiency and accuracy of TALE-gene synthesis. TALE arrays of more than 20 repeats can be constructed, and the majority of the synthesized constructs have perfect sequences. In addition, this novel oligonucleotide-based method can readily accommodate design changes to the TALE repeats. We demonstrated an increased gene targeting efficiency against a genomic site containing a potentially methylated cytosine by incorporating non-conventional repeat variable di-residue (RVD) sequences.

  16. Advances in SVM-Based System Using GMM Super Vectors for Text-Independent Speaker Verification

    ZHAO Jian; DONG Yuan; ZHAO Xianyu; YANG Hao; LU Liang; WANG Haila

    2008-01-01

    For text-independent speaker verification,the Gaussian mixture model (GMM) using a universal background model strategy and the GMM using support vector machines are the two most commonly used methodologies.Recently,a new SVM-based speaker verification method using GMM super vectors has been proposed.This paper describes the construction of a new speaker verification system and investigates the use of nuisance attribute projection and test normalization to further enhance performance.Experiments were conducted on the core test of the 2006 NIST speaker recognition evaluation corpus.The experimental results indicate that an SVM-based speaker verification system using GMM super vectors can achieve ap-pealing performance.With the use of nuisance attribute projection and test normalization,the system per-formance can be significantly improved,with improvements in the equal error rate from 7.78% to 4.92% and detection cost function from 0.0376 to 0.0251.

  17. SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling.

    Shahid, Mohammad; Shahzad Cheema, Muhammad; Klenner, Alexander; Younesi, Erfan; Hofmann-Apitius, Martin

    2013-03-01

    Systems pharmacological modeling of drug mode of action for the next generation of multitarget drugs may open new routes for drug design and discovery. Computational methods are widely used in this context amongst which support vector machines (SVM) have proven successful in addressing the challenge of classifying drugs with similar features. We have applied a variety of such SVM-based approaches, namely SVM-based recursive feature elimination (SVM-RFE). We use the approach to predict the pharmacological properties of drugs widely used against complex neurodegenerative disorders (NDD) and to build an in-silico computational model for the binary classification of NDD drugs from other drugs. Application of an SVM-RFE model to a set of drugs successfully classified NDD drugs from non-NDD drugs and resulted in overall accuracy of ∼80 % with 10 fold cross validation using 40 top ranked molecular descriptors selected out of total 314 descriptors. Moreover, SVM-RFE method outperformed linear discriminant analysis (LDA) based feature selection and classification. The model reduced the multidimensional descriptors space of drugs dramatically and predicted NDD drugs with high accuracy, while avoiding over fitting. Based on these results, NDD-specific focused libraries of drug-like compounds can be designed and existing NDD-specific drugs can be characterized by a well-characterized set of molecular descriptors.

  18. Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression

    Melo Francisco

    2006-11-01

    Full Text Available Abstract Background In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE. The method relies on current genome information and annotation, incorporation of several new features, and key improvements over alternative methods, all of which are important to determine gene expression levels more accurately. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. Results We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. In addition, we report new insights from the analysis of existing SAGE data. First, we found that experimental SAGE tags mapping onto introns, intron-exon boundaries, and non-coding RNA elements are observed in all available SAGE data. Second, a significant fraction of experimental SAGE tags was found to map onto genomic regions currently annotated as intergenic. Third, a significant number of existing experimental SAGE tags for yeast has been derived from truncated cDNAs, which are synthesized through oligo-d(T priming to internal poly-(A regions during reverse transcription. Conclusion We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments. This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications.

  19. Accurate prediction of secondary metabolite gene clusters in filamentous fungi

    Andersen, Mikael Rørdam; Nielsen, Jakob Blæsbjerg; Klitgaard, Andreas

    2013-01-01

    Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify suppo...... used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom....

  20. Diagnosis of Elevator Faults with LS-SVM Based on Optimization by K-CV

    Zhou Wan

    2015-01-01

    Full Text Available Several common elevator malfunctions were diagnosed with a least square support vector machine (LS-SVM. After acquiring vibration signals of various elevator functions, their energy characteristics and time domain indicators were extracted by theoretically analyzing the optimal wavelet packet, in order to construct a feature vector of malfunctions for identifying causes of the malfunctions as input of LS-SVM. Meanwhile, parameters about LS-SVM were optimized by K-fold cross validation (K-CV. After diagnosing deviated elevator guide rail, deviated shape of guide shoe, abnormal running of tractor, erroneous rope groove of traction sheave, deviated guide wheel, and tension of wire rope, the results suggested that the LS-SVM based on K-CV optimization was one of effective methods for diagnosing elevator malfunctions.

  1. Accurate Gene Expression-Based Biodosimetry Using a Minimal Set of Human Gene Transcripts

    Tucker, James D., E-mail: jtucker@biology.biosci.wayne.edu [Department of Biological Sciences, Wayne State University, Detroit, Michigan (United States); Joiner, Michael C. [Department of Radiation Oncology, Wayne State University, Detroit, Michigan (United States); Thomas, Robert A.; Grever, William E.; Bakhmutsky, Marina V. [Department of Biological Sciences, Wayne State University, Detroit, Michigan (United States); Chinkhota, Chantelle N.; Smolinski, Joseph M. [Department of Electrical and Computer Engineering, Wayne State University, Detroit, Michigan (United States); Divine, George W. [Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan (United States); Auner, Gregory W. [Department of Electrical and Computer Engineering, Wayne State University, Detroit, Michigan (United States)

    2014-03-15

    Purpose: Rapid and reliable methods for conducting biological dosimetry are a necessity in the event of a large-scale nuclear event. Conventional biodosimetry methods lack the speed, portability, ease of use, and low cost required for triaging numerous victims. Here we address this need by showing that polymerase chain reaction (PCR) on a small number of gene transcripts can provide accurate and rapid dosimetry. The low cost and relative ease of PCR compared with existing dosimetry methods suggest that this approach may be useful in mass-casualty triage situations. Methods and Materials: Human peripheral blood from 60 adult donors was acutely exposed to cobalt-60 gamma rays at doses of 0 (control) to 10 Gy. mRNA expression levels of 121 selected genes were obtained 0.5, 1, and 2 days after exposure by reverse-transcriptase real-time PCR. Optimal dosimetry at each time point was obtained by stepwise regression of dose received against individual gene transcript expression levels. Results: Only 3 to 4 different gene transcripts, ASTN2, CDKN1A, GDF15, and ATM, are needed to explain ≥0.87 of the variance (R{sup 2}). Receiver-operator characteristics, a measure of sensitivity and specificity, of 0.98 for these statistical models were achieved at each time point. Conclusions: The actual and predicted radiation doses agree very closely up to 6 Gy. Dosimetry at 8 and 10 Gy shows some effect of saturation, thereby slightly diminishing the ability to quantify higher exposures. Analyses of these gene transcripts may be advantageous for use in a field-portable device designed to assess exposures in mass casualty situations or in clinical radiation emergencies.

  2. A hybrid PSO-SVM-based method for predicting the friction coefficient between aircraft tire and coating

    Zhan, Liwei; Li, Chengwei

    2017-02-01

    A hybrid PSO-SVM-based model is proposed to predict the friction coefficient between aircraft tire and coating. The presented hybrid model combines a support vector machine (SVM) with particle swarm optimization (PSO) technique. SVM has been adopted to solve regression problems successfully. Its regression accuracy is greatly related to optimizing parameters such as the regularization constant C , the parameter gamma γ corresponding to RBF kernel and the epsilon parameter \\varepsilon in the SVM training procedure. However, the friction coefficient which is predicted based on SVM has yet to be explored between aircraft tire and coating. The experiment reveals that drop height and tire rotational speed are the factors affecting friction coefficient. Bearing in mind, the friction coefficient can been predicted using the hybrid PSO-SVM-based model by the measured friction coefficient between aircraft tire and coating. To compare regression accuracy, a grid search (GS) method and a genetic algorithm (GA) are used to optimize the relevant parameters (C , γ and \\varepsilon ), respectively. The regression accuracy could be reflected by the coefficient of determination ({{R}2} ). The result shows that the hybrid PSO-RBF-SVM-based model has better accuracy compared with the GS-RBF-SVM- and GA-RBF-SVM-based models. The agreement of this model (PSO-RBF-SVM) with experiment data confirms its good performance.

  3. LDA-SVM-based EGFR mutation model for NSCLC brain metastases: an observational study.

    Hu, Nan; Wang, Ge; Wu, Yu-Hao; Chen, Shi-Feng; Liu, Guo-Dong; Chen, Chuan; Wang, Dong; He, Zhong-Shi; Yang, Xue-Qin; He, Yong; Xiao, Hua-Liang; Huang, Ding-De; Xiong, Kun-Lin; Wu, Yan; Huang, Ming; Yang, Zhen-Zhou

    2015-02-01

    Epidermal growth factor receptor (EGFR) activating mutations are a predictor of tyrosine kinase inhibitor effectiveness in the treatment of non-small-cell lung cancer (NSCLC). The objective of this study is to build a model for predicting the EGFR mutation status of brain metastasis in patients with NSCLC. Observation and model set-up. This study was conducted between January 2003 and December 2011 in 6 medical centers in Southwest China. The study included 31 NSCLC patients with brain metastases. Eligibility requirements were histological proof of NSCLC, as well as sufficient quantity of paraffin-embedded lung and brain metastases specimens for EGFR mutation detection. The linear discriminant analysis (LDA) method was used for analyzing the dimensional reduction of clinical features, and a support vector machine (SVM) algorithm was employed to generate an EGFR mutation model for NSCLC brain metastases. Training-testing-validation (3 : 1 : 1) processes were applied to find the best fit in 12 patients (validation test set) with NSCLC and brain metastases treated with a tyrosine kinase inhibitor and whole-brain radiotherapy. Primary and secondary outcome measures: EGFR mutation analysis in patients with NSCLC and brain metastases and the development of a LDA-SVM-based EGFR mutation model for NSCLC brain metastases patients. EGFR mutation discordance between the primary lung tumor and brain metastases was found in 5 patients. Using LDA, 13 clinical features were transformed into 9 characteristics, and 3 were selected as primary vectors. The EGFR mutation model constructed with SVM algorithms had an accuracy, sensitivity, and specificity for determining the mutation status of brain metastases of 0.879, 0.886, and 0.875, respectively. Furthermore, the replicability of our model was confirmed by testing 100 random combinations of input values. The LDA-SVM-based model developed in this study could predict the EGFR status of brain metastases in this small cohort of

  4. LDA-SVM-Based EGFR Mutation Model for NSCLC Brain Metastases

    Hu, Nan; Wang, Ge; Wu, Yu-Hao; Chen, Shi-Feng; Liu, Guo-Dong; Chen, Chuan; Wang, Dong; He, Zhong-Shi; Yang, Xue-Qin; He, Yong; Xiao, Hua-Liang; Huang, Ding-De; Xiong, Kun-Lin; Wu, Yan; Huang, Ming; Yang, Zhen-Zhou

    2015-01-01

    Abstract Epidermal growth factor receptor (EGFR) activating mutations are a predictor of tyrosine kinase inhibitor effectiveness in the treatment of non–small-cell lung cancer (NSCLC). The objective of this study is to build a model for predicting the EGFR mutation status of brain metastasis in patients with NSCLC. Observation and model set-up. This study was conducted between January 2003 and December 2011 in 6 medical centers in Southwest China. The study included 31 NSCLC patients with brain metastases. Eligibility requirements were histological proof of NSCLC, as well as sufficient quantity of paraffin-embedded lung and brain metastases specimens for EGFR mutation detection. The linear discriminant analysis (LDA) method was used for analyzing the dimensional reduction of clinical features, and a support vector machine (SVM) algorithm was employed to generate an EGFR mutation model for NSCLC brain metastases. Training-testing-validation (3 : 1 : 1) processes were applied to find the best fit in 12 patients (validation test set) with NSCLC and brain metastases treated with a tyrosine kinase inhibitor and whole-brain radiotherapy. Primary and secondary outcome measures: EGFR mutation analysis in patients with NSCLC and brain metastases and the development of a LDA-SVM-based EGFR mutation model for NSCLC brain metastases patients. EGFR mutation discordance between the primary lung tumor and brain metastases was found in 5 patients. Using LDA, 13 clinical features were transformed into 9 characteristics, and 3 were selected as primary vectors. The EGFR mutation model constructed with SVM algorithms had an accuracy, sensitivity, and specificity for determining the mutation status of brain metastases of 0.879, 0.886, and 0.875, respectively. Furthermore, the replicability of our model was confirmed by testing 100 random combinations of input values. The LDA-SVM-based model developed in this study could predict the EGFR status of brain metastases in this

  5. Evaluation of new reference genes in papaya for accurate transcript normalization under different experimental conditions.

    Zhu, Xiaoyang; Li, Xueping; Chen, Weixin; Chen, Jianye; Lu, Wangjin; Chen, Lei; Fu, Danwen

    2012-01-01

    Real-time reverse transcription PCR (RT-qPCR) is a preferred method for rapid and accurate quantification of gene expression studies. Appropriate application of RT-qPCR requires accurate normalization though the use of reference genes. As no single reference gene is universally suitable for all experiments, thus reference gene(s) validation under different experimental conditions is crucial for RT-qPCR analysis. To date, only a few studies on reference genes have been done in other plants but none in papaya. In the present work, we selected 21 candidate reference genes, and evaluated their expression stability in 246 papaya fruit samples using three algorithms, geNorm, NormFinder and RefFinder. The samples consisted of 13 sets collected under different experimental conditions, including various tissues, different storage temperatures, different cultivars, developmental stages, postharvest ripening, modified atmosphere packaging, 1-methylcyclopropene (1-MCP) treatment, hot water treatment, biotic stress and hormone treatment. Our results demonstrated that expression stability varied greatly between reference genes and that different suitable reference gene(s) or combination of reference genes for normalization should be validated according to the experimental conditions. In general, the internal reference genes EIF (Eukaryotic initiation factor 4A), TBP1 (TATA binding protein 1) and TBP2 (TATA binding protein 2) genes had a good performance under most experimental conditions, whereas the most widely present used reference genes, ACTIN (Actin 2), 18S rRNA (18S ribosomal RNA) and GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) were not suitable in many experimental conditions. In addition, two commonly used programs, geNorm and Normfinder, were proved sufficient for the validation. This work provides the first systematic analysis for the selection of superior reference genes for accurate transcript normalization in papaya under different experimental conditions.

  6. Evaluation of new reference genes in papaya for accurate transcript normalization under different experimental conditions.

    Xiaoyang Zhu

    Full Text Available Real-time reverse transcription PCR (RT-qPCR is a preferred method for rapid and accurate quantification of gene expression studies. Appropriate application of RT-qPCR requires accurate normalization though the use of reference genes. As no single reference gene is universally suitable for all experiments, thus reference gene(s validation under different experimental conditions is crucial for RT-qPCR analysis. To date, only a few studies on reference genes have been done in other plants but none in papaya. In the present work, we selected 21 candidate reference genes, and evaluated their expression stability in 246 papaya fruit samples using three algorithms, geNorm, NormFinder and RefFinder. The samples consisted of 13 sets collected under different experimental conditions, including various tissues, different storage temperatures, different cultivars, developmental stages, postharvest ripening, modified atmosphere packaging, 1-methylcyclopropene (1-MCP treatment, hot water treatment, biotic stress and hormone treatment. Our results demonstrated that expression stability varied greatly between reference genes and that different suitable reference gene(s or combination of reference genes for normalization should be validated according to the experimental conditions. In general, the internal reference genes EIF (Eukaryotic initiation factor 4A, TBP1 (TATA binding protein 1 and TBP2 (TATA binding protein 2 genes had a good performance under most experimental conditions, whereas the most widely present used reference genes, ACTIN (Actin 2, 18S rRNA (18S ribosomal RNA and GAPDH (Glyceraldehyde-3-phosphate dehydrogenase were not suitable in many experimental conditions. In addition, two commonly used programs, geNorm and Normfinder, were proved sufficient for the validation. This work provides the first systematic analysis for the selection of superior reference genes for accurate transcript normalization in papaya under different experimental

  7. A SVM-based quantitative fMRI method for resting-state functional network detection.

    Song, Xiaomu; Chen, Nan-kuei

    2014-09-01

    Resting-state functional magnetic resonance imaging (fMRI) aims to measure baseline neuronal connectivity independent of specific functional tasks and to capture changes in the connectivity due to neurological diseases. Most existing network detection methods rely on a fixed threshold to identify functionally connected voxels under the resting state. Due to fMRI non-stationarity, the threshold cannot adapt to variation of data characteristics across sessions and subjects, and generates unreliable mapping results. In this study, a new method is presented for resting-state fMRI data analysis. Specifically, the resting-state network mapping is formulated as an outlier detection process that is implemented using one-class support vector machine (SVM). The results are refined by using a spatial-feature domain prototype selection method and two-class SVM reclassification. The final decision on each voxel is made by comparing its probabilities of functionally connected and unconnected instead of a threshold. Multiple features for resting-state analysis were extracted and examined using an SVM-based feature selection method, and the most representative features were identified. The proposed method was evaluated using synthetic and experimental fMRI data. A comparison study was also performed with independent component analysis (ICA) and correlation analysis. The experimental results show that the proposed method can provide comparable or better network detection performance than ICA and correlation analysis. The method is potentially applicable to various resting-state quantitative fMRI studies.

  8. MATEPRED-A-SVM-Based Prediction Method for Multidrug And Toxin Extrusion (MATE) Proteins.

    Tamanna; Ramana, Jayashree

    2015-10-01

    The growth and spread of drug resistance in bacteria have been well established in both mankind and beasts and thus is a serious public health concern. Due to the increasing problem of drug resistance, control of infectious diseases like diarrhea, pneumonia etc. is becoming more difficult. Hence, it is crucial to understand the underlying mechanism of drug resistance mechanism and devising novel solution to address this problem. Multidrug And Toxin Extrusion (MATE) proteins, first characterized as bacterial drug transporters, are present in almost all species. It plays a very important function in the secretion of cationic drugs across the cell membrane. In this work, we propose SVM based method for prediction of MATE proteins. The data set employed for training consists of 189 non-redundant protein sequences, that are further classified as positive (63 sequences) set comprising of sequences from MATE family, and negative (126 sequences) set having protein sequences from other transporters families proteins and random protein sequences taken from NCBI while in the test set, there are 120 protein sequences in all (8 in positive and 112 in negative set). The model was derived using Position Specific Scoring Matrix (PSSM) composition and achieved an overall accuracy 92.06%. The five-fold cross validation was used to optimize SVM parameter and select the best model. The prediction algorithm presented here is implemented as a freely available web server MATEPred, which will assist in rapid identification of MATE proteins.

  9. PSO-SVM-Based Online Locomotion Mode Identification for Rehabilitation Robotic Exoskeletons

    Yi Long

    2016-09-01

    Full Text Available Locomotion mode identification is essential for the control of a robotic rehabilitation exoskeletons. This paper proposes an online support vector machine (SVM optimized by particle swarm optimization (PSO to identify different locomotion modes to realize a smooth and automatic locomotion transition. A PSO algorithm is used to obtain the optimal parameters of SVM for a better overall performance. Signals measured by the foot pressure sensors integrated in the insoles of wearable shoes and the MEMS-based attitude and heading reference systems (AHRS attached on the shoes and shanks of leg segments are fused together as the input information of SVM. Based on the chosen window whose size is 200 ms (with sampling frequency of 40 Hz, a three-layer wavelet packet analysis (WPA is used for feature extraction, after which, the kernel principal component analysis (kPCA is utilized to reduce the dimension of the feature set to reduce computation cost of the SVM. Since the signals are from two types of different sensors, the normalization is conducted to scale the input into the interval of [0, 1]. Five-fold cross validation is adapted to train the classifier, which prevents the classifier over-fitting. Based on the SVM model obtained offline in MATLAB, an online SVM algorithm is constructed for locomotion mode identification. Experiments are performed for different locomotion modes and experimental results show the effectiveness of the proposed algorithm with an accuracy of 96.00% ± 2.45%. To improve its accuracy, majority vote algorithm (MVA is used for post-processing, with which the identification accuracy is better than 98.35% ± 1.65%. The proposed algorithm can be extended and employed in the field of robotic rehabilitation and assistance.

  10. PSO-SVM-Based Online Locomotion Mode Identification for Rehabilitation Robotic Exoskeletons

    Long, Yi; Du, Zhi-Jiang; Wang, Wei-Dong; Zhao, Guang-Yu; Xu, Guo-Qiang; He, Long; Mao, Xi-Wang; Dong, Wei

    2016-01-01

    Locomotion mode identification is essential for the control of a robotic rehabilitation exoskeletons. This paper proposes an online support vector machine (SVM) optimized by particle swarm optimization (PSO) to identify different locomotion modes to realize a smooth and automatic locomotion transition. A PSO algorithm is used to obtain the optimal parameters of SVM for a better overall performance. Signals measured by the foot pressure sensors integrated in the insoles of wearable shoes and the MEMS-based attitude and heading reference systems (AHRS) attached on the shoes and shanks of leg segments are fused together as the input information of SVM. Based on the chosen window whose size is 200 ms (with sampling frequency of 40 Hz), a three-layer wavelet packet analysis (WPA) is used for feature extraction, after which, the kernel principal component analysis (kPCA) is utilized to reduce the dimension of the feature set to reduce computation cost of the SVM. Since the signals are from two types of different sensors, the normalization is conducted to scale the input into the interval of [0, 1]. Five-fold cross validation is adapted to train the classifier, which prevents the classifier over-fitting. Based on the SVM model obtained offline in MATLAB, an online SVM algorithm is constructed for locomotion mode identification. Experiments are performed for different locomotion modes and experimental results show the effectiveness of the proposed algorithm with an accuracy of 96.00% ± 2.45%. To improve its accuracy, majority vote algorithm (MVA) is used for post-processing, with which the identification accuracy is better than 98.35% ± 1.65%. The proposed algorithm can be extended and employed in the field of robotic rehabilitation and assistance. PMID:27598160

  11. PSO-SVM-Based Online Locomotion Mode Identification for Rehabilitation Robotic Exoskeletons.

    Long, Yi; Du, Zhi-Jiang; Wang, Wei-Dong; Zhao, Guang-Yu; Xu, Guo-Qiang; He, Long; Mao, Xi-Wang; Dong, Wei

    2016-09-02

    Locomotion mode identification is essential for the control of a robotic rehabilitation exoskeletons. This paper proposes an online support vector machine (SVM) optimized by particle swarm optimization (PSO) to identify different locomotion modes to realize a smooth and automatic locomotion transition. A PSO algorithm is used to obtain the optimal parameters of SVM for a better overall performance. Signals measured by the foot pressure sensors integrated in the insoles of wearable shoes and the MEMS-based attitude and heading reference systems (AHRS) attached on the shoes and shanks of leg segments are fused together as the input information of SVM. Based on the chosen window whose size is 200 ms (with sampling frequency of 40 Hz), a three-layer wavelet packet analysis (WPA) is used for feature extraction, after which, the kernel principal component analysis (kPCA) is utilized to reduce the dimension of the feature set to reduce computation cost of the SVM. Since the signals are from two types of different sensors, the normalization is conducted to scale the input into the interval of [0, 1]. Five-fold cross validation is adapted to train the classifier, which prevents the classifier over-fitting. Based on the SVM model obtained offline in MATLAB, an online SVM algorithm is constructed for locomotion mode identification. Experiments are performed for different locomotion modes and experimental results show the effectiveness of the proposed algorithm with an accuracy of 96.00% ± 2.45%. To improve its accuracy, majority vote algorithm (MVA) is used for post-processing, with which the identification accuracy is better than 98.35% ± 1.65%. The proposed algorithm can be extended and employed in the field of robotic rehabilitation and assistance.

  12. mGene.web: a web service for accurate computational gene finding.

    Schweikert, Gabriele; Behr, Jonas; Zien, Alexander; Zeller, Georg; Ong, Cheng Soon; Sonnenburg, Sören; Rätsch, Gunnar

    2009-07-01

    We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to train the system with their own data for other organisms on the push of a button, a functionality that will greatly accelerate the annotation of newly sequenced genomes. The system is built in a highly modular way, such that individual components of the framework, like the promoter prediction tool or the splice site predictor, can be used autonomously. The underlying gene finding system mGene is based on discriminative machine learning techniques and its high accuracy has been demonstrated in an international competition on nematode genomes. mGene.web is available at http://www.mgene.org/web, it is free of charge and can be used for eukaryotic genomes of small to moderate size (several hundred Mbp).

  13. An SVM-Based Classifier for Estimating the State of Various Rotating Components in Agro-Industrial Machinery with a Vibration Signal Acquired from a Single Point on the Machine Chassis

    Ruben Ruiz-Gonzalez

    2014-11-01

    Full Text Available The goal of this article is to assess the feasibility of estimating the state of various rotating components in agro-industrial machinery by employing just one vibration signal acquired from a single point on the machine chassis. To do so, a Support Vector Machine (SVM-based system is employed. Experimental tests evaluated this system by acquiring vibration data from a single point of an agricultural harvester, while varying several of its working conditions. The whole process included two major steps. Initially, the vibration data were preprocessed through twelve feature extraction algorithms, after which the Exhaustive Search method selected the most suitable features. Secondly, the SVM-based system accuracy was evaluated by using Leave-One-Out cross-validation, with the selected features as the input data. The results of this study provide evidence that (i accurate estimation of the status of various rotating components in agro-industrial machinery is possible by processing the vibration signal acquired from a single point on the machine structure; (ii the vibration signal can be acquired with a uniaxial accelerometer, the orientation of which does not significantly affect the classification accuracy; and, (iii when using an SVM classifier, an 85% mean cross-validation accuracy can be reached, which only requires a maximum of seven features as its input, and no significant improvements are noted between the use of either nonlinear or linear kernels.

  14. Modeling the milling tool wear by using an evolutionary SVM-based model from milling runs experimental data

    Nieto, Paulino José García; García-Gonzalo, Esperanza; Vilán, José Antonio Vilán; Robleda, Abraham Segade

    2015-12-01

    The main aim of this research work is to build a new practical hybrid regression model to predict the milling tool wear in a regular cut as well as entry cut and exit cut of a milling tool. The model was based on Particle Swarm Optimization (PSO) in combination with support vector machines (SVMs). This optimization mechanism involved kernel parameter setting in the SVM training procedure, which significantly influences the regression accuracy. Bearing this in mind, a PSO-SVM-based model, which is based on the statistical learning theory, was successfully used here to predict the milling tool flank wear (output variable) as a function of the following input variables: the time duration of experiment, depth of cut, feed, type of material, etc. To accomplish the objective of this study, the experimental dataset represents experiments from runs on a milling machine under various operating conditions. In this way, data sampled by three different types of sensors (acoustic emission sensor, vibration sensor and current sensor) were acquired at several positions. A second aim is to determine the factors with the greatest bearing on the milling tool flank wear with a view to proposing milling machine's improvements. Firstly, this hybrid PSO-SVM-based regression model captures the main perception of statistical learning theory in order to obtain a good prediction of the dependence among the flank wear (output variable) and input variables (time, depth of cut, feed, etc.). Indeed, regression with optimal hyperparameters was performed and a determination coefficient of 0.95 was obtained. The agreement of this model with experimental data confirmed its good performance. Secondly, the main advantages of this PSO-SVM-based model are its capacity to produce a simple, easy-to-interpret model, its ability to estimate the contributions of the input variables, and its computational efficiency. Finally, the main conclusions of this study are exposed.

  15. Gene expression accurately distinguishes liver metastases of small bowel and pancreas neuroendocrine tumors.

    Sherman, Scott K; Maxwell, Jessica E; Carr, Jennifer C; Wang, Donghong; Bellizzi, Andrew M; Sue O'Dorisio, M; O'Dorisio, Thomas M; Howe, James R

    2014-12-01

    Small bowel (SBNETs) and pancreatic neuroendocrine tumors (PNETs) often present with liver metastases. Although liver biopsy establishes a neuroendocrine diagnosis, the primary tumor site is frequently unknown without exploratory surgery. Gene expression differences in metastases may distinguish primary SBNETs and PNETs. This study sought to determine expression differences of four genes in neuroendocrine metastases and to create a gene expression algorithm to distinguish the primary site. Nodal and liver metastases from SBNETs and PNETs (n = 136) were collected at surgery under an Institutional Review Board-approved protocol. Quantitative PCR measured expression of bombesin-like receptor-3, opioid receptor kappa-1, oxytocin receptor, and secretin receptor in metastases. Logistic regression models defined an algorithm predicting the primary tumor site. Models were developed on a training set of 21 nodal metastases and performance was validated on an independent set of nodal and liver metastases. Expression of all four genes was significantly different in SBNET compared to PNET metastases. The optimal model employed expression of bombesin-like receptor-3 and opioid receptor kappa-1. When these genes did not amplify, the algorithm used oxytocin receptor and secretin receptor expression, which allowed classification of all 136 metastases with 94.1 % accuracy. In the independent liver metastasis validation set, 52/56 (92.9 %) were correctly classified. Positive predictive values were 92.5 % for SBNETs and 93.8 % for PNETs. This validated algorithm accurately distinguishes SBNET and PNET metastases based on their expression of four genes. High accuracy in liver metastases demonstrates applicability to the clinical setting. Studies assessing this algorithm's utility in prospective clinical decision-making are warranted.

  16. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K.; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G.; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H.

    2017-01-01

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. PMID:27899623

  17. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics

    Ronen, Michal; Rosenberg, Revital; Shraiman, Boris I.; Alon, Uri

    2002-08-01

    A basic challenge in systems biology is to understand the dynamical behavior of gene regulation networks. Current approaches aim at determining the network structure based on genomic-scale data. However, the network connectivity alone is not sufficient to define its dynamics; one needs to also specify the kinetic parameters for the regulation reactions. Here, we ask whether effective kinetic parameters can be assigned to a transcriptional network based on expression data. We present a combined experimental and theoretical approach based on accurate high temporal-resolution measurement of promoter activities from living cells by using green fluorescent protein (GFP) reporter plasmids. We present algorithms that use these data to assign effective kinetic parameters within a mathematical model of the network. To demonstrate this, we employ a well defined network, the SOS DNA repair system of Escherichia coli. We find a strikingly detailed temporal program of expression that correlates with the functional role of the SOS genes and is driven by a hierarchy of effective kinetic parameter strengths for the various promoters. The calculated parameters can be used to determine the kinetics of all SOS genes given the expression profile of just one representative, allowing a significant reduction in complexity. The concentration profile of the master SOS transcriptional repressor can be calculated, demonstrating that relative protein levels may be determined from purely transcriptional data. This finding opens the possibility of assigning kinetic parameters to transcriptional networks on a genomic scale.

  18. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H

    2017-01-09

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively.

  19. In-Vivo Imaging of Cell Migration Using Contrast Enhanced MRI and SVM Based Post-Processing.

    Christian Weis

    Full Text Available The migration of cells within a living organism can be observed with magnetic resonance imaging (MRI in combination with iron oxide nanoparticles as an intracellular contrast agent. This method, however, suffers from low sensitivity and specificty. Here, we developed a quantitative non-invasive in-vivo cell localization method using contrast enhanced multiparametric MRI and support vector machines (SVM based post-processing. Imaging phantoms consisting of agarose with compartments containing different concentrations of cancer cells labeled with iron oxide nanoparticles were used to train and evaluate the SVM for cell localization. From the magnitude and phase data acquired with a series of T2*-weighted gradient-echo scans at different echo-times, we extracted features that are characteristic for the presence of superparamagnetic nanoparticles, in particular hyper- and hypointensities, relaxation rates, short-range phase perturbations, and perturbation dynamics. High detection quality was achieved by SVM analysis of the multiparametric feature-space. The in-vivo applicability was validated in animal studies. The SVM detected the presence of iron oxide nanoparticles in the imaging phantoms with high specificity and sensitivity with a detection limit of 30 labeled cells per mm3, corresponding to 19 μM of iron oxide. As proof-of-concept, we applied the method to follow the migration of labeled cancer cells injected in rats. The combination of iron oxide labeled cells, multiparametric MRI and a SVM based post processing provides high spatial resolution, specificity, and sensitivity, and is therefore suitable for non-invasive in-vivo cell detection and cell migration studies over prolonged time periods.

  20. In-Vivo Imaging of Cell Migration Using Contrast Enhanced MRI and SVM Based Post-Processing.

    Weis, Christian; Hess, Andreas; Budinsky, Lubos; Fabry, Ben

    2015-01-01

    The migration of cells within a living organism can be observed with magnetic resonance imaging (MRI) in combination with iron oxide nanoparticles as an intracellular contrast agent. This method, however, suffers from low sensitivity and specificty. Here, we developed a quantitative non-invasive in-vivo cell localization method using contrast enhanced multiparametric MRI and support vector machines (SVM) based post-processing. Imaging phantoms consisting of agarose with compartments containing different concentrations of cancer cells labeled with iron oxide nanoparticles were used to train and evaluate the SVM for cell localization. From the magnitude and phase data acquired with a series of T2*-weighted gradient-echo scans at different echo-times, we extracted features that are characteristic for the presence of superparamagnetic nanoparticles, in particular hyper- and hypointensities, relaxation rates, short-range phase perturbations, and perturbation dynamics. High detection quality was achieved by SVM analysis of the multiparametric feature-space. The in-vivo applicability was validated in animal studies. The SVM detected the presence of iron oxide nanoparticles in the imaging phantoms with high specificity and sensitivity with a detection limit of 30 labeled cells per mm3, corresponding to 19 μM of iron oxide. As proof-of-concept, we applied the method to follow the migration of labeled cancer cells injected in rats. The combination of iron oxide labeled cells, multiparametric MRI and a SVM based post processing provides high spatial resolution, specificity, and sensitivity, and is therefore suitable for non-invasive in-vivo cell detection and cell migration studies over prolonged time periods.

  1. A Multi-Classification Method of Improved SVM-based Information Fusion for Traffic Parameters Forecasting

    Hongzhuan Zhao

    2016-04-01

    Full Text Available With the enrichment of perception methods, modern transportation system has many physical objects whose states are influenced by many information factors so that it is a typical Cyber-Physical System (CPS. Thus, the traffic information is generally multi-sourced, heterogeneous and hierarchical. Existing research results show that the multisourced traffic information through accurate classification in the process of information fusion can achieve better parameters forecasting performance. For solving the problem of traffic information accurate classification, via analysing the characteristics of the multi-sourced traffic information and using redefined binary tree to overcome the shortcomings of the original Support Vector Machine (SVM classification in information fusion, a multi-classification method using improved SVM in information fusion for traffic parameters forecasting is proposed. The experiment was conducted to examine the performance of the proposed scheme, and the results reveal that the method can get more accurate and practical outcomes.

  2. A machine learned classifier that uses gene expression data to accurately predict estrogen receptor status.

    Meysam Bastani

    Full Text Available BACKGROUND: Selecting the appropriate treatment for breast cancer requires accurately determining the estrogen receptor (ER status of the tumor. However, the standard for determining this status, immunohistochemical analysis of formalin-fixed paraffin embedded samples, suffers from numerous technical and reproducibility issues. Assessment of ER-status based on RNA expression can provide more objective, quantitative and reproducible test results. METHODS: To learn a parsimonious RNA-based classifier of hormone receptor status, we applied a machine learning tool to a training dataset of gene expression microarray data obtained from 176 frozen breast tumors, whose ER-status was determined by applying ASCO-CAP guidelines to standardized immunohistochemical testing of formalin fixed tumor. RESULTS: This produced a three-gene classifier that can predict the ER-status of a novel tumor, with a cross-validation accuracy of 93.17±2.44%. When applied to an independent validation set and to four other public databases, some on different platforms, this classifier obtained over 90% accuracy in each. In addition, we found that this prediction rule separated the patients' recurrence-free survival curves with a hazard ratio lower than the one based on the IHC analysis of ER-status. CONCLUSIONS: Our efficient and parsimonious classifier lends itself to high throughput, highly accurate and low-cost RNA-based assessments of ER-status, suitable for routine high-throughput clinical use. This analytic method provides a proof-of-principle that may be applicable to developing effective RNA-based tests for other biomarkers and conditions.

  3. A Statistical Parameter Analysis and SVM Based Fault Diagnosis Strategy for Dynamically Tuned Gyroscopes

    2007-01-01

    Gyro's fault diagnosis plays a critical role in inertia navigation systems for higher reliability and precision. A new fault diagnosis strategy based on the statistical parameter analysis (SPA) and support vector machine(SVM) classification model was proposed for dynamically tuned gyroscopes (DTG). The SPA, a kind of time domain analysis approach, was introduced to compute a set of statistical parameters of vibration signal as the state features of DTG, with which the SVM model, a novel learning machine based on statistical learning theory (SLT), was applied and constructed to train and identify the working state of DTG. The experimental results verify that the proposed diagnostic strategy can simply and effectively extract the state features of DTG, and it outperforms the radial-basis function (RBF) neural network based diagnostic method and can more reliably and accurately diagnose the working state of DTG.

  4. SVM-based method for protein structural class prediction using secondary structural content and structural information of amino acids.

    Mohammad, Tabrez Anwar Shamim; Nagarajaram, Hampapathalu Adimurthy

    2011-08-01

    The knowledge collated from the known protein structures has revealed that the proteins are usually folded into the four structural classes: all-α, all-β, α/β and α + β. A number of methods have been proposed to predict the protein's structural class from its primary structure; however, it has been observed that these methods fail or perform poorly in the cases of distantly related sequences. In this paper, we propose a new method for protein structural class prediction using low homology (twilight-zone) protein sequences dataset. Since protein structural class prediction is a typical classification problem, we have developed a Support Vector Machine (SVM)-based method for protein structural class prediction that uses features derived from the predicted secondary structure and predicted burial information of amino acid residues. The examination of different individual as well as feature combinations revealed that the combination of secondary structural content, secondary structural and solvent accessibility state frequencies of amino acids gave rise to the best leave-one-out cross-validation accuracy of ~81% which is comparable to the best accuracy reported in the literature so far.

  5. LS-SVM Based AGC of an Asynchronous Power System with Dynamic Participation from DFIG Based Wind Turbines

    Gulshan Sharma

    2014-08-01

    Full Text Available Modern power systems are large and interconnected with growing trends to integrate wind energy to the power system and meet the ever rising energy demand in an economical manner. The penetration of wind energy has motivated power engineers and researchers to investigate the dynamic participation of Doubly Fed Induction Generators (DFIG based wind turbines in Automatic Generation Control (AGC services. However, with dynamic participation of DFIG, the AGC problem becomes more complex and under these conditions classical AGC are not suitable. Therefore, a new non-linear Least Squares Support Vector Machines (LS-SVM based regulator for solution of AGC problem is proposed in this study. The proposed AGC regulator is trained for a wide range of operating conditions and load changes using an off-line data set generated from the robust control technique. A two-area power system connected via parallel AC/DC tie-lines with DFIG based wind turbines in each area is considered to demonstrate the effectiveness of the proposed AGC regulator and compared with results obtained using Multi-Layer Perceptron (MLP neural networks and conventional PI regulators under various operating conditions and load changes.

  6. FaaPred: a SVM-based prediction method for fungal adhesins and adhesin-like proteins.

    Jayashree Ramana

    Full Text Available Adhesion constitutes one of the initial stages of infection in microbial diseases and is mediated by adhesins. Hence, identification and comprehensive knowledge of adhesins and adhesin-like proteins is essential to understand adhesin mediated pathogenesis and how to exploit its therapeutic potential. However, the knowledge about fungal adhesins is rudimentary compared to that of bacterial adhesins. In addition to host cell attachment and mating, the fungal adhesins play a significant role in homotypic and xenotypic aggregation, foraging and biofilm formation. Experimental identification of fungal adhesins is labor- as well as time-intensive. In this work, we present a Support Vector Machine (SVM based method for the prediction of fungal adhesins and adhesin-like proteins. The SVM models were trained with different compositional features, namely, amino acid, dipeptide, multiplet fractions, charge and hydrophobic compositions, as well as PSI-BLAST derived PSSM matrices. The best classifiers are based on compositional properties as well as PSSM and yield an overall accuracy of 86%. The prediction method based on best classifiers is freely accessible as a world wide web based server at http://bioinfo.icgeb.res.in/faap. This work will aid rapid and rational identification of fungal adhesins, expedite the pace of experimental characterization of novel fungal adhesins and enhance our knowledge about role of adhesins in fungal infections.

  7. AREA DETERMINATION OF DIABETIC FOOT ULCER IMAGES USING A CASCADED TWO-STAGE SVM BASED CLASSIFICATION.

    Wang, Lei; Pedersen, Peder; Agu, Emmanuel; Strong, Diane; Tulu, Bengisu

    2016-11-23

    It is standard practice for clinicians and nurses to primarily assess patients' wounds via visual examination. This subjective method can be inaccurate in wound assessment and also represents a significant clinical workload. Hence, computer-based systems, especially implemented on mobile devices, can provide automatic, quantitative wound assessment and can thus be valuable for accurately monitoring wound healing status. Out of all wound assessment parameters, the measurement of the wound area is the most suitable for automated analysis. Most of the current wound boundary determination methods only process the image of the wound area along with a small amount of surrounding healthy skin. In this paper, we present a novel approach that uses Support Vector Machine (SVM) to determine the wound boundary on a foot ulcer image captured with an image capture box, which provides controlled lighting, angle and range conditions. The Simple Linear Iterative Clustering (SLIC) method is applied for effective super-pixel segmentation. A cascaded two-stage classifier is trained as follows: in the first stage a set of k binary SVM classifiers are trained and applied to different subsets of the entire training images dataset, and a set of incorrectly classified instances are collected. In the second stage, another binary SVM classifier is trained on the incorrectly classified set. We extracted various color and texture descriptors from super-pixels that are used as input for each stage in the classifier training. Specifically, we apply the color and Bag-of-Word (BoW) representation of local Dense SIFT features (DSIFT) as the descriptor for ruling out irrelevant regions (first stage), and apply color and wavelet based features as descriptors for distinguishing healthy tissue from wound regions (second stage). Finally, the detected wound boundary is refined by applying a Conditional Random Field (CRF) image processing technique. We have implemented the wound classification on a Nexus

  8. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Jiang-Ke Yang

    Full Text Available In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp and Aspergillus niger phytase gene phyA (1404 bp. Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  9. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Yang, Jiang-Ke; Chen, Fang-Yuan; Yan, Xiang-Xiang; Miao, Li-Hong; Dai, Jiang-Hong

    2012-01-01

    In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE) was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp) and Aspergillus niger phytase gene phyA (1404 bp). Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  10. Gene expression accurately distinguishes liver metastases of small bowel and pancreas neuroendocrine tumors

    Sherman, Scott K.; Maxwell, Jessica E.; Carr, Jennifer C.; Wang, Donghong; Bellizzi, Andrew M.; O’Dorisio, M. Sue; O’Dorisio, Thomas M.; Howe, James R.

    2014-01-01

    Small bowel (SBNETs) and pancreatic neuroendocrine tumors (PNETs) often present with liver metastases. Although liver biopsy establishes a neuroendocrine diagnosis, the primary tumor site is frequently unknown without exploratory surgery. Gene expression differences in metastases may distinguish primary SBNETs and PNETs. This study sought to determine expression differences of four genes in neuroendocrine metastases and to create a gene expression algorithm to distinguish the primary site. No...

  11. Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells

    Lim Qing-En

    2010-01-01

    Full Text Available Abstract Background Gene regulation at transcript level can provide a good indication of the complex signaling mechanisms underlying physiological and pathological processes. Transcriptomic methods such as microarray and quantitative real-time PCR require stable reference genes for accurate normalization of gene expression. Some but not all studies have shown that housekeeping genes (HGKs, β-actin (ACTB and glyceraldehyde-3-phosphate dehydrogenase (GAPDH, which are routinely used for normalization, may vary significantly depending on the cell/tissue type and experimental conditions. It is currently unclear if these genes are stably expressed in cells undergoing drastic morphological changes during neuronal differentiation. Recent meta-analysis of microarray datasets showed that some but not all of the ribosomal protein genes are stably expressed. To test the hypothesis that some ribosomal protein genes can serve as reference genes for neuronal differentiation, a genome-wide analysis was performed and putative reference genes were identified based on stability of expressions. The stabilities of these potential reference genes were then analyzed by reverse transcription quantitative real-time PCR in six differentiation conditions. Results Twenty stably expressed genes, including thirteen ribosomal protein genes, were selected from microarray analysis of the gene expression profiles of GDNF and NGF induced differentiation of PC12 cells. The expression levels of these candidate genes as well as ACTB and GAPDH were further analyzed by reverse transcription quantitative real-time PCR in PC12 cells differentiated with a variety of stimuli including NGF, GDNF, Forskolin, KCl and ROCK inhibitor, Y27632. The performances of these candidate genes as stable reference genes were evaluated with two independent statistical approaches, geNorm and NormFinder. Conclusions The ribosomal protein genes, RPL19 and RPL29, were identified as suitable reference genes

  12. An endometrial gene expression signature accurately predicts recurrent implantation failure after IVF

    Koot, Yvonne E. M.; van Hooff, Sander R.; Boomsma, Carolien M.; van Leenen, Dik; Groot Koerkamp, Marian J. A.; Goddijn, Mariëtte; Eijkemans, Marinus J. C.; Fauser, Bart C. J. M.; Holstege, Frank C. P.; Macklon, Nick S.

    2016-01-01

    The primary limiting factor for effective IVF treatment is successful embryo implantation. Recurrent implantation failure (RIF) is a condition whereby couples fail to achieve pregnancy despite consecutive embryo transfers. Here we describe the collection of gene expression profiles from mid-luteal phase endometrial biopsies (n = 115) from women experiencing RIF and healthy controls. Using a signature discovery set (n = 81) we identify a signature containing 303 genes predictive of RIF. Independent validation in 34 samples shows that the gene signature predicts RIF with 100% positive predictive value (PPV). The strength of the RIF associated expression signature also stratifies RIF patients into distinct groups with different subsequent implantation success rates. Exploration of the expression changes suggests that RIF is primarily associated with reduced cellular proliferation. The gene signature will be of value in counselling and guiding further treatment of women who fail to conceive upon IVF and suggests new avenues for developing intervention. PMID:26797113

  13. Suitable reference genes for accurate gene expression analysis in parsley (Petroselinum crispum for abiotic stresses and hormone stimuli

    Meng-Yao Li

    2016-09-01

    Full Text Available Parsley is one of the most important vegetable in Apiaceae family and widely used in food industry, medicinal and cosmetic. The recent studies in parsley are mainly focus on chemical composition, further research involving the analysis of the gene functions and expressions will be required. qPCR is a powerful method for detecting very low quantities of target transcript levels and widely used for gene expression studies. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, three software geNorm, NormFinder, and BestKeeper were used to evaluate the expression stabilities of eight candidate reference genes (GAPDH, ACTIN, eIF-4α, SAND, UBC, TIP41, EF-1α, and TUB under various conditions including abiotic stresses (heat, cold, salt, and drought and hormone stimuli treatments (GA, SA, MeJA, and ABA. The results showed that EF-1α and TUB were identified as the most stable genes for abiotic stresses, while EF-1α, GAPDH, and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1α and TUB were the most stable reference genes across all the tested samples, while UBC was the least stable one. The expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study provides a guideline for selection the suitable reference genes in gene expression in parsley.

  14. Accurate assessment of intragenic recombination frequency within the Duchenne muscular dystrophy gene.

    Abbs, S; Roberts, R G; Mathew, C G; Bentley, D R; Bobrow, M

    1990-08-01

    Polymorphic loci that lie at the two extremities of the Duchenne/Becker muscular dystrophy (DMD/BMD) gene have been used to estimate intragenic recombination rates. Multipoint linkage analysis of the CEPH panel of families suggests a total intragenic recombination frequency of nearly 0.12 (confidence intervals 0.041-0.226) over the genomic length of approximately 2 Mb.

  15. Comprehensive and accurate mutation scanning of the CFTR gene by two-dimensional DNA electrophoresis

    Wu, Y; Hofstra, RMW; Scheffer, H; Uitterlinden, AG; Mullaart, E; Buys, CHCM; Vijg, J

    1996-01-01

    The large number of possible disease causing mutations in the 27 exons of the cystic fibrosis transmembrane conductance regulator (CFTR) gene has severely limited direct diagnosis of cystic fibrosis (CF) patients and carriers by mutation detection. Here we show that in principle testing for mutation

  16. 基于信息熵的SVM入侵检测技术%Exploring SVM-based intrusion detection through information entropy theory

    朱文杰; 王强; 翟献军

    2013-01-01

    在传统基于SVM的入侵检测中,核函数构造和特征选择采用先验知识,普遍存在准确度不高、效率低下的问题.通过信息熵理论与SVM算法相结合的方法改进为基于信息熵的SVM入侵检测算法,可以提高入侵检测的准确性,提升入侵检测的效率.基于信息熵的SVM入侵检测算法包括两个方面:一方面,根据样本包含的用户信息熵和方差,将样本特征统一,以特征是否属于置信区间来度量.将得到的样本特征置信向量作为SVM核函数的构造参数,既可保证训练样本集与最优分类面之间的对应关系,又可得到入侵检测需要的最大分类间隔;另一方面,将样本包含的用户信息量作为度量大幅度约简样本特征子集,不但降低了样本计算规模,而且提高了分类器的训练速度.实验表明,该算法在入侵检测系统中的应用优于传统的SVM算法.%In traditional SVM based intrusion detection approaches,both core function construction and feature selection use prior knowdege.Due to this,they are not only inefficient but also inaccurate.It is observed that integrating information entropy theory into SVM-based intrusion detection can enhance both the precision and the speed.Concludely speaking,SVM-based entropy intrusion detection algorithms are made up of two aspects:on one hand,setting sample confidence vector as core function's constructor of SVM algorithm can guarantee the mapping relationship between training sample and optimization classification plane.Also,the intrusion detection's maximum interval can be acquired.On the other hand,simplifying feature subset with samples's entropy as metric standard can not only shrink the computing scale but also improve the speed.Experiments prove that the SVM based entropy intrusion detection algoritm outperfomrs other tradional algorithms.

  17. 基于支持向量机无限集成学习方法的遥感图像分类%Remotely sensed imagery classification by SVM-based Infinite Ensemble Learning method

    杨娜; 秦志远; 张俊

    2013-01-01

    基于支持向量机的无限集成学习方法(SVM-based IEL)是机器学习领域新兴起的一种集成学习方法.本文将SVM-based IEL引入遥感图像的分类领域,并同时将SVM、Bagging、AdaBoost和SVM-based IEL等方法应用于遥感图像分类.实验表明:Bagging方法可以提高遥感图像的分类精度,而AdaBoost却降低了遥感图像的分类精度;同时,与SVM、有限集成的学习方法相比,SVM-based IEL方法具有可以显著地提高遥感图像的分类精度、分类效率的优势.%Support-vector-machines-based Infinite Ensemble Learning method ( SVM-based IEL) is one of the ensemble learning methods in the field of machine learning. In this paper, the SVM-based IEL was applied to the classification of remotely sensed imagery besides classic ensemble learning methods such as Bagging, AdaBoost and SVM etc. SVM was taken as the base classifier in Bagging, AdaBoost The experiments showed that the classic ensemble learning methods have different performances compared to SVM. In detail , the Bagging was capable of enhancing the classification accuracy but the AdaBoost was decreasing the classification accuracy. Furthermore, the experiments suggested that compared to SVM and classic ensemble learning methods, SVM-based IEL has many merits such as increasing both of the classification accuracy and classification efficiency.

  18. Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees.

    Groussin, Mathieu; Hobbs, Joanne K; Szöllősi, Gergely J; Gribaldo, Simonetta; Arcus, Vickery L; Gouy, Manolo

    2015-01-01

    The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the species phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using species tree-aware gene trees on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify.

  19. Validation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in strawberry fruits using different cultivars and osmotic stresses.

    Galli, Vanessa; Borowski, Joyce Moura; Perin, Ellen Cristina; Messias, Rafael da Silva; Labonde, Julia; Pereira, Ivan dos Santos; Silva, Sérgio Delmar Dos Anjos; Rombaldi, Cesar Valmor

    2015-01-10

    The increasing demand of strawberry (Fragaria×ananassa Duch) fruits is associated mainly with their sensorial characteristics and the content of antioxidant compounds. Nevertheless, the strawberry production has been hampered due to its sensitivity to abiotic stresses. Therefore, to understand the molecular mechanisms highlighting stress response is of great importance to enable genetic engineering approaches aiming to improve strawberry tolerance. However, the study of expression of genes in strawberry requires the use of suitable reference genes. In the present study, seven traditional and novel candidate reference genes were evaluated for transcript normalization in fruits of ten strawberry cultivars and two abiotic stresses, using RefFinder, which integrates the four major currently available software programs: geNorm, NormFinder, BestKeeper and the comparative delta-Ct method. The results indicate that the expression stability is dependent on the experimental conditions. The candidate reference gene DBP (DNA binding protein) was considered the most suitable to normalize expression data in samples of strawberry cultivars and under drought stress condition, and the candidate reference gene HISTH4 (histone H4) was the most stable under osmotic stresses and salt stress. The traditional genes GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and 18S (18S ribosomal RNA) were considered the most unstable genes in all conditions. The expression of phenylalanine ammonia lyase (PAL) and 9-cis epoxycarotenoid dioxygenase (NCED1) genes were used to further confirm the validated candidate reference genes, showing that the use of an inappropriate reference gene may induce erroneous results. This study is the first survey on the stability of reference genes in strawberry cultivars and osmotic stresses and provides guidelines to obtain more accurate RT-qPCR results for future breeding efforts.

  20. ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes.

    Hua, Zhi-Gang; Lin, Yan; Yuan, Ya-Zhou; Yang, De-Chang; Wei, Wen; Guo, Feng-Biao

    2015-07-01

    In 2003, we developed an ab initio program, ZCURVE 1.0, to find genes in bacterial and archaeal genomes. In this work, we present the updated version (i.e. ZCURVE 3.0). Using 422 prokaryotic genomes, the average accuracy was 93.7% with the updated version, compared with 88.7% with the original version. Such results also demonstrate that ZCURVE 3.0 is comparable with Glimmer 3.02 and may provide complementary predictions to it. In fact, the joint application of the two programs generated better results by correctly finding more annotated genes while also containing fewer false-positive predictions. As the exclusive function, ZCURVE 3.0 contains one post-processing program that can identify essential genes with high accuracy (generally >90%). We hope ZCURVE 3.0 will receive wide use with the web-based running mode. The updated ZCURVE can be freely accessed from http://cefg.uestc.edu.cn/zcurve/ or http://tubic.tju.edu.cn/zcurveb/ without any restrictions.

  1. Staphylococcus aureus interaction with phospholipid vesicles--a new method to accurately determine accessory gene regulator (agr activity.

    Maisem Laabei

    Full Text Available The staphylococcal accessory gene regulatory (agr operon is a well-characterised global regulatory element that is important in the control of virulence gene expression for Staphylococcus aureus, a major human pathogen. Hence, accurate and sensitive measurement of Agr activity is central in understanding the virulence potential of Staphylococcus aureus, especially in the context of Agr dysfunction, which has been linked with persistent bacteraemia and reduced susceptibility to glycopeptide antibiotics. Agr function is typically measured using a synergistic haemolysis CAMP assay, which is believe to report on the level of expression of one of the translated products of the agr locus, delta toxin. In this study we develop a vesicle lysis test (VLT that is specific to small amphipathic peptides, most notably delta and Phenol Soluble Modulin (PSM toxins. To determine the accuracy of this VLT method in assaying Agr activity, we compared it to the CAMP assay using 89 clinical Staphylococcus aureus isolates. Of the 89 isolates, 16 were designated as having dysfunctional Agr systems by the CAMP assay, whereas only three were designated as such by VLT. Molecular analysis demonstrated that of these 16 isolates, the 13 designated as having a functional Agr system by VLT transcribed rnaIII and secreted delta toxin, demonstrating they have a functional Agr system despite the results of the CAMP assay. The agr locus of all 16 isolates was sequenced, and only the 3 designated as having a dysfunctional Agr system contained mutations, explaining their Agr dysfunction. Given the potentially important link between Agr dysfunction and clinical outcome, we have developed an assay that determines this more accurately than the conventional CAMP assay.

  2. A method to improve the stability and accuracy of ANN- and SVM-based time series models for long-term groundwater level predictions

    Yoon, Heesung; Hyun, Yunjung; Ha, Kyoochul; Lee, Kang-Kun; Kim, Gyoo-Bum

    2016-05-01

    The prediction of long-term groundwater level fluctuations is necessary to effectively manage groundwater resources and to assess the effects of changes in rainfall patterns on groundwater resources. In the present study, a weighted error function approach was utilised to improve the performance of artificial neural network (ANN)- and support vector machine (SVM)-based recursive prediction models for the long-term prediction of groundwater levels in response to rainfall. The developed time series models were applied to groundwater level data from 5 groundwater-monitoring stations in South Korea. The results demonstrated that the weighted error function approach can improve the stability and accuracy of recursive prediction models, especially for ANN models. The comparison of the model performance showed that the recursive prediction performance of the SVM was superior to the performance of the ANN in this case study.

  3. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

    Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

    2015-02-01

    The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp.

  4. VICMpred: An SVM-based Method for the Prediction of Functional Proteins of Gram-negative Bacteria Using Amino Acid Patterns and Composition

    Sudipto Saha; G.P.S. Raghava

    2006-01-01

    In this study, an attempt has been made to predict the major functions of gramnegative bacterial proteins from their amino acid sequences. The dataset used for training and testing consists of 670 non-redundant gram-negative bacterial proteins (255 ofcellular process, 60 of information molecules, 285 of metabolism, and 70 of virulence factors). First we developed an SVM-based method using amino acid and dipeptide composition and achieved the overall accuracy of 52.39% and 47.01%, respectively. We introduced a new concept for the classification of proteins based on tetrapeptides, in which we identified the unique tetrapeptides significantly found in a class of proteins. These tetrapeptides were used as the input feature for predicting the function of a protein and achieved the overall accuracy of 68.66%. We also developed a hybrid method in which the tetrapeptide information was used with amino acid composition and achieved the overall accuracy of 70.75%. A five-fold cross validation was used to evaluate the performance of these methods. The web server VICMpred has been developed for predicting the function of gram-negative bacterial proteins (http://www.imtech.res.in/raghava/vicmpred/).

  5. Microcalcification detection in full-field digital mammograms with PFCM clustering and weighted SVM-based method

    Liu, Xiaoming; Mei, Ming; Liu, Jun; Hu, Wei

    2015-12-01

    Clustered microcalcifications (MCs) in mammograms are an important early sign of breast cancer in women. Their accurate detection is important in computer-aided detection (CADe). In this paper, we integrated the possibilistic fuzzy c-means (PFCM) clustering algorithm and weighted support vector machine (WSVM) for the detection of MC clusters in full-field digital mammograms (FFDM). For each image, suspicious MC regions are extracted with region growing and active contour segmentation. Then geometry and texture features are extracted for each suspicious MC, a mutual information-based supervised criterion is used to select important features, and PFCM is applied to cluster the samples into two clusters. Weights of the samples are calculated based on possibilities and typicality values from the PFCM, and the ground truth labels. A weighted nonlinear SVM is trained. During the test process, when an unknown image is presented, suspicious regions are located with the segmentation step, selected features are extracted, and the suspicious MC regions are classified as containing MC or not by the trained weighted nonlinear SVM. Finally, the MC regions are analyzed with spatial information to locate MC clusters. The proposed method is evaluated using a database of 410 clinical mammograms and compared with a standard unweighted support vector machine (SVM) classifier. The detection performance is evaluated using response receiver operating (ROC) curves and free-response receiver operating characteristic (FROC) curves. The proposed method obtained an area under the ROC curve of 0.8676, while the standard SVM obtained an area of 0.8268 for MC detection. For MC cluster detection, the proposed method obtained a high sensitivity of 92 % with a false-positive rate of 2.3 clusters/image, and it is also better than standard SVM with 4.7 false-positive clusters/image at the same sensitivity.

  6. A multi-class SVM based on FCOWA-ER%一种基于FCOWA-ER的SVM多分类方法

    刘卫兵; 杨艺; 韩德强

    2015-01-01

    支持向量机(SVM)在处理多分类问题时,需要综合利用多个二分类SVM,以获得多分类判决结果。传统多分类拓展方法使用的是SVM的硬输出,在一定程度上造成了信息的丢失。为了更加充分地利用信息,提出一种基于证据推理-多属性决策方法的SVM多分类算法,将多分类问题视为一个多属性决策问题,使用证据推理-模糊谨慎有序加权平均方法(FCOWA-ER)实现SVM的多分类判决。实验结果表明,所提出方法可以获得更高的分类精度。%Multiple bi-class SVMs are used together to obtain the final decision when the support vector machine(SVM) is applied to multi-class classification problems. The conventional methods of applying the SVM to multiple classification tasks are all based on the hard output of SVM, which can bring the loss of information to some extent. Therefore, a multi-class SVM based on an evidential reasoning based multiple attribute decision approach is proposed to use more information. The multi-class classification problem is modelled as a multi-criteria decision making problem. Then a fuzzy-cautious OWA(ordered weighted averaging) approach with evidential reasoning(FCOWA-ER) is used to implement multi-class classification and obtain the final decision. The simulation results show that the method proposed has better accuracy compared with conventional methods.

  7. Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function.

    Raychaudhuri, Soumya; Korn, Joshua M; McCarroll, Steven A; Altshuler, David; Sklar, Pamela; Purcell, Shaun; Daly, Mark J

    2010-09-09

    Investigators have linked rare copy number variation (CNVs) to neuropsychiatric diseases, such as schizophrenia. One hypothesis is that CNV events cause disease by affecting genes with specific brain functions. Under these circumstances, we expect that CNV events in cases should impact brain-function genes more frequently than those events in controls. Previous publications have applied "pathway" analyses to genes within neuropsychiatric case CNVs to show enrichment for brain-functions. While such analyses have been suggestive, they often have not rigorously compared the rates of CNVs impacting genes with brain function in cases to controls, and therefore do not address important confounders such as the large size of brain genes and overall differences in rates and sizes of CNVs. To demonstrate the potential impact of confounders, we genotyped rare CNV events in 2,415 unaffected controls with Affymetrix 6.0; we then applied standard pathway analyses using four sets of brain-function genes and observed an apparently highly significant enrichment for each set. The enrichment is simply driven by the large size of brain-function genes. Instead, we propose a case-control statistical test, cnv-enrichment-test, to compare the rate of CNVs impacting specific gene sets in cases versus controls. With simulations, we demonstrate that cnv-enrichment-test is robust to case-control differences in CNV size, CNV rate, and systematic differences in gene size. Finally, we apply cnv-enrichment-test to rare CNV events published by the International Schizophrenia Consortium (ISC). This approach reveals nominal evidence of case-association in neuronal-activity and the learning gene sets, but not the other two examined gene sets. The neuronal-activity genes have been associated in a separate set of schizophrenia cases and controls; however, testing in independent samples is necessary to definitively confirm this association. Our method is implemented in the PLINK software package.

  8. A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

    Zhang, Yuan; Sun, Yanni; Cole, James R

    2014-08-01

    Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.

  9. A scalable and accurate targeted gene assembly tool (SAT-Assembler for next-generation sequencing data.

    Yuan Zhang

    2014-08-01

    Full Text Available Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.

  10. Identification of a 251 gene expression signature that can accurately detect M. tuberculosis in patients with and without HIV co-infection.

    Noor Dawany

    Full Text Available BACKGROUND: Co-infection with tuberculosis (TB is the leading cause of death in HIV-infected individuals. However, diagnosis of TB, especially in the presence of an HIV co-infection, can be limiting due to the high inaccuracy associated with the use of conventional diagnostic methods. Here we report a gene signature that can identify a tuberculosis infection in patients co-infected with HIV as well as in the absence of HIV. METHODS: We analyzed global gene expression data from peripheral blood mononuclear cell (PBMC samples of patients that were either mono-infected with HIV or co-infected with HIV/TB and used support vector machines to identify a gene signature that can distinguish between the two classes. We then validated our results using publically available gene expression data from patients mono-infected with TB. RESULTS: Our analysis successfully identified a 251-gene signature that accurately distinguishes patients co-infected with HIV/TB from those infected with HIV only, with an overall accuracy of 81.4% (sensitivity = 76.2%, specificity = 86.4%. Furthermore, we show that our 251-gene signature can also accurately distinguish patients with active TB in the absence of an HIV infection from both patients with a latent TB infection and healthy controls (88.9-94.7% accuracy; 69.2-90% sensitivity and 90.3-100% specificity. We also demonstrate that the expression levels of the 251-gene signature diminish as a correlate of the length of TB treatment. CONCLUSIONS: A 251-gene signature is described to (a detect TB in the presence or absence of an HIV co-infection, and (b assess response to treatment following anti-TB therapy.

  11. Identification and validation of reference genes for accurate normalization of real-time quantitative PCR data in kiwifruit.

    Ferradás, Yolanda; Rey, Laura; Martínez, Óscar; Rey, Manuel; González, Ma Victoria

    2016-05-01

    Identification and validation of reference genes are required for the normalization of qPCR data. We studied the expression stability produced by eight primer pairs amplifying four common genes used as references for normalization. Samples representing different tissues, organs and developmental stages in kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) were used. A total of 117 kiwifruit samples were divided into five sample sets (mature leaves, axillary buds, stigmatic arms, fruit flesh and seeds). All samples were also analysed as a single set. The expression stability of the candidate primer pairs was tested using three algorithms (geNorm, NormFinder and BestKeeper). The minimum number of reference genes necessary for normalization was also determined. A unique primer pair was selected for amplifying the 18S rRNA gene. The primer pair selected for amplifying the ACTIN gene was different depending on the sample set. 18S 2 and ACT 2 were the candidate primer pairs selected for normalization in the three sample sets (mature leaves, fruit flesh and stigmatic arms). 18S 2 and ACT 3 were the primer pairs selected for normalization in axillary buds. No primer pair could be selected for use as the reference for the seed sample set. The analysis of all samples in a single set did not produce the selection of any stably expressing primer pair. Considering data previously reported in the literature, we validated the selected primer pairs amplifying the FLOWERING LOCUS T gene for use in the normalization of gene expression in kiwifruit.

  12. Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages.

    Reddy, Anupama; Growney, Joseph D; Wilson, Nick S; Emery, Caroline M; Johnson, Jennifer A; Ward, Rebecca; Monaco, Kelli A; Korn, Joshua; Monahan, John E; Stump, Mark D; Mapa, Felipa A; Wilson, Christopher J; Steiger, Janine; Ledell, Jebediah; Rickles, Richard J; Myer, Vic E; Ettenberg, Seth A; Schlegel, Robert; Sellers, William R; Huet, Heather A; Lehár, Joseph

    2015-01-01

    Death Receptor 5 (DR5) agonists demonstrate anti-tumor activity in preclinical models but have yet to demonstrate robust clinical responses. A key limitation may be the lack of patient selection strategies to identify those most likely to respond to treatment. To overcome this limitation, we screened a DR5 agonist Nanobody across >600 cell lines representing 21 tumor lineages and assessed molecular features associated with response. High expression of DR5 and Casp8 were significantly associated with sensitivity, but their expression thresholds were difficult to translate due to low dynamic ranges. To address the translational challenge of establishing thresholds of gene expression, we developed a classifier based on ratios of genes that predicted response across lineages. The ratio classifier outperformed the DR5+Casp8 classifier, as well as standard approaches for feature selection and classification using genes, instead of ratios. This classifier was independently validated using 11 primary patient-derived pancreatic xenograft models showing perfect predictions as well as a striking linearity between prediction probability and anti-tumor response. A network analysis of the genes in the ratio classifier captured important biological relationships mediating drug response, specifically identifying key positive and negative regulators of DR5 mediated apoptosis, including DR5, CASP8, BID, cFLIP, XIAP and PEA15. Importantly, the ratio classifier shows translatability across gene expression platforms (from Affymetrix microarrays to RNA-seq) and across model systems (in vitro to in vivo). Our approach of using gene expression ratios presents a robust and novel method for constructing translatable biomarkers of compound response, which can also probe the underlying biology of treatment response.

  13. Evaluation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in Pyrus pyrifolia using different tissue samples and seasonal conditions.

    Imai, Tsuyoshi; Ubi, Benjamin E; Saito, Takanori; Moriguchi, Takaya

    2014-01-01

    We have evaluated suitable reference genes for real time (RT)-quantitative PCR (qPCR) analysis in Japanese pear (Pyrus pyrifolia). We tested most frequently used genes in the literature such as β-Tubulin, Histone H3, Actin, Elongation factor-1α, Glyceraldehyde-3-phosphate dehydrogenase, together with newly added genes Annexin, SAND and TIP41. A total of 17 primer combinations for these eight genes were evaluated using cDNAs synthesized from 16 tissue samples from four groups, namely: flower bud, flower organ, fruit flesh and fruit skin. Gene expression stabilities were analyzed using geNorm and NormFinder software packages or by ΔCt method. geNorm analysis indicated three best performing genes as being sufficient for reliable normalization of RT-qPCR data. Suitable reference genes were different among sample groups, suggesting the importance of validation of gene expression stability of reference genes in the samples of interest. Ranking of stability was basically similar between geNorm and NormFinder, suggesting usefulness of these programs based on different algorithms. ΔCt method suggested somewhat different results in some groups such as flower organ or fruit skin; though the overall results were in good correlation with geNorm or NormFinder. Gene expression of two cold-inducible genes PpCBF2 and PpCBF4 were quantified using the three most and the three least stable reference genes suggested by geNorm. Although normalized quantities were different between them, the relative quantities within a group of samples were similar even when the least stable reference genes were used. Our data suggested that using the geometric mean value of three reference genes for normalization is quite a reliable approach to evaluating gene expression by RT-qPCR. We propose that the initial evaluation of gene expression stability by ΔCt method, and subsequent evaluation by geNorm or NormFinder for limited number of superior gene candidates will be a practical way of finding out

  14. TMO: time and memory optimized algorithm applicable for more accurate alignment of trinucleotide repeat disorders associated genes

    Done Stojanov

    2016-03-01

    Full Text Available In this study, time and memory optimized (TMO algorithm is presented. Compared with Smith–Waterman's algorithm, TMO is applicable for a more accurate detection of continuous insertion/deletions (indels in genes’ fragments, associated with disorders caused by over-repetition of a certain codon. The improvement comes from the tendency to pinpoint indels in the least preserved nucleotide pairs. All nucleotide pairs that occur less frequently are classified as less preserved and they are considered as mutated codons whose mid-nucleotides were deleted. Other benefit of the proposed algorithm is its general tendency to maximize the number of matching nucleotides included per alignment, regardless of any specific alignment metrics. Since the structure of the solution, when applying Smith–Waterman, depends on the adjustment of the alignment parameters and, therefore, an incomplete (shortened solution may be derived, our algorithm does not reject any of the consistent matching nucleotides that can be included in the final solution. In terms of computational aspects, our algorithm runs faster than Smith–Waterman for very similar DNA and requires less memory than the most memory efficient dynamic programming algorithms. The speed up comes from the reduced number of nucleotide comparisons that have to be performed, without having to imperil the completeness of the solution. Due to the fact that four integers (16 Bytes are required for tracking matching fragment, regardless its length, our algorithm requires less memory than Huang's algorithm.

  15. Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays

    Jiang Nan

    2006-08-01

    Full Text Available Abstract Background Gene expression profiling using microarrays has become an important genetic tool. Spotted arrays prepared in academic labs have the advantage of low cost and high design and content flexibility, but are often limited by their susceptibility to quality control (QC issues. Previously, we have reported a novel 3-color microarray technology that enabled array fabrication QC. In this report we further investigated its advantage in spot-level data QC. Results We found that inadequate amount of bound probes available for hybridization led to significant, gene-specific compression in ratio measurements, increased data variability, and printing pin dependent heterogeneities. The impact of such problems can be captured through the definition of quality scores, and efficiently controlled through quality-dependent filtering and normalization. We compared gene expression measurements derived using our data processing pipeline with the known input ratios of spiked in control clones, and with the measurements by quantitative real time RT-PCR. In each case, highly linear relationships (R2>0.94 were observed, with modest compression in the microarray measurements (correction factor Conclusion Our microarray analytical and technical advancements enabled a better dissection of the sources of data variability and hence a more efficient QC. With that highly accurate gene expression measurements can be achieved using the cDNA microarray technology.

  16. Identification and evaluation of reference genes for accurate gene expression normalization of fresh and frozen-thawed spermatozoa of water buffalo (Bubalus bubalis).

    Ashish, Shende; Bhure, S K; Harikrishna, Pillai; Ramteke, S S; Muhammed Kutty, V H; Shruthi, N; Ravi Kumar, G V P P S; Manish, Mahawar; Ghosh, S K; Mihir, Sarkar

    2017-04-01

    The quantitative real time PCR (qRT-PCR) has become an important tool for gene-expression analysis for a selected number of genes in life science. Although large dynamic range, sensitivity and reproducibility of qRT-PCR is good, the reliability majorly depend on the selection of proper reference genes (RGs) employed for normalization. Although, RGs expression has been reported to vary considerably within same cell type with different experimental treatments. No systematic study has been conducted to identify and evaluate the appropriate RGs in spermatozoa of domestic animals. Therefore, this study was conducted to analyze suitable stable RGs in fresh and frozen-thawed spermatozoa. We have assessed 13 candidate RGs (BACT, RPS18s, RPS15A, ATP5F1, HMBS, ATP2B4, RPL13, EEF2, TBP, EIF2B2, MDH1, B2M and GLUT5) of different functions and pathways using five algorithms. Regardless of the approach, the ranking of the most and the least candidate RGs remained almost same. The comprehensive ranking by RefFinder showed GLUT5, ATP2B4 and B2M, MDH1 as the top two stable and least stable RGs, respectively. The expression levels of four heat shock proteins (HSP) were employed as a target gene to evaluate RGs efficiency for normalization. The results demonstrated an exponential difference in expression levels of the four HSP genes upon normalization of the data with the most stable and the least stable RGs. Our study, provides a convenient RGs for normalization of gene-expression of key metabolic pathways effected during freezing and thawing of spermatozoa of buffalo and other closely related bovines.

  17. Rapid and accurate identification of Mycobacterium tuberculosis complex and common non-tuberculous mycobacteria by multiplex real-time PCR targeting different housekeeping genes.

    Nasr Esfahani, Bahram; Rezaei Yazdi, Hadi; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Zarkesh Esfahani, Hamid

    2012-11-01

    Rapid and accurate identification of mycobacteria isolates from primary culture is important due to timely and appropriate antibiotic therapy. Conventional methods for identification of Mycobacterium species based on biochemical tests needs several weeks and may remain inconclusive. In this study, a novel multiplex real-time PCR was developed for rapid identification of Mycobacterium genus, Mycobacterium tuberculosis complex (MTC) and the most common non-tuberculosis mycobacteria species including M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and the M. gordonae in three reaction tubes but under same PCR condition. Genetic targets for primer designing included the 16S rDNA gene, the dnaJ gene, the gyrB gene and internal transcribed spacer (ITS). Multiplex real-time PCR was setup with reference Mycobacterium strains and was subsequently tested with 66 clinical isolates. Results of multiplex real-time PCR were analyzed with melting curves and melting temperature (T (m)) of Mycobacterium genus, MTC, and each of non-tuberculosis Mycobacterium species were determined. Multiplex real-time PCR results were compared with amplification and sequencing of 16S-23S rDNA ITS for identification of Mycobacterium species. Sensitivity and specificity of designed primers were each 100 % for MTC, M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and M. gordonae. Sensitivity and specificity of designed primer for genus Mycobacterium was 96 and 100 %, respectively. According to the obtained results, we conclude that this multiplex real-time PCR with melting curve analysis and these novel primers can be used for rapid and accurate identification of genus Mycobacterium, MTC, and the most common non-tuberculosis Mycobacterium species.

  18. Enzymic colorimetry-based DNA chip: a rapid and accurate assay for detecting mutations for clarithromycin resistance in the 23S rRNA gene of Helicobacter pylori.

    Xuan, Shi-Hai; Zhou, Yu-Gui; Shao, Bo; Cui, Ya-Lin; Li, Jian; Yin, Hong-Bo; Song, Xiao-Ping; Cong, Hui; Jing, Feng-Xiang; Jin, Qing-Hui; Wang, Hui-Min; Zhou, Jie

    2009-11-01

    Macrolide drugs, such as clarithromycin (CAM), are a key component of many combination therapies used to eradicate Helicobacter pylori. However, resistance to CAM is increasing in H. pylori and is becoming a serious problem in H. pylori eradication therapy. CAM resistance in H. pylori is mostly due to point mutations (A2142G/C, A2143G) in the peptidyltransferase-encoding region of the 23S rRNA gene. In this study an enzymic colorimetry-based DNA chip was developed to analyse single-nucleotide polymorphisms of the 23S rRNA gene to determine the prevalence of mutations in CAM-related resistance in H. pylori-positive patients. The results of the colorimetric DNA chip were confirmed by direct DNA sequencing. In 63 samples, the incidence of the A2143G mutation was 17.46 % (11/63). The results of the colorimetric DNA chip were concordant with DNA sequencing in 96.83 % of results (61/63). The colorimetric DNA chip could detect wild-type and mutant signals at every site, even at a DNA concentration of 1.53 x 10(2) copies microl(-1). Thus, the colorimetric DNA chip is a reliable assay for rapid and accurate detection of mutations in the 23S rRNA gene of H. pylori that lead to CAM-related resistance, directly from gastric tissues.

  19. An AS-PCR assay for accurate genotyping of FAD2A/FAD2B genes in peanuts (Arachis hypogaea L.

    Yu, H. T.

    2013-09-01

    Full Text Available FAD2A and FAD2B are homoeologous genes from A and B genomes in cultivated peanuts (Arachis hypogaea L. encoding fatty acid desaturates which convert oleate to linoleate. To study the genetics of oleate and breed high oleate peanut cultivars, a simple allele specific-PCR (AS-PCR protocol for the accurate genotyping of FAD2A/FAD2B was developed to discriminate the wild and mutant allele of both genes (FAD2A 448 G > A and FAD2B 441_442insA. The results may serve to develop a feasible procedure for producing highly desired high oleate peanut cultivars through hybridization.FAD2A y FAD2B son genes homólogos de genomas A y B en cacahuete cultivado (Arachis hypogaea L. que codifican las desaturasas de ácidos grasos que convierten oleato a linoleato. Para estudiar la genética de las variedades mejoradas de cacahuete alto oleato, fue desarrollado un protocolo sencillo del alelo específico PCR-(AS-PCR para la determinación precisa del genotipo de FAD2A/FAD2B y discriminar el alelo silvestre y el mutante de ambos genes (FAD2A 448 G > A y FAD2B 441_442insA. Los resultados pueden servir para desarrollar un procedimiento viable para la producción de cultivares deseados de cacahuetes alto oleato a través de hibridación.

  20. IMPre: an accurate and efficient software for prediction of T- and B-cell receptor germline genes and alleles from rearranged repertoire data

    Wei Zhang

    2016-11-01

    Full Text Available Large-scale study of the properties of T-cell receptor (TCR and B-cell receptor (BCR repertoires through next-generation sequencing is providing excellent insights into the understanding of adaptive immune responses. Variable(DiversityJoining V(DJ germline genes and alleles must be characterized in detail to facilitate repertoire analyses. However, most species do not have well-characterized TCR/BCR germline genes because of their high homology. Also, more germline alleles are required for humans and other species, which limits the capacity for studying immune repertoires. Herein, we developed Immune Germline Prediction (IMPre, a tool for predicting germline V/J genes and alleles using deep-sequencing data derived from TCR/BCR repertoires. We developed a new algorithm, Seed_Clust, for clustering, produced a multiway tree for assembly and optimized the sequence according to the characteristics of rearrangement. We trained IMPre on human samples of T-cell receptor beta (TRB and immunoglobulin heavy chain (IGH, and then tested it on additional human samples. Accuracy of 97.7%, 100%, 92.9% and 100% was obtained for TRBV, TRBJ, IGHV and IGHJ, respectively. Analyses of subsampling performance for these samples showed IMPre to be robust using different data quantities. Subsequently, IMPre was tested on samples from rhesus monkeys and human long sequences: the highly accurate results demonstrated IMPre to be stable with animal and multiple data types. With rapid accumulation of high-throughput sequence data for TCR and BCR repertoires, IMPre can be applied broadly for obtaining novel genes and a large number of novel alleles. IMPre is available at https://github.com/zhangwei2015/IMPre.

  1. 基于支持向量机MPLS的间歇过程故障诊断方法%On-line Fault Detection Using SVM-based Dynamic MPLS for Batch Processes

    李运锋; 汪志锋; 袁景淇

    2006-01-01

    In this article, a nonlinear dynamic multiway partial least squares (MPLS) based on support vector machines (SVM) is developed for on-line fault detection in batch processes. The approach, referred to as SVM-based DMPLS, integrates the SVM with the MPLS model. Process data from normal historical batches are used to develop the MPLS model, and a series of single-input-single-output SVM networks are adopted to approximate nonlinear inner relationship between input and output variables. In addition, the application of a time-lagged window technique not only makes the complementarities of unmeasured data of the monitored batch unnecessary, but also significantly reduces the computation and storage requirements in comparison with the traditional MPLS. The proposed approach is validated by a simulation study of on-line fault detection for a fed-batch penicillin production.

  2. The detection of the methylated Wif-1 gene is more accurate than a fecal occult blood test for colorectal cancer screening

    Amiot, Aurelien

    2014-07-15

    Background: The clinical benefit of guaiac fecal occult blood tests (FOBT) is now well established for colorectal cancer screening. Growing evidence has demonstrated that epigenetic modifications and fecal microbiota changes, also known as dysbiosis, are associated with CRC pathogenesis and might be used as surrogate markers of CRC. Patients and Methods: We performed a cross-sectional study that included all consecutive subjects that were referred (from 2003 to 2007) for screening colonoscopies. Prior to colonoscopy, effluents (fresh stools, sera-S and urine-U) were harvested and FOBTs performed. Methylation levels were measured in stools, S and U for 3 genes (Wif1, ALX-4, and Vimentin) selected from a panel of 63 genes; Kras mutations and seven dominant and subdominant bacterial populations in stools were quantified. Calibration was assessed with the Hosmer-Lemeshow chi-square, and discrimination was determined by calculating the C-statistic (Area Under Curve) and Net Reclassification Improvement index. Results: There were 247 individuals (mean age 60.8±12.4 years, 52% of males) in the study group, and 90 (36%) of these individuals were patients with advanced polyps or invasive adenocarcinomas. A multivariate model adjusted for age and FOBT led to a C-statistic of 0.83 [0.77-0.88]. After supplementary sequential (one-by-one) adjustment, Wif-1 methylation (S or U) and fecal microbiota dysbiosis led to increases of the C-statistic to 0.90 [0.84-0.94] (p = 0.02) and 0.81 [0.74-0.86] (p = 0.49), respectively. When adjusted jointly for FOBT and Wif-1 methylation or fecal microbiota dysbiosis, the increase of the C-statistic was even more significant (0.91 and 0.85, p<0.001 and p = 0.10, respectively). Conclusion: The detection of methylated Wif-1 in either S or U has a higher performance accuracy compared to guaiac FOBT for advanced colorectal neoplasia screening. Conversely, fecal microbiota dysbiosis detection was not more accurate. Blood and urine testing could be

  3. An SVM-based method for predicting cigarette sales volume%一种基于支持向量机的卷烟销量预测方法

    武牧; 林慧苹; 李素科; 吴明治; 王治国; 吴高峰

    2016-01-01

    为解决现有线性回归方法对市级卷烟销量预测研究效果不佳等问题,基于支持向量机(SVM,Support vector machine)设计并实现了一种市级卷烟销量预测方法.以湖南中烟工业有限责任公司卷烟销量为研究对象,将支持向量机(SVM)方法应用到卷烟销量预测中,提出了基于SVM的卷烟销量预测混合方法(SHPM,SVM-based hybrid prediction method).将SHPM与线性回归方法、ARIMA(Autoregressive integrated moving average)方法、SVM方法进行了市级卷烟销量预测的对比实验,结果表明:将SVM方法应用到卷烟销量预测中是可行的.在市级卷烟销量预测上,SHPM预测结果误差相比SVM方法降低9.58%,比线性回归方法降低11.83%,比ARIMA方法降低45.79%.因此,SHPM是一种有效的市级卷烟销量预测方法.%Not satisfied with the accuracy of cigarette sales volume prediction with linear regression method, an SHPM (SVM-based hybrid prediction method) was proposed based on SVM (Support vector machine) by taking the sales volume of China Tobacco Hunan Industrial Company Limited as objects. Municipal level cigarette sales volume predicted separately by SHPM, linear regression, ARIMA (autoregressive integrated moving average) and SVM were compared and analyzed. The results showed that it was feasible to predict cigarette sales volumes with SVM method. The prediction errors against SVM, linear regression and ARIMA reduced by 9.58%, 11.83% and 45.79%, respectively; SHPM prediction method was more effective.

  4. Validating Internal Control Genes for the Accurate Normalization of qPCR Expression Analysis of the Novel Model Plant Setaria viridis.

    Julia Lambret-Frotté

    Full Text Available Employing reference genes to normalize the data generated with quantitative PCR (qPCR can increase the accuracy and reliability of this method. Previous results have shown that no single housekeeping gene can be universally applied to all experiments. Thus, the identification of a suitable reference gene represents a critical step of any qPCR analysis. Setaria viridis has recently been proposed as a model system for the study of Panicoid grasses, a crop family of major agronomic importance. Therefore, this paper aims to identify suitable S. viridis reference genes that can enhance the analysis of gene expression in this novel model plant. The first aim of this study was the identification of a suitable RNA extraction method that could retrieve a high quality and yield of RNA. After this, two distinct algorithms were used to assess the gene expression of fifteen different candidate genes in eighteen different samples, which were divided into two major datasets, the developmental and the leaf gradient. The best-ranked pair of reference genes from the developmental dataset included genes that encoded a phosphoglucomutase and a folylpolyglutamate synthase; genes that encoded a cullin and the same phosphoglucomutase as above were the most stable genes in the leaf gradient dataset. Additionally, the expression pattern of two target genes, a SvAP3/PI MADS-box transcription factor and the carbon-fixation enzyme PEPC, were assessed to illustrate the reliability of the chosen reference genes. This study has shown that novel reference genes may perform better than traditional housekeeping genes, a phenomenon which has been previously reported. These results illustrate the importance of carefully validating reference gene candidates for each experimental set before employing them as universal standards. Additionally, the robustness of the expression of the target genes may increase the utility of S. viridis as a model for Panicoid grasses.

  5. 一种基于 QBC 的 SVM 主动学习算法%Active learning algorithm for SVM based on QBC

    徐海龙; 别晓峰; 冯卉; 吴天爱

    2015-01-01

    To the problem that large-scale labeled samples is not easy to acquire and the class-unbalanced dataset in the course of souport vector machine (SVM)training,an active learning algorithm based on query by committee (QBC)for SVM(QBC-ASVM)is proposed,which efficiently combines the improved QBC active learning and the weighted SVM.In this method,QBC active learning is used to select the samples which are the most valuable to the current SVM classifier,and the weighted SVM is used to reduce the impact of the unba-lanced data set on SVMs active learning.The experimental results show that the proposed approach can consid-erably reduce the labeled samples and costs compared with the passive SVM,and at the same time,it can ensure that the accurate classification performance is kept as the passive SVM,and the proposed method improves gen-eralization performance and also expedites the SVM training.%针对支持向量机(souport vector machine,SVM)训练学习过程中样本分布不均衡、难以获得大量带有类标注样本的问题,提出一种基于委员会投票选择(query by committee,QBC)的 SVM 主动学习算法 QBC-AS-VM,将改进的 QBC 主动学习方法与加权 SVM 方法有机地结合应用于 SVM 训练学习中,通过改进的 QBC 主动学习,主动选择那些对当前 SVM 分类器最有价值的样本进行标注,在 SVM 主动学习中应用改进的加权 SVM,减少了样本分布不均衡对 SVM 主动学习性能的影响,实验结果表明在保证不影响分类精度的情况下,所提出的算法需要标记的样本数量大大少于随机采样法需要标记的样本数量,降低了学习的样本标记代价,提高了 SVM 泛化性能而且训练速度同样有所提高。

  6. A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks.

    Mei, Suyu; Zhu, Hao

    2015-01-26

    Protein-protein interaction (PPI) prediction is generally treated as a problem of binary classification wherein negative data sampling is still an open problem to be addressed. The commonly used random sampling is prone to yield less representative negative data with considerable false negatives. Meanwhile rational constraints are seldom exerted on model selection to reduce the risk of false positive predictions for most of the existing computational methods. In this work, we propose a novel negative data sampling method based on one-class SVM (support vector machine, SVM) to predict proteome-wide protein interactions between HTLV retrovirus and Homo sapiens, wherein one-class SVM is used to choose reliable and representative negative data, and two-class SVM is used to yield proteome-wide outcomes as predictive feedback for rational model selection. Computational results suggest that one-class SVM is more suited to be used as negative data sampling method than two-class PPI predictor, and the predictive feedback constrained model selection helps to yield a rational predictive model that reduces the risk of false positive predictions. Some predictions have been validated by the recent literature. Lastly, gene ontology based clustering of the predicted PPI networks is conducted to provide valuable cues for the pathogenesis of HTLV retrovirus.

  7. An accurate prostate cancer prognosticator using a seven-gene signature plus Gleason score and taking cell type heterogeneity into account.

    Xin Chen

    Full Text Available One of the major challenges in the development of prostate cancer prognostic biomarkers is the cellular heterogeneity in tissue samples. We developed an objective Cluster-Correlation (CC analysis to identify gene expression changes in various cell types that are associated with progression. In the Cluster step, samples were clustered (unsupervised based on the expression values of each gene through a mixture model combined with a multiple linear regression model in which cell-type percent data were used for decomposition. In the Correlation step, a Chi-square test was used to select potential prognostic genes. With CC analysis, we identified 324 significantly expressed genes (68 tumor and 256 stroma cell expressed genes which were strongly associated with the observed biochemical relapse status. Significance Analysis of Microarray (SAM was then utilized to develop a seven-gene classifier. The Classifier has been validated using two independent Data Sets. The overall prediction accuracy and sensitivity is 71% and 76%, respectively. The inclusion of the Gleason sum to the seven-gene classifier raised the prediction accuracy and sensitivity to 83% and 76% respectively based on independent testing. These results indicated that our prognostic model that includes cell type adjustments and using Gleason score and the seven-gene signature has some utility for predicting outcomes for prostate cancer for individual patients at the time of prognosis. The strategy could have applications for improving marker performance in other cancers and other diseases.

  8. Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies

    Yuan Shinsheng

    2011-09-01

    Full Text Available Abstract Background To elucidate the molecular complications in many complex diseases, we argue for the priority to construct a model representing the normal physiological state of a cell/tissue. Results By analyzing three independent microarray datasets on normal human tissues, we established a quantitative molecular model GET, which consists of 24 tissue-specific Gene Expression Templates constructed from a set of 56 genes, for predicting 24 distinct tissue types under disease-free condition. 99.2% correctness was reached when a large-scale validation was performed on 61 new datasets to test the tissue-prediction power of GET. Network analysis based on molecular interactions suggests a potential role of these 56 genes in tissue differentiation and carcinogenesis. Applying GET to transcriptomic datasets produced from tissue development studies the results correlated well with developmental stages. Cancerous tissues and cell lines yielded significantly lower correlation with GET than the normal tissues. GET distinguished melanoma from normal skin tissue or benign skin tumor with 96% sensitivity and 89% specificity. Conclusions These results strongly suggest that a normal tissue or cell may uphold its normal functioning and morphology by maintaining specific chemical stoichiometry among genes. The state of stoichiometry can be depicted by a compact set of representative genes such as the 56 genes obtained here. A significant deviation from normal stoichiometry may result in malfunction or abnormal growth of the cells.

  9. Immediate-Early Gene Transcriptional Activation in Hippocampus Ca1 and Ca3 Does Not Accurately Reflect Rapid, Pattern Completion-Based Retrieval of Context Memory

    Pevzner, Aleksandr; Guzowski, John F.

    2015-01-01

    No studies to date have examined whether immediate-early gene (IEG) activation is driven by context memory recall. To address this question, we utilized the context preexposure facilitation effect (CPFE) paradigm. In CPFE, animals acquire contextual fear conditioning through hippocampus-dependent rapid retrieval of a previously formed contextual…

  10. Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions

    Merkl Rainer

    2010-11-01

    Full Text Available Abstract Background In many microbial genomes, a strong preference for a small number of codons can be observed in genes whose products are needed by the cell in large quantities. This codon usage bias (CUB improves translational accuracy and speed and is one of several factors optimizing cell growth. Whereas CUB and the overrepresentation of individual proteins have been studied in detail, it is still unclear which high-level metabolic categories are subject to translational optimization in different habitats. Results In a systematic study of 388 microbial species, we have identified for each genome a specific subset of genes characterized by a marked CUB, which we named the effectome. As expected, gene products related to protein synthesis are abundant in both archaeal and bacterial effectomes. In addition, enzymes contributing to energy production and gene products involved in protein folding and stabilization are overrepresented. The comparison of genomes from eleven habitats shows that the environment has only a minor effect on the composition of the effectomes. As a paradigmatic example, we detailed the effectome content of 37 bacterial genomes that are most likely exposed to strongest selective pressure towards translational optimization. These effectomes accommodate a broad range of protein functions like enzymes related to glycolysis/gluconeogenesis and the TCA cycle, ATP synthases, aminoacyl-tRNA synthetases, chaperones, proteases that degrade misfolded proteins, protectants against oxidative damage, as well as cold shock and outer membrane proteins. Conclusions We made clear that effectomes consist of specific subsets of the proteome being involved in several cellular functions. As expected, some functions are related to cell growth and affect speed and quality of protein synthesis. Additionally, the effectomes contain enzymes of central metabolic pathways and cellular functions sustaining microbial life under stress situations. These

  11. Selection and Validation of Reference Genes for Accurate RT-qPCR Data Normalization in Coffea spp. under a Climate Changes Context of Interacting Elevated [CO2] and Temperature

    Martins, Madlles Q.; Fortunato, Ana S.; Rodrigues, Weverton P.; Partelli, Fábio L.; Campostrini, Eliemar; Lidon, Fernando C.; DaMatta, Fábio M.; Ramalho, José C.; Ribeiro-Barros, Ana I.

    2017-01-01

    /oxygenase (RLS), results from the in silico aggregation and experimental validation of the best number of reference genes showed that two reference genes are adequate to normalize RT-qPCR data. Altogether, this work highlights the importance of an adequate selection of reference genes for each single or combined experimental condition and constitutes the basis to accurately study molecular responses of Coffea spp. in a context of climate changes and global warming. PMID:28326094

  12. Direct and accurate measurement of CAG repeat configuration in the ataxin-1 (ATXN-1) gene by "dual-fluorescence labeled PCR-restriction fragment length analysis".

    Lin, Jiang X; Ishikawa, Kinya; Sakamoto, Masaki; Tsunemi, Taiji; Ishiguro, Taro; Amino, Takeshi; Toru, Shuta; Kondo, Ikuko; Mizusawa, Hidehiro

    2008-01-01

    Spinocerebellar ataxia type 1 (SCA1; OMIM: #164400) is an autosomal dominant cerebellar ataxia caused by an expansion of CAG repeat, which encodes polyglutamine, in the ataxin-1 (ATXN1) gene. Length of polyglutamine in the ATXN1 protein is the critical determinant of pathogenesis of this disease. Molecular diagnosis of SCA1 is usually undertaken by assessing the length of CAG repeat configuration using primers spanning this configuration. However, this conventional method may potentially lead to misdiagnosis in assessing polyglutamine-encoding CAG repeat length, since CAT interruptions may be present within the CAG repeat configuration, not only in normal controls but also in neurologically symptomatic subjects. We developed a new method for assessing actual CAG repeat numbers not interrupted by CAT sequences. Polymerase chain reaction using a primer pair labeled with two different fluorescences followed by restriction enzyme digestion with SfaNI which recognizes the sequence "GCATC(N)(5)", lengths of actual CAG repeats that encode polyglutamine were directly detected. We named this method "dual fluorescence labeled PCR-restriction fragment length analysis". We found that numbers of actual CAG repeat encoding polyglutamine do not overlap between our cohorts of normal chromosomes (n=385) and SCA1 chromosomes (n=5). We conclude that the present method is a useful way for molecular diagnosis of SCA1.

  13. Rapid and accurate detection of the CFTR gene mutation 1811+1.6 kbA>G by real-time fluorescence resonance energy transfer PCR.

    Reboul, Marie-Pierre; Higueret, Laurent; Biteau, Nicolas; Iron, Albert

    2005-10-01

    The CFTR gene mutation 1811+1.6 kbA>G has been reported as associated with a severe phenotype of cystic fibrosis with pancreatic insufficiency. This mutation has been identified as a rather common one in the South West of France and in the Iberian Peninsula. Because of the precise geographical origin of the subjects and its frequency, the mutation has to be investigated with accuracy. We have developed an original real-time Fluorescence Resonance Energy Transfer (FRET) PCR assay for genotyping the mutation 1811+1.6 kbA>G. It is based on the amplification of a region spanning the mutation with simultaneous detection of the amplicon by hybridization with a bi-probe followed by a melting curve analysis. The results obtained are identical with those resulting from either restriction fragment length polymorphism analysis or sequencing. The distinction between the wild type and the mutation 1811+1.6 kbA>G is easy because the corresponding melting points shows a difference of 6 or 9.5 degrees C depending on the associated SNP A/T located 16 bp downstream. We demonstrated that a FRET assay showed enough sensitivity to discriminate between two nucleotide polymorphisms (SNPs) in the sequence of the sensor. In conclusion, this method is specific, fast, easy to perform, reproducible, inexpensive as it uses only one bi-probe and well adapted to daily practice.

  14. Speaking Fluently And Accurately

    JosephDeVeto

    2004-01-01

    Even after many years of study,students make frequent mistakes in English. In addition, many students still need a long time to think of what they want to say. For some reason, in spite of all the studying, students are still not quite fluent.When I teach, I use one technique that helps students not only speak more accurately, but also more fluently. That technique is dictations.

  15. 基于NIR-PCA-SVM联用技术的烤烟烟叶产地模式识别%NIR-PCA-SVM Based Pattern Recognition of Growing Area of Flue-cured Tobacco

    束茹欣; 孙平; 杨凯; 张建平; 刘太昂

    2011-01-01

    To accurately identify the growing area of flue - cured tobacco, the contents of chemical components, including total sugar, reducing sugar, total nitrogen, nicotine, total chlorine and total potassium, in 402 cured tobacco samples collected from Yunnan, Henan, Anhui, Fujian, Guizhou and Jilin Provinces in 2010 were tested, and the samples were scanned by near infrared spectrometer. The near infrared spectra (NIR) pattern recognition models of growing area were developed by principal component analysis (PCA) and support vector machine (SVM) algorithms, and the growing areas of the samples were recognized. The results indicated that: 1) The prediction accuracy recognized by NIR-PCA-SVM models reached 97%, while that by chemical component-SVM and NIR-SVM models were lower. 2) The NIR - PCA - SVM, and chemical component - SVM models all offered better recoginition for Yunnan tobacco samples. NIR-PCA-SVM model could be applied to pattern recognition of flue-cured tobacco samples of different origins.%为了更准确地对烟叶样品进行产地模式识别,检测了云南、河南、安徽、福建、贵州、吉林6省2010年生产的402个初烤烟叶样品的总糖、还原糖、总氮、烟碱、总氯、总钾含量,同时进行了近红外( NIR)光谱扫描,利用主成分分析( PCA)法和支持向量机算法(SVM)建立了烟叶产地模式识别模型,并对云南、河南、安徽、福建、贵州、吉林6省烟叶样品进行了产地模式识别.结果表明:①NIR-PCA-SVM模型对6省烟叶样品识别的预报正确率高达97%,而化学成分-SVM模型和NIR-SVM模型对6省烟叶产地的识别效果差;②NIR-PCA-SVM、化学成分-SVM和NIR-SVM 3个模型对云南省烟叶都有着较好的识别效果.NIR-PCA-SVM模型可用于不同烟叶样品产地的模式识别.

  16. 用兴趣点凸包和SVM加权反馈实现图像检索%Image Retrieval by Convex Hulls of Interest Points and SVM-Based Weighted Feedback

    苏小红; 丁进; 马培军

    2009-01-01

    针对采用环状颜色直方图的图像检索方法存在的不足,提出一种基于兴趣点凸包的图像特征提取方法,通过对用小波变换检测出的必趣点递归求出它们的凸包,并将每个凸包上的兴趣点按一定的算法安插在相应的桶内,对每个桶求出颜色直方图,利用桶与桶之间的相似度定义两幅图像的相似度.这种特征提取方法可有效抑制兴趣点集合中出现游离兴趣点的情况,结合基于兴趣点的空间离散度和Gabor小波纹理等特征实现图像检索,可有效提高图像检索精度.最后,提出一种新的相关反馈方法,通过利用支持向量机分类结果设置权值来改进移动查询点相关反馈方法.实际图像数据库上的实验表明,引入这种反馈方法后可将图像检索的查准率提高20%左右,查全率提高10%左右.%To solve the problem of image retrieval method based on annular color histogram, a new image characteristics extraction method based on convex hulls of interest points is presented. Firstly, the interest points on an image are detected by wavelet transform. Then, convex hulls of interest points are calculated recursively and these points are assigned to some buckets by a spe-cific algorithm to form a color histogram for every bucket. The similarity of two images is calcu-lated by the similarity between histograms of two buckets. Combined with spatial distribution feature and Gabor texture feature based on convex hulls of interest points, the system of image retrieval is built. Experiments on image database show that this method works well when isolated points exist in the interest points set and so provide more accurate retrieval performance compa-ring with other retrieval method based on interest points. Further more, a novel relevance feed-back method is presented. It improves the query point movement relevance feedback method by setting weights based on support vector machine cluster results. The experiments show

  17. A GA-SVM based model for throwing rate prediction in the open-pit cast blasting%基于GA-SVM的露天矿抛掷爆破抛掷率预测

    刘希亮; 赵学胜; 陆锋; 孙文彬

    2012-01-01

    This paper probed into the whole height bench cast blasting process and described the influence factors from 3 major perspectives:natural geological,blasting scheming and factitious ones,and selected the throwing rate which was generally accepted in the cast blasting field to assess the blasting performance.Then a novel GA-SVM model was constructed to analyze the real collected explosion data from open pit mining,and verified in a certain open-pit.Also the MIV method was employed to analyze the influence factor at each input factor.The study indicate that:① the presented GA-SVM model performs more robust and accurate than other artificial intelligence models such as BP,RBF,GRNN and GA-BP,which has a more stable prediction accuracy of 83.75%.Moreover,due to the ubiquitous paradigm of the presented approach,it provides a single,unified approach to evaluating other blasting performance factors such as the longest thrown distance and loose coefficient etc;② for this certain open pit which maintains a steady lithological character and design parameters,the bench height,explosive specific charge possess a positive correlation coefficient with the throwing rate,while line of least resistance,the slope angle and the profile width perform the opposite.%分析了高台阶抛掷爆破的机理过程,并从自然地质、爆破设计和人为操作3个角度出发,结合某矿区的实际开采情况,提取其中10个参数作为影响该矿区抛掷爆破效果的主要因素,以爆破领域中广泛接受的抛掷率作为抛掷爆破效果的评价因子,采用此矿区爆破生产中的实际数据建立了基于遗传算法优化的支持向量机模型GA-SVM。基于建立的GA-SVM模型,采用平均影响值(Mean Impact Value,MIV)作为评价标准,对各因素的影响程度进行了评定。结果表明:①GA-SVM模型能够比较快速、准确地根据此矿区的爆破设计参数预测出抛掷爆破的抛掷率,平均预测精度稳定在83.75%,

  18. Face Detection Using Adaboosted SVM-Based Component Classifier

    Valiollahzadeh, Seyyed Majid; Nazari, Mohammad

    2008-01-01

    Recently, Adaboost has been widely used to improve the accuracy of any given learning algorithm. In this paper we focus on designing an algorithm to employ combination of Adaboost with Support Vector Machine as weak component classifiers to be used in Face Detection Task. To obtain a set of effective SVM-weaklearner Classifier, this algorithm adaptively adjusts the kernel parameter in SVM instead of using a fixed one. Proposed combination outperforms in generalization in comparison with SVM on imbalanced classification problem. The proposed here method is compared, in terms of classification accuracy, to other commonly used Adaboost methods, such as Decision Trees and Neural Networks, on CMU+MIT face database. Results indicate that the performance of the proposed method is overall superior to previous Adaboost approaches.

  19. Incremental Training for SVM-Based Classification with Keyword Adjusting

    SUN Jin-wen; YANG Jian-wu; LU Bin; XIAO Jian-guo

    2004-01-01

    This paper analyzed the theory of incremental learning of SVM (support vector machine) and pointed out it is a shortage that the support vector optimization is only considered in present research of SVM incremental learning.According to the significance of keyword in training, a new incremental training method considering keyword adjusting was proposed, which eliminates the difference between incremental learning and batch learning through the keyword adjusting.The experimental results show that the improved method outperforms the method without the keyword adjusting and achieve the same precision as the batch method.

  20. Hyperellipsoidal SVM-Based Outlier Detection Technique for Geosensor Networks

    Zhang, Yang; Meratnia, N.; Havinga, P.J.M.

    2009-01-01

    Recently, wireless sensor networks providing fine-grained spatio-temporal observations have become one of the major monitoring platforms for geo-applications. Along side data acquisition, outlier detection is essential in geosensor networks to ensure data quality, secure monitoring and re- liable de

  1. A NEW SVM BASED EMOTIONAL CLASSIFICATION OF IMAGE

    Wang Weining; Yu Yinglin; Zhang Jianchao

    2005-01-01

    How high-level emotional representation of art paintings can be inferred from percep tual level features suited for the particular classes (dynamic vs. static classification)is presented. The key points are feature selection and classification. According to the strong relationship between notable lines of image and human sensations, a novel feature vector WLDLV (Weighted Line Direction-Length Vector) is proposed, which includes both orientation and length information of lines in an image. Classification is performed by SVM (Support Vector Machine) and images can be classified into dynamic and static. Experimental results demonstrate the effectiveness and superiority of the algorithm.

  2. SVM-Based Control System for a Robot Manipulator

    Foudil Abdessemed

    2012-12-01

    Full Text Available Real systems are usually non‐linear, ill‐defined, have variable parameters and are subject to external disturbances. Modelling these systems is often an approximation of the physical phenomena involved. However, it is from this approximate system of representation that we propose ‐ in this paper ‐ to build a robust control, in the sense that it must ensure low sensitivity towards parameters, uncertainties, variations and external disturbances. The computed torque method is a well‐established robot control technique which takes account of the dynamic coupling between the robot links. However, its main disadvantage lies on the assumption of an exactly known dynamic model which is not realizable in practice. To overcome this issue, we propose the estimation of the dynamics model of the nonlinear system with a machine learning regression method. The output of this regressor is used in conjunction with a PD controller to achieve the tracking trajectory task of a robot manipulator. In cases where some of the parameters of the plant undergo a change in their values, poor performance may result. To cope with this drawback, a fuzzy precompensator is inserted to reinforce the SVM computed torque‐based controller and avoid any deterioration. The theory is developed and the simulation results are carried out on a two‐degree of freedom robot manipulator to demonstrate the validity of the proposed approach.

  3. Automatic Parameters Selection for SVM Based on PSO

    ZHANG Mingfeng; ZHU Yinghua; ZHENG Xu; LIU Yu

    2007-01-01

    Motivated by the fact that automatic parameters selection for Support Vector Machine (SVM) is an important issue to make SVM practically useful and the common used Leave-One-Out (LOO) method is complex calculation and time consuming,an effective strategy for automatic parameters selection for SVM is proposed by using the Particle Swarm Optimization (PSO) in this paper.Simulation results of practice data model demonstrate the effectiveness and high efficiency of the proposed approach.

  4. Oil spill detection from SAR image using SVM based classification

    A. A. Matkan

    2013-09-01

    Full Text Available In this paper, the potential of fully polarimetric L-band SAR data for detecting sea oil spills is investigated using polarimetric decompositions and texture analysis based on SVM classifier. First, power and magnitude measurements of HH and VV polarization modes and, Pauli, Freeman and Krogager decompositions are computed and applied in SVM classifier. Texture analysis is used for identification using SVM method. The texture features i.e. Mean, Variance, Contrast and Dissimilarity from them are then extracted. Experiments are conducted on full polarimetric SAR data acquired from PALSAR sensor of ALOS satellite on August 25, 2006. An accuracy assessment indicated overall accuracy of 78.92% and 96.46% for the power measurement of the VV polarization and the Krogager decomposition respectively in first step. But by use of texture analysis the results are improved to 96.44% and 96.65% quality for mean of power and magnitude measurements of HH and VV polarizations and the Krogager decomposition. Results show that the Krogager polarimetric decomposition method has the satisfying result for detection of sea oil spill on the sea surface and the texture analysis presents the good results.

  5. SVM Based Identification of Psychological Personality Using Handwritten Text

    Syeda Asra

    2016-04-01

    Full Text Available Identification of Personality is a complex process. To ease this process, a model is developed using cursive handwriting. Area based, width based and height based thresholds are set for only character selection, word selection and line selection. The rest is considered as noise. Followed by feature vector construction. Slope feature using slope calculation, shape features and edge detection done using Sobel filter and direction histogram is considered. Based on the direction of handwriting the analysis was done. Writing which rises to the right shows optimism and cheerfulness. Sagging to the right shows physical or mental weariness. The lines which are straight, reveals over-control to compensate for an inner fear of loss of control.The analysis was done using single line and multiple lines. Simple techniques have provided good results. The results using single line were 95% and multiple lines were 91%.The classification is done using SVM classifier.

  6. GA-SVM Based Lungs Nodule Detection and Classification

    Jaffar, M. Arfan; Hussain, Ayyaz; Jabeen, Fauzia; Nazir, M.; Mirza, Anwar M.

    In this paper we have proposed a method for lungs nodule detection from computed tomography (CT) scanned images by using Genetic Algorithms (GA) and morphological techniques. First of all, GA has been used for automated segmentation of lungs. Region of interests (ROIs) have been extracted by using 8 directional searches slice by slice and then features extraction have been performed. Finally SVM have been used to classify ROI that contain nodule. The proposed system is capable to perform fully automatic segmentation and nodule detection from CT Scan Lungs images. The technique was tested against the 50 datasets of different patients received from Aga Khan Medical University, Pakistan and Lung Image Database Consortium (LIDC) dataset.

  7. Gene

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  8. Efficient and accurate fragmentation methods.

    Pruitt, Spencer R; Bertoni, Colleen; Brorsen, Kurt R; Gordon, Mark S

    2014-09-16

    Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum

  9. Accurate determination of antenna directivity

    Dich, Mikael

    1997-01-01

    The derivation of a formula for accurate estimation of the total radiated power from a transmitting antenna for which the radiated power density is known in a finite number of points on the far-field sphere is presented. The main application of the formula is determination of directivity from power......-pattern measurements. The derivation is based on the theory of spherical wave expansion of electromagnetic fields, which also establishes a simple criterion for the required number of samples of the power density. An array antenna consisting of Hertzian dipoles is used to test the accuracy and rate of convergence...

  10. Accurate molecular classification of cancer using simple rules

    Gotoh Osamu

    2009-10-01

    Full Text Available Abstract Background One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to remove the effects of noise. Feature selection is often used to address this problem by selecting informative genes from among thousands or tens of thousands of genes. However, most of the existing methods of microarray-based cancer classification utilize too many genes to achieve accurate classification, which often hampers the interpretability of the models. For a better understanding of the classification results, it is desirable to develop simpler rule-based models with as few marker genes as possible. Methods We screened a small number of informative single genes and gene pairs on the basis of their depended degrees proposed in rough sets. Applying the decision rules induced by the selected genes or gene pairs, we constructed cancer classifiers. We tested the efficacy of the classifiers by leave-one-out cross-validation (LOOCV of training sets and classification of independent test sets. Results We applied our methods to five cancerous gene expression datasets: leukemia (acute lymphoblastic leukemia [ALL] vs. acute myeloid leukemia [AML], lung cancer, prostate cancer, breast cancer, and leukemia (ALL vs. mixed-lineage leukemia [MLL] vs. AML. Accurate classification outcomes were obtained by utilizing just one or two genes. Some genes that correlated closely with the pathogenesis of relevant cancers were identified. In terms of both classification performance and algorithm simplicity, our approach outperformed or at least matched existing methods. Conclusion In cancerous gene expression datasets, a small number of genes, even one or two if selected correctly, is capable of achieving an ideal cancer classification effect. This finding also means that very simple rules may perform well for cancerous class prediction.

  11. Accurate Modeling of Advanced Reflectarrays

    Zhou, Min

    Analysis and optimization methods for the design of advanced printed re ectarrays have been investigated, and the study is focused on developing an accurate and efficient simulation tool. For the analysis, a good compromise between accuracy and efficiency can be obtained using the spectral domain...... to the POT. The GDOT can optimize for the size as well as the orientation and position of arbitrarily shaped array elements. Both co- and cross-polar radiation can be optimized for multiple frequencies, dual polarization, and several feed illuminations. Several contoured beam reflectarrays have been designed...... using the GDOT to demonstrate its capabilities. To verify the accuracy of the GDOT, two offset contoured beam reflectarrays that radiate a high-gain beam on a European coverage have been designed and manufactured, and subsequently measured at the DTU-ESA Spherical Near-Field Antenna Test Facility...

  12. The Accurate Particle Tracer Code

    Wang, Yulei; Qin, Hong; Yu, Zhi

    2016-01-01

    The Accurate Particle Tracer (APT) code is designed for large-scale particle simulations on dynamical systems. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and non-linear problems. Under the well-designed integrated and modularized framework, APT serves as a universal platform for researchers from different fields, such as plasma physics, accelerator physics, space science, fusion energy research, computational mathematics, software engineering, and high-performance computation. The APT code consists of seven main modules, including the I/O module, the initialization module, the particle pusher module, the parallelization module, the field configuration module, the external force-field module, and the extendible module. The I/O module, supported by Lua and Hdf5 projects, provides a user-friendly interface for both numerical simulation and data analysis. A series of new geometric numerical methods...

  13. Accurate ab initio spin densities

    Boguslawski, Katharina; Legeza, Örs; Reiher, Markus

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...

  14. Accurate thickness measurement of graphene.

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T

    2016-03-29

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  15. Accurate thickness measurement of graphene

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  16. A More Accurate Fourier Transform

    Courtney, Elya

    2015-01-01

    Fourier transform methods are used to analyze functions and data sets to provide frequencies, amplitudes, and phases of underlying oscillatory components. Fast Fourier transform (FFT) methods offer speed advantages over evaluation of explicit integrals (EI) that define Fourier transforms. This paper compares frequency, amplitude, and phase accuracy of the two methods for well resolved peaks over a wide array of data sets including cosine series with and without random noise and a variety of physical data sets, including atmospheric $\\mathrm{CO_2}$ concentrations, tides, temperatures, sound waveforms, and atomic spectra. The FFT uses MIT's FFTW3 library. The EI method uses the rectangle method to compute the areas under the curve via complex math. Results support the hypothesis that EI methods are more accurate than FFT methods. Errors range from 5 to 10 times higher when determining peak frequency by FFT, 1.4 to 60 times higher for peak amplitude, and 6 to 10 times higher for phase under a peak. The ability t...

  17. 38 CFR 4.46 - Accurate measurement.

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  18. Clinical application and comparison of rapid and accurate identification of mycobacterium by gene chip microarray and smear acid-fast staining%基因芯片快速分枝杆菌鉴定技术与涂片抗酸染色技术的临床应用比较∗

    侯沪; 李爱敏; 唐曙明

    2015-01-01

    目的:比较基因芯片快速鉴定分枝杆菌与经典涂片抗酸染色镜检技术的临床应用效果,评估两种方法的优劣性。方法2011~2014年间以基因芯片与涂片抗酸染色两种技术对深圳市所有综合性医院临床怀疑有分枝杆菌感染的标本进行检验。χ%Objective To compare the clinical effect of application of gene chip microscopy technique for rapid identification of Mycobacterium and classic smear acid-fast staining,and to assess the advantages and disadvantages of the wo methods.Methods From 201 1 to 2014,gene chip microarray and smear acid fast staining were used to identify the mycobacterium tuberculosis in speci-mens suspicious of the infection from all the general hospitals of Shenzhen city.Chi-square test was used to compare the positive rates of the two methods.Results A total of 2 481 specimens were collected from clinic.With smear acid-fast staining technique, the positive specimens of 1 93 cases werefound and the positive rate was 7.8%.Meanwhile,31 7 positive samples were detected by the technology of gene chip microarray,and the positive rate was 12.8%.The positive rate of Gene chip microarray technology was higher than that of the smear acid fast staining,and there was significant difference between them (P < 0.05 ).The 31 7 positive samples identified by Gene chip microarray,included 263 cases of Mycobacterium tuberculosis,27 cases of Mycobacterium absces-sus,18 cases of Mycobacterium intracellulare,3 cases of Mycobacterium gastric uLcer,3 cases of Mycobacterium avium,1 case of Mycobacterium Gordonae,1 case of Mycobacterium marinum and 1 case of Mycobacterium Kansas.Conclusion The gene chip mi-croarray technology is fast,accurate,and its positive rate is higher than that of smear acid-fast staining technique.Classification and identification of Mycobacterium is very helpful for clinical individualized treatment of anti mycobacterium infection.

  19. Optimizing cell arrays for accurate functional genomics

    Fengler Sven

    2012-07-01

    Full Text Available Abstract Background Cellular responses emerge from a complex network of dynamic biochemical reactions. In order to investigate them is necessary to develop methods that allow perturbing a high number of gene products in a flexible and fast way. Cell arrays (CA enable such experiments on microscope slides via reverse transfection of cellular colonies growing on spotted genetic material. In contrast to multi-well plates, CA are susceptible to contamination among neighboring spots hindering accurate quantification in cell-based screening projects. Here we have developed a quality control protocol for quantifying and minimizing contamination in CA. Results We imaged checkered CA that express two distinct fluorescent proteins and segmented images into single cells to quantify the transfection efficiency and interspot contamination. Compared with standard procedures, we measured a 3-fold reduction of contaminants when arrays containing HeLa cells were washed shortly after cell seeding. We proved that nucleic acid uptake during cell seeding rather than migration among neighboring spots was the major source of contamination. Arrays of MCF7 cells developed without the washing step showed 7-fold lower percentage of contaminant cells, demonstrating that contamination is dependent on specific cell properties. Conclusions Previously published methodological works have focused on achieving high transfection rate in densely packed CA. Here, we focused in an equally important parameter: The interspot contamination. The presented quality control is essential for estimating the rate of contamination, a major source of false positives and negatives in current microscopy based functional genomics screenings. We have demonstrated that a washing step after seeding enhances CA quality for HeLA but is not necessary for MCF7. The described method provides a way to find optimal seeding protocols for cell lines intended to be used for the first time in CA.

  20. Laboratory Building for Accurate Determination of Plutonium

    2008-01-01

    <正>The accurate determination of plutonium is one of the most important assay techniques of nuclear fuel, also the key of the chemical measurement transfer and the base of the nuclear material balance. An

  1. Understanding the Code: keeping accurate records.

    Griffith, Richard

    2015-10-01

    In his continuing series looking at the legal and professional implications of the Nursing and Midwifery Council's revised Code of Conduct, Richard Griffith discusses the elements of accurate record keeping under Standard 10 of the Code. This article considers the importance of accurate record keeping for the safety of patients and protection of district nurses. The legal implications of records are explained along with how district nurses should write records to ensure these legal requirements are met.

  2. Accurate tracking control in LOM application

    2003-01-01

    The fabrication of accurate prototype from CAD model directly in short time depends on the accurate tracking control and reference trajectory planning in (Laminated Object Manufacture) LOM application. An improvement on contour accuracy is acquired by the introduction of a tracking controller and a trajectory generation policy. A model of the X-Y positioning system of LOM machine is developed as the design basis of tracking controller. The ZPETC (Zero Phase Error Tracking Controller) is used to eliminate single axis following error, thus reduce the contour error. The simulation is developed on a Maltab model based on a retrofitted LOM machine and the satisfied result is acquired.

  3. BASIC: A Simple and Accurate Modular DNA Assembly Method.

    Storch, Marko; Casini, Arturo; Mackrow, Ben; Ellis, Tom; Baldwin, Geoff S

    2017-01-01

    Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2].

  4. Accurate Switched-Voltage voltage averaging circuit

    金光, 一幸; 松本, 寛樹

    2006-01-01

    Abstract ###This paper proposes an accurate Switched-Voltage (SV) voltage averaging circuit. It is presented ###to compensated for NMOS missmatch error at MOS differential type voltage averaging circuit. ###The proposed circuit consists of a voltage averaging and a SV sample/hold (S/H) circuit. It can ###operate using nonoverlapping three phase clocks. Performance of this circuit is verified by PSpice ###simulations.

  5. Accurate overlaying for mobile augmented reality

    Pasman, W; van der Schaaf, A; Lagendijk, RL; Jansen, F.W.

    1999-01-01

    Mobile augmented reality requires accurate alignment of virtual information with objects visible in the real world. We describe a system for mobile communications to be developed to meet these strict alignment criteria using a combination of computer vision. inertial tracking and low-latency renderi

  6. Accurate colorimetric feedback for RGB LED clusters

    Man, Kwong; Ashdown, Ian

    2006-08-01

    We present an empirical model of LED emission spectra that is applicable to both InGaN and AlInGaP high-flux LEDs, and which accurately predicts their relative spectral power distributions over a wide range of LED junction temperatures. We further demonstrate with laboratory measurements that changes in LED spectral power distribution with temperature can be accurately predicted with first- or second-order equations. This provides the basis for a real-time colorimetric feedback system for RGB LED clusters that can maintain the chromaticity of white light at constant intensity to within +/-0.003 Δuv over a range of 45 degrees Celsius, and to within 0.01 Δuv when dimmed over an intensity range of 10:1.

  7. Accurate guitar tuning by cochlear implant musicians.

    Thomas Lu

    Full Text Available Modern cochlear implant (CI users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  8. Efficient Accurate Context-Sensitive Anomaly Detection

    2007-01-01

    For program behavior-based anomaly detection, the only way to ensure accurate monitoring is to construct an efficient and precise program behavior model. A new program behavior-based anomaly detection model,called combined pushdown automaton (CPDA) model was proposed, which is based on static binary executable analysis. The CPDA model incorporates the optimized call stack walk and code instrumentation technique to gain complete context information. Thereby the proposed method can detect more attacks, while retaining good performance.

  9. On accurate determination of contact angle

    Concus, P.; Finn, R.

    1992-01-01

    Methods are proposed that exploit a microgravity environment to obtain highly accurate measurement of contact angle. These methods, which are based on our earlier mathematical results, do not require detailed measurement of a liquid free-surface, as they incorporate discontinuous or nearly-discontinuous behavior of the liquid bulk in certain container geometries. Physical testing is planned in the forthcoming IML-2 space flight and in related preparatory ground-based experiments.

  10. Accurate Control of Josephson Phase Qubits

    2016-04-14

    61 ~1986!. 23 K. Kraus, States, Effects, and Operations: Fundamental Notions of Quantum Theory, Lecture Notes in Physics , Vol. 190 ~Springer-Verlag... PHYSICAL REVIEW B 68, 224518 ~2003!Accurate control of Josephson phase qubits Matthias Steffen,1,2,* John M. Martinis,3 and Isaac L. Chuang1 1Center...for Bits and Atoms and Department of Physics , MIT, Cambridge, Massachusetts 02139, USA 2Solid State and Photonics Laboratory, Stanford University

  11. Accurate guitar tuning by cochlear implant musicians.

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang

    2014-01-01

    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  12. Synthesizing Accurate Floating-Point Formulas

    Ioualalen, Arnault; Martel, Matthieu

    2013-01-01

    International audience; Many critical embedded systems perform floating-point computations yet their accuracy is difficult to assert and strongly depends on how formulas are written in programs. In this article, we focus on the synthesis of accurate formulas mathematically equal to the original formulas occurring in source codes. In general, an expression may be rewritten in many ways. To avoid any combinatorial explosion, we use an intermediate representation, called APEG, enabling us to rep...

  13. Accurate structural correlations from maximum likelihood superpositions.

    Douglas L Theobald

    2008-02-01

    Full Text Available The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method ("PCA plots" for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology.

  14. Accurate measurement of unsteady state fluid temperature

    Jaremkiewicz, Magdalena

    2017-03-01

    In this paper, two accurate methods for determining the transient fluid temperature were presented. Measurements were conducted for boiling water since its temperature is known. At the beginning the thermometers are at the ambient temperature and next they are immediately immersed into saturated water. The measurements were carried out with two thermometers of different construction but with the same housing outer diameter equal to 15 mm. One of them is a K-type industrial thermometer widely available commercially. The temperature indicated by the thermometer was corrected considering the thermometers as the first or second order inertia devices. The new design of a thermometer was proposed and also used to measure the temperature of boiling water. Its characteristic feature is a cylinder-shaped housing with the sheath thermocouple located in its center. The temperature of the fluid was determined based on measurements taken in the axis of the solid cylindrical element (housing) using the inverse space marching method. Measurements of the transient temperature of the air flowing through the wind tunnel using the same thermometers were also carried out. The proposed measurement technique provides more accurate results compared with measurements using industrial thermometers in conjunction with simple temperature correction using the inertial thermometer model of the first or second order. By comparing the results, it was demonstrated that the new thermometer allows obtaining the fluid temperature much faster and with higher accuracy in comparison to the industrial thermometer. Accurate measurements of the fast changing fluid temperature are possible due to the low inertia thermometer and fast space marching method applied for solving the inverse heat conduction problem.

  15. Niche Genetic Algorithm with Accurate Optimization Performance

    LIU Jian-hua; YAN De-kun

    2005-01-01

    Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolutionary direction dynamically during evolution. After evolution, the solutions's precision can be greatly improved by means of the local searching along the recorded direction. Simulation shows that this algorithm can not only keep population diversity but also find accurate solutions. Although using this method has to take more time compared with the standard GA, it is really worth applying to some cases that have to meet a demand for high solution precision.

  16. Accurate estimation of indoor travel times

    Prentow, Thor Siiger; Blunck, Henrik; Stisen, Allan

    2014-01-01

    the InTraTime method for accurately estimating indoor travel times via mining of historical and real-time indoor position traces. The method learns during operation both travel routes, travel times and their respective likelihood---both for routes traveled as well as for sub-routes thereof. In...... are collected within the building complex. Results indicate that InTraTime is superior with respect to metrics such as deployment cost, maintenance cost and estimation accuracy, yielding an average deviation from actual travel times of 11.7 %. This accuracy was achieved despite using a minimal-effort setup...

  17. Accurate diagnosis is essential for amebiasis

    2004-01-01

    @@ Amebiasis is one of the three most common causes of death from parasitic disease, and Entamoeba histolytica is the most widely distributed parasites in the world. Particularly, Entamoeba histolytica infection in the developing countries is a significant health problem in amebiasis-endemic areas with a significant impact on infant mortality[1]. In recent years a world wide increase in the number of patients with amebiasis has refocused attention on this important infection. On the other hand, improving the quality of parasitological methods and widespread use of accurate tecniques have improved our knowledge about the disease.

  18. The first accurate description of an aurora

    Schröder, Wilfried

    2006-12-01

    As technology has advanced, the scientific study of auroral phenomena has increased by leaps and bounds. A look back at the earliest descriptions of aurorae offers an interesting look into how medieval scholars viewed the subjects that we study.Although there are earlier fragmentary references in the literature, the first accurate description of the aurora borealis appears to be that published by the German Catholic scholar Konrad von Megenberg (1309-1374) in his book Das Buch der Natur (The Book of Nature). The book was written between 1349 and 1350.

  19. New law requires 'medically accurate' lesson plans.

    1999-09-17

    The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material.

  20. Universality: Accurate Checks in Dyson's Hierarchical Model

    Godina, J. J.; Meurice, Y.; Oktay, M. B.

    2003-06-01

    In this talk we present high-accuracy calculations of the susceptibility near βc for Dyson's hierarchical model in D = 3. Using linear fitting, we estimate the leading (γ) and subleading (Δ) exponents. Independent estimates are obtained by calculating the first two eigenvalues of the linearized renormalization group transformation. We found γ = 1.29914073 ± 10 -8 and, Δ = 0.4259469 ± 10-7 independently of the choice of local integration measure (Ising or Landau-Ginzburg). After a suitable rescaling, the approximate fixed points for a large class of local measure coincide accurately with a fixed point constructed by Koch and Wittwer.

  1. How Accurately can we Calculate Thermal Systems?

    Cullen, D; Blomquist, R N; Dean, C; Heinrichs, D; Kalugin, M A; Lee, M; Lee, Y; MacFarlan, R; Nagaya, Y; Trkov, A

    2004-04-20

    I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it would be more precise to say that I would like to determine the spread in answers that we obtain from a variety of code packages. This spread should serve as an excellent indicator of how accurately we can really model and calculate such systems today. Hopefully, eventually this will lead to improvements in both our codes and the thermal scattering models that they use in the future. In order to accomplish this I propose a number of extremely simple systems that involve thermal neutron scattering that can be easily modeled and calculated by a variety of neutron transport codes. These are theoretical systems designed to emphasize the effects of thermal scattering, since that is what we are interested in studying. I have attempted to keep these systems very simple, and yet at the same time they include most, if not all, of the important thermal scattering effects encountered in a large, water-moderated, uranium fueled thermal system, i.e., our typical thermal reactors.

  2. Accurate pattern registration for integrated circuit tomography

    Levine, Zachary H.; Grantham, Steven; Neogi, Suneeta; Frigo, Sean P.; McNulty, Ian; Retsch, Cornelia C.; Wang, Yuxin; Lucatorto, Thomas B.

    2001-07-15

    As part of an effort to develop high resolution microtomography for engineered structures, a two-level copper integrated circuit interconnect was imaged using 1.83 keV x rays at 14 angles employing a full-field Fresnel zone plate microscope. A major requirement for high resolution microtomography is the accurate registration of the reference axes in each of the many views needed for a reconstruction. A reconstruction with 100 nm resolution would require registration accuracy of 30 nm or better. This work demonstrates that even images that have strong interference fringes can be used to obtain accurate fiducials through the use of Radon transforms. We show that we are able to locate the coordinates of the rectilinear circuit patterns to 28 nm. The procedure is validated by agreement between an x-ray parallax measurement of 1.41{+-}0.17 {mu}m and a measurement of 1.58{+-}0.08 {mu}m from a scanning electron microscope image of a cross section.

  3. Accurate determination of characteristic relative permeability curves

    Krause, Michael H.; Benson, Sally M.

    2015-09-01

    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  4. Accurate pose estimation for forensic identification

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk

    2010-04-01

    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  5. Accurate taxonomic assignment of short pyrosequencing reads.

    Clemente, José C; Jansson, Jesper; Valiente, Gabriel

    2010-01-01

    Ambiguities in the taxonomy dependent assignment of pyrosequencing reads are usually resolved by mapping each read to the lowest common ancestor in a reference taxonomy of all those sequences that match the read. This conservative approach has the drawback of mapping a read to a possibly large clade that may also contain many sequences not matching the read. A more accurate taxonomic assignment of short reads can be made by mapping each read to the node in the reference taxonomy that provides the best precision and recall. We show that given a suffix array for the sequences in the reference taxonomy, a short read can be mapped to the node of the reference taxonomy with the best combined value of precision and recall in time linear in the size of the taxonomy subtree rooted at the lowest common ancestor of the matching sequences. An accurate taxonomic assignment of short reads can thus be made with about the same efficiency as when mapping each read to the lowest common ancestor of all matching sequences in a reference taxonomy. We demonstrate the effectiveness of our approach on several metagenomic datasets of marine and gut microbiota.

  6. Accurate phylogenetic classification of DNA fragments based onsequence composition

    McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis; Hugenholtz, Philip; Rigoutsos, Isidore

    2006-05-01

    Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequence characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.

  7. Toward Accurate and Quantitative Comparative Metagenomics

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  8. Apparatus for accurately measuring high temperatures

    Smith, D.D.

    The present invention is a thermometer used for measuring furnace temperatures in the range of about 1800/sup 0/ to 2700/sup 0/C. The thermometer comprises a broadband multicolor thermal radiation sensor positioned to be in optical alignment with the end of a blackbody sight tube extending into the furnace. A valve-shutter arrangement is positioned between the radiation sensor and the sight tube and a chamber for containing a charge of high pressure gas is positioned between the valve-shutter arrangement and the radiation sensor. A momentary opening of the valve shutter arrangement allows a pulse of the high gas to purge the sight tube of air-borne thermal radiation contaminants which permits the radiation sensor to accurately measure the thermal radiation emanating from the end of the sight tube.

  9. Accurate renormalization group analyses in neutrino sector

    Haba, Naoyuki [Graduate School of Science and Engineering, Shimane University, Matsue 690-8504 (Japan); Kaneta, Kunio [Kavli IPMU (WPI), The University of Tokyo, Kashiwa, Chiba 277-8568 (Japan); Takahashi, Ryo [Graduate School of Science and Engineering, Shimane University, Matsue 690-8504 (Japan); Yamaguchi, Yuya [Department of Physics, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan)

    2014-08-15

    We investigate accurate renormalization group analyses in neutrino sector between ν-oscillation and seesaw energy scales. We consider decoupling effects of top quark and Higgs boson on the renormalization group equations of light neutrino mass matrix. Since the decoupling effects are given in the standard model scale and independent of high energy physics, our method can basically apply to any models beyond the standard model. We find that the decoupling effects of Higgs boson are negligible, while those of top quark are not. Particularly, the decoupling effects of top quark affect neutrino mass eigenvalues, which are important for analyzing predictions such as mass squared differences and neutrinoless double beta decay in an underlying theory existing at high energy scale.

  10. Accurate Weather Forecasting for Radio Astronomy

    Maddalena, Ronald J.

    2010-01-01

    The NRAO Green Bank Telescope routinely observes at wavelengths from 3 mm to 1 m. As with all mm-wave telescopes, observing conditions depend upon the variable atmospheric water content. The site provides over 100 days/yr when opacities are low enough for good observing at 3 mm, but winds on the open-air structure reduce the time suitable for 3-mm observing where pointing is critical. Thus, to maximum productivity the observing wavelength needs to match weather conditions. For 6 years the telescope has used a dynamic scheduling system (recently upgraded; www.gb.nrao.edu/DSS) that requires accurate multi-day forecasts for winds and opacities. Since opacity forecasts are not provided by the National Weather Services (NWS), I have developed an automated system that takes available forecasts, derives forecasted opacities, and deploys the results on the web in user-friendly graphical overviews (www.gb.nrao.edu/ rmaddale/Weather). The system relies on the "North American Mesoscale" models, which are updated by the NWS every 6 hrs, have a 12 km horizontal resolution, 1 hr temporal resolution, run to 84 hrs, and have 60 vertical layers that extend to 20 km. Each forecast consists of a time series of ground conditions, cloud coverage, etc, and, most importantly, temperature, pressure, humidity as a function of height. I use the Liebe's MWP model (Radio Science, 20, 1069, 1985) to determine the absorption in each layer for each hour for 30 observing wavelengths. Radiative transfer provides, for each hour and wavelength, the total opacity and the radio brightness of the atmosphere, which contributes substantially at some wavelengths to Tsys and the observational noise. Comparisons of measured and forecasted Tsys at 22.2 and 44 GHz imply that the forecasted opacities are good to about 0.01 Nepers, which is sufficient for forecasting and accurate calibration. Reliability is high out to 2 days and degrades slowly for longer-range forecasts.

  11. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  12. Fast and accurate exhaled breath ammonia measurement.

    Solga, Steven F; Mudalel, Matthew L; Spacek, Lisa A; Risby, Terence H

    2014-06-11

    This exhaled breath ammonia method uses a fast and highly sensitive spectroscopic method known as quartz enhanced photoacoustic spectroscopy (QEPAS) that uses a quantum cascade based laser. The monitor is coupled to a sampler that measures mouth pressure and carbon dioxide. The system is temperature controlled and specifically designed to address the reactivity of this compound. The sampler provides immediate feedback to the subject and the technician on the quality of the breath effort. Together with the quick response time of the monitor, this system is capable of accurately measuring exhaled breath ammonia representative of deep lung systemic levels. Because the system is easy to use and produces real time results, it has enabled experiments to identify factors that influence measurements. For example, mouth rinse and oral pH reproducibly and significantly affect results and therefore must be controlled. Temperature and mode of breathing are other examples. As our understanding of these factors evolves, error is reduced, and clinical studies become more meaningful. This system is very reliable and individual measurements are inexpensive. The sampler is relatively inexpensive and quite portable, but the monitor is neither. This limits options for some clinical studies and provides rational for future innovations.

  13. Noninvasive hemoglobin monitoring: how accurate is enough?

    Rice, Mark J; Gravenstein, Nikolaus; Morey, Timothy E

    2013-10-01

    Evaluating the accuracy of medical devices has traditionally been a blend of statistical analyses, at times without contextualizing the clinical application. There have been a number of recent publications on the accuracy of a continuous noninvasive hemoglobin measurement device, the Masimo Radical-7 Pulse Co-oximeter, focusing on the traditional statistical metrics of bias and precision. In this review, which contains material presented at the Innovations and Applications of Monitoring Perfusion, Oxygenation, and Ventilation (IAMPOV) Symposium at Yale University in 2012, we critically investigated these metrics as applied to the new technology, exploring what is required of a noninvasive hemoglobin monitor and whether the conventional statistics adequately answer our questions about clinical accuracy. We discuss the glucose error grid, well known in the glucose monitoring literature, and describe an analogous version for hemoglobin monitoring. This hemoglobin error grid can be used to evaluate the required clinical accuracy (±g/dL) of a hemoglobin measurement device to provide more conclusive evidence on whether to transfuse an individual patient. The important decision to transfuse a patient usually requires both an accurate hemoglobin measurement and a physiologic reason to elect transfusion. It is our opinion that the published accuracy data of the Masimo Radical-7 is not good enough to make the transfusion decision.

  14. Accurate free energy calculation along optimized paths.

    Chen, Changjun; Xiao, Yi

    2010-05-01

    The path-based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10-ALA peptide and find that the calculated free energy changes in helix-helix and helix-hairpin transitions are both self-convergent and cross-convergent. We also calculate the free energy differences between different stable states of beta-hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation.

  15. Accurate fission data for nuclear safety

    Solders, A; Jokinen, A; Kolhinen, V S; Lantz, M; Mattera, A; Penttila, H; Pomp, S; Rakopoulos, V; Rinta-Antila, S

    2013-01-01

    The Accurate fission data for nuclear safety (AlFONS) project aims at high precision measurements of fission yields, using the renewed IGISOL mass separator facility in combination with a new high current light ion cyclotron at the University of Jyvaskyla. The 30 MeV proton beam will be used to create fast and thermal neutron spectra for the study of neutron induced fission yields. Thanks to a series of mass separating elements, culminating with the JYFLTRAP Penning trap, it is possible to achieve a mass resolving power in the order of a few hundred thousands. In this paper we present the experimental setup and the design of a neutron converter target for IGISOL. The goal is to have a flexible design. For studies of exotic nuclei far from stability a high neutron flux (10^12 neutrons/s) at energies 1 - 30 MeV is desired while for reactor applications neutron spectra that resembles those of thermal and fast nuclear reactors are preferred. It is also desirable to be able to produce (semi-)monoenergetic neutrons...

  16. Towards Accurate Modeling of Moving Contact Lines

    Holmgren, Hanna

    2015-01-01

    A main challenge in numerical simulations of moving contact line problems is that the adherence, or no-slip boundary condition leads to a non-integrable stress singularity at the contact line. In this report we perform the first steps in developing the macroscopic part of an accurate multiscale model for a moving contact line problem in two space dimensions. We assume that a micro model has been used to determine a relation between the contact angle and the contact line velocity. An intermediate region is introduced where an analytical expression for the velocity exists. This expression is used to implement boundary conditions for the moving contact line at a macroscopic scale, along a fictitious boundary located a small distance away from the physical boundary. Model problems where the shape of the interface is constant thought the simulation are introduced. For these problems, experiments show that the errors in the resulting contact line velocities converge with the grid size $h$ at a rate of convergence $...

  17. Does a pneumotach accurately characterize voice function?

    Walters, Gage; Krane, Michael

    2016-11-01

    A study is presented which addresses how a pneumotach might adversely affect clinical measurements of voice function. A pneumotach is a device, typically a mask, worn over the mouth, in order to measure time-varying glottal volume flow. By measuring the time-varying difference in pressure across a known aerodynamic resistance element in the mask, the glottal volume flow waveform is estimated. Because it adds aerodynamic resistance to the vocal system, there is some concern that using a pneumotach may not accurately portray the behavior of the voice. To test this hypothesis, experiments were performed in a simplified airway model with the principal dimensions of an adult human upper airway. A compliant constriction, fabricated from silicone rubber, modeled the vocal folds. Variations of transglottal pressure, time-averaged volume flow, model vocal fold vibration amplitude, and radiated sound with subglottal pressure were performed, with and without the pneumotach in place, and differences noted. Acknowledge support of NIH Grant 2R01DC005642-10A1.

  18. Accurate lineshape spectroscopy and the Boltzmann constant.

    Truong, G-W; Anstie, J D; May, E F; Stace, T M; Luiten, A N

    2015-10-14

    Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m.

  19. Accurate upper body rehabilitation system using kinect.

    Sinha, Sanjana; Bhowmick, Brojeshwar; Chakravarty, Kingshuk; Sinha, Aniruddha; Das, Abhijit

    2016-08-01

    The growing importance of Kinect as a tool for clinical assessment and rehabilitation is due to its portability, low cost and markerless system for human motion capture. However, the accuracy of Kinect in measuring three-dimensional body joint center locations often fails to meet clinical standards of accuracy when compared to marker-based motion capture systems such as Vicon. The length of the body segment connecting any two joints, measured as the distance between three-dimensional Kinect skeleton joint coordinates, has been observed to vary with time. The orientation of the line connecting adjoining Kinect skeletal coordinates has also been seen to differ from the actual orientation of the physical body segment. Hence we have proposed an optimization method that utilizes Kinect Depth and RGB information to search for the joint center location that satisfies constraints on body segment length and as well as orientation. An experimental study have been carried out on ten healthy participants performing upper body range of motion exercises. The results report 72% reduction in body segment length variance and 2° improvement in Range of Motion (ROM) angle hence enabling to more accurate measurements for upper limb exercises.

  20. Accurate thermoplasmonic simulation of metallic nanoparticles

    Yu, Da-Miao; Liu, Yan-Nan; Tian, Fa-Lin; Pan, Xiao-Min; Sheng, Xin-Qing

    2017-01-01

    Thermoplasmonics leads to enhanced heat generation due to the localized surface plasmon resonances. The measurement of heat generation is fundamentally a complicated task, which necessitates the development of theoretical simulation techniques. In this paper, an efficient and accurate numerical scheme is proposed for applications with complex metallic nanostructures. Light absorption and temperature increase are, respectively, obtained by solving the volume integral equation (VIE) and the steady-state heat diffusion equation through the method of moments (MoM). Previously, methods based on surface integral equations (SIEs) were utilized to obtain light absorption. However, computing light absorption from the equivalent current is as expensive as O(NsNv), where Ns and Nv, respectively, denote the number of surface and volumetric unknowns. Our approach reduces the cost to O(Nv) by using VIE. The accuracy, efficiency and capability of the proposed scheme are validated by multiple simulations. The simulations show that our proposed method is more efficient than the approach based on SIEs under comparable accuracy, especially for the case where many incidents are of interest. The simulations also indicate that the temperature profile can be tuned by several factors, such as the geometry configuration of array, beam direction, and light wavelength.

  1. Fast and Provably Accurate Bilateral Filtering.

    Chaudhury, Kunal N; Dabhade, Swapnil D

    2016-06-01

    The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires O(S) operations per pixel, where S is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to O(1) per pixel for any arbitrary S . The algorithm has a simple implementation involving N+1 spatial filterings, where N is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to estimate the order N required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with the state-of-the-art methods in terms of speed and accuracy.

  2. Towards Accurate Application Characterization for Exascale (APEX)

    Hammond, Simon David [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    Sandia National Laboratories has been engaged in hardware and software codesign activities for a number of years, indeed, it might be argued that prototyping of clusters as far back as the CPLANT machines and many large capability resources including ASCI Red and RedStorm were examples of codesigned solutions. As the research supporting our codesign activities has moved closer to investigating on-node runtime behavior a nature hunger has grown for detailed analysis of both hardware and algorithm performance from the perspective of low-level operations. The Application Characterization for Exascale (APEX) LDRD was a project concieved of addressing some of these concerns. Primarily the research was to intended to focus on generating accurate and reproducible low-level performance metrics using tools that could scale to production-class code bases. Along side this research was an advocacy and analysis role associated with evaluating tools for production use, working with leading industry vendors to develop and refine solutions required by our code teams and to directly engage with production code developers to form a context for the application analysis and a bridge to the research community within Sandia. On each of these accounts significant progress has been made, particularly, as this report will cover, in the low-level analysis of operations for important classes of algorithms. This report summarizes the development of a collection of tools under the APEX research program and leaves to other SAND and L2 milestone reports the description of codesign progress with Sandia’s production users/developers.

  3. Accurate paleointensities - the multi-method approach

    de Groot, Lennart

    2016-04-01

    The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.

  4. How flatbed scanners upset accurate film dosimetry.

    van Battum, L J; Huizenga, H; Verdaasdonk, R M; Heukelom, S

    2016-01-21

    Film is an excellent dosimeter for verification of dose distributions due to its high spatial resolution. Irradiated film can be digitized with low-cost, transmission, flatbed scanners. However, a disadvantage is their lateral scan effect (LSE): a scanner readout change over its lateral scan axis. Although anisotropic light scattering was presented as the origin of the LSE, this paper presents an alternative cause. Hereto, LSE for two flatbed scanners (Epson 1680 Expression Pro and Epson 10000XL), and Gafchromic film (EBT, EBT2, EBT3) was investigated, focused on three effects: cross talk, optical path length and polarization. Cross talk was examined using triangular sheets of various optical densities. The optical path length effect was studied using absorptive and reflective neutral density filters with well-defined optical characteristics (OD range 0.2-2.0). Linear polarizer sheets were used to investigate light polarization on the CCD signal in absence and presence of (un)irradiated Gafchromic film. Film dose values ranged between 0.2 to 9 Gy, i.e. an optical density range between 0.25 to 1.1. Measurements were performed in the scanner's transmission mode, with red-green-blue channels. LSE was found to depend on scanner construction and film type. Its magnitude depends on dose: for 9 Gy increasing up to 14% at maximum lateral position. Cross talk was only significant in high contrast regions, up to 2% for very small fields. The optical path length effect introduced by film on the scanner causes 3% for pixels in the extreme lateral position. Light polarization due to film and the scanner's optical mirror system is the main contributor, different in magnitude for the red, green and blue channel. We concluded that any Gafchromic EBT type film scanned with a flatbed scanner will face these optical effects. Accurate dosimetry requires correction of LSE, therefore, determination of the LSE per color channel and dose delivered to the film.

  5. Accurate atom-mapping computation for biochemical reactions.

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  6. Rapid and accurate pyrosequencing of angiosperm plastid genomes

    Farmerie William G

    2006-08-01

    Full Text Available Abstract Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20 System (454 Life Sciences Corporation, to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae and Platanus occidentalis (Platanaceae. Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy

  7. Genes and Gene Therapy

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  8. SVM-based base-metal prospectivity modeling of the Aravalli Orogen, Northwestern India

    Porwal, Alok; Yu, Le; Gessner, Klaus

    2010-05-01

    The Proterozoic Aravalli orogen in the state of Rajasthan, northwestern India, constitutes the most important metallogenic province for base-metal deposits in India and hosts the entire economically viable lead-zinc resource-base of the country. The orogen evolved through near-orderly Wilson cycles of repeated extensional and compressional tectonics resulting in sequential opening and closing of intracratonic rifts and amalgamation of crustal domains during a circa 1.0-Ga geological history from 2.2 Ga to 1.0 Ga. This study develops a conceptual tectonostratigraphic model of the orogen based on a synthesis of the available geological, geophysical and geochronological data followed by deep-seismic-reflectivity-constrained 2-D forward gravity modeling, and links it to the Proterozoic base-metal metallogeny in the orogen in order to identify key geological controls on the base-metal mineralization. These controls are translated into exploration criteria for base-metal deposits, validated using empirical spatial analysis, and used to derive input spatial variables for model-based base-metal prospectivity mapping of the orogen. A support vector machine (SVM) algorithm augmented by incorporating a feature selection procedure is used in a GIS environment to implement the prospectivity mapping. A comparison of the SVM-derived prospectivity map with the ones derived using other established models such as neural-networks, logistic regression, and Bayesian weights-of-evidence indicates that the SVM outperforms other models, which is attributed to the capability of the SVM to return robust classification based on small training datasets.

  9. Settlement Prediction of Road Soft Foundation Using a Support Vector Machine (SVM Based on Measured Data

    Yu Huiling

    2016-01-01

    Full Text Available The suppor1t vector machine (SVM is a relatively new artificial intelligence technique which is increasingly being applied to geotechnical problems and is yielding encouraging results. SVM is a new machine learning method based on the statistical learning theory. A case study based on road foundation engineering project shows that the forecast results are in good agreement with the measured data. The SVM model is also compared with BP artificial neural network model and traditional hyperbola method. The prediction results indicate that the SVM model has a better prediction ability than BP neural network model and hyperbola method. Therefore, settlement prediction based on SVM model can reflect actual settlement process more correctly. The results indicate that it is effective and feasible to use this method and the nonlinear mapping relation between foundation settlement and its influence factor can be expressed well. It will provide a new method to predict foundation settlement.

  10. Restoring the Generalizability of SVM Based Decoding in High Dimensional Neuroimage Data

    Abrahamsen, Trine Julie; Hansen, Lars Kai

    2011-01-01

    for Support Vector Machines. However, good generalization may be recovered in part by a simple renormalization procedure. We show that with proper renormalization, cross-validation based parameter optimization leads to the acceptance of more non-linearity in neuroimage classifiers than would have been...

  11. SVM-based classification of LV wall motion in cardiac MRI with the assessment of STE

    Mantilla, Juan; Garreau, Mireille; Bellanger, Jean-Jacques; Paredes, José Luis

    2015-01-01

    In this paper, we propose an automated method to classify normal/abnormal wall motion in Left Ventricle (LV) function in cardiac cine-Magnetic Resonance Imaging (MRI), taking as reference, strain information obtained from 2D Speckle Tracking Echocardiography (STE). Without the need of pre-processing and by exploiting all the images acquired during a cardiac cycle, spatio-temporal profiles are extracted from a subset of radial lines from the ventricle centroid to points outside the epicardial border. Classical Support Vector Machines (SVM) are used to classify features extracted from gray levels of the spatio-temporal profile as well as their representations in the Wavelet domain under the assumption that the data may be sparse in that domain. Based on information obtained from radial strain curves in 2D-STE studies, we label all the spatio-temporal profiles that belong to a particular segment as normal if the peak systolic radial strain curve of this segment presents normal kinesis, or abnormal if the peak systolic radial strain curve presents hypokinesis or akinesis. For this study, short-axis cine- MR images are collected from 9 patients with cardiac dyssynchrony for which we have the radial strain tracings at the mid-papilary muscle obtained by 2D STE; and from one control group formed by 9 healthy subjects. The best classification performance is obtained with the gray level information of the spatio-temporal profiles using a RBF kernel with 91.88% of accuracy, 92.75% of sensitivity and 91.52% of specificity.

  12. Classification of EEG data using FHT and SVM based on Bayesian Network

    V. Baby Deepa

    2011-09-01

    Full Text Available Brain Computer Interface (BCI enables the capturing and processing of motor imagery related brain signals which can be interpreted by computers. BCI systems capture the motor imagery signals via Electroencephalogram or Electrocorticogram. The processing of the signal is usually attempted by extracting feature vectors in the frequency domain and using classification algorithms to interpret the motor imagery action. In this paper we investigate the motor imagery signals obtained from BCI competition dataset IVA using the Fast Hartley Transform (FHT for feature vector extraction and feature reduction using support vector machine. The processed data is trained and classified using the Bayes Net.

  13. An SVM-based solution for fault detection in wind turbines.

    Santos, Pedro; Villa, Luisa F; Reñones, Aníbal; Bustillo, Andres; Maudes, Jesús

    2015-03-09

    Research into fault diagnosis in machines with a wide range of variable loads and speeds, such as wind turbines, is of great industrial interest. Analysis of the power signals emitted by wind turbines for the diagnosis of mechanical faults in their mechanical transmission chain is insufficient. A successful diagnosis requires the inclusion of accelerometers to evaluate vibrations. This work presents a multi-sensory system for fault diagnosis in wind turbines, combined with a data-mining solution for the classification of the operational state of the turbine. The selected sensors are accelerometers, in which vibration signals are processed using angular resampling techniques and electrical, torque and speed measurements. Support vector machines (SVMs) are selected for the classification task, including two traditional and two promising new kernels. This multi-sensory system has been validated on a test-bed that simulates the real conditions of wind turbines with two fault typologies: misalignment and imbalance. Comparison of SVM performance with the results of artificial neural networks (ANNs) shows that linear kernel SVM outperforms other kernels and ANNs in terms of accuracy, training and tuning times. The suitability and superior performance of linear SVM is also experimentally analyzed, to conclude that this data acquisition technique generates linearly separable datasets.

  14. Linear SVM-Based Android Malware Detection for Reliable IoT Services

    Hyo-Sik Ham

    2014-01-01

    Full Text Available Current many Internet of Things (IoT services are monitored and controlled through smartphone applications. By combining IoT with smartphones, many convenient IoT services have been provided to users. However, there are adverse underlying effects in such services including invasion of privacy and information leakage. In most cases, mobile devices have become cluttered with important personal user information as various services and contents are provided through them. Accordingly, attackers are expanding the scope of their attacks beyond the existing PC and Internet environment into mobile devices. In this paper, we apply a linear support vector machine (SVM to detect Android malware and compare the malware detection performance of SVM with that of other machine learning classifiers. Through experimental validation, we show that the SVM outperforms other machine learning classifiers.

  15. EHPred: an SVM-based method for epoxide hydrolases recognition and classification

    JIA Jia; YANG Liang; ZHANG Zi-zhang

    2006-01-01

    A two-layer method based on support vector machines (SVMs) has been developed to distinguish epoxide hydrolases (EHs) from other enzymes and to classify its subfamilies using its primary protein sequences. SVM classifiers were built using three different feature vectors extracted from the primary sequence of EHs: the amino acid composition (AAC), the dipeptide composition (DPC), and the pseudo-amino acid composition (PAAC). Validated by 5-fold cross tests, the first layer SVM classifier can differentiate EHs and non-EHs with an accuracy of 94.2% and has a Matthew,s correlation coefficient (MCC) of 0.84.Using 2-fold cross validation, PAAC-based second layer SVM can further classify EH subfamilies with an overall accuracy of 90.7% and MCC of 0.87 as compared to AAC (80.0%) and DPC (84.9%). A program called EHPred has also been developed to assist readers to recognize EHs and to classify their subfamilies using primary protein sequences with greater accuracy.

  16. Deriving statistical significance maps for SVM based image classification and group comparisons

    Gaonkar, Bilwaj; Davatzikos, Christos

    2012-01-01

    Population based pattern analysis and classification for quantifying structural and functional differences between diverse groups has been shown to be a powerful tool for the study of a number of diseases, and is quite commonly used especially in neuroimaging. The alternative to these pattern analysis methods, namely mass univariate methods such as voxel based analysis and all related methods, cannot detect multivariate patterns associated with group differences, and are not particularly suit...

  17. Deriving statistical significance maps for SVM based image classification and group comparisons.

    Gaonkar, Bilwaj; Davatzikos, Christos

    2012-01-01

    Population based pattern analysis and classification for quantifying structural and functional differences between diverse groups has been shown to be a powerful tool for the study of a number of diseases, and is quite commonly used especially in neuroimaging. The alternative to these pattern analysis methods, namely mass univariate methods such as voxel based analysis and all related methods, cannot detect multivariate patterns associated with group differences, and are not particularly suitable for developing individual-based diagnostic and prognostic biomarkers. A commonly used pattern analysis tool is the support vector machine (SVM). Unlike univariate statistical frameworks for morphometry, analytical tools for statistical inference are unavailable for the SVM. In this paper, we show that null distributions ordinarily obtained by permutation tests using SVMs can be analytically approximated from the data. The analytical computation takes a small fraction of the time it takes to do an actual permutation test, thereby rendering it possible to quickly create statistical significance maps derived from SVMs. Such maps are critical for understanding imaging patterns of group differences and interpreting which anatomical regions are important in determining the classifier's decision.

  18. Better Kernels and Coding Schemes Lead to Improvements in SVM-Based Secondary Structure Prediction

    2005-07-29

    NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND...set of proteins derived from SCOP 1.67 [17] as follows. We used Astral [2] to obtain a set of protein domains whose pairwise sequence identity was less...Walker, L. Lo Conte, P. Koehl, M. Levitt, and S. E. Brenner. The astral compendium in 2004. Nucleic Acids Research, 32:D189– D192, 2004. [3]G. E

  19. A SVM-based method for sentiment analysis in Persian language

    Hajmohammadi, Mohammad Sadegh; Ibrahim, Roliana

    2013-03-01

    Persian language is the official language of Iran, Tajikistan and Afghanistan. Local online users often represent their opinions and experiences on the web with written Persian. Although the information in those reviews is valuable to potential consumers and sellers, the huge amount of web reviews make it difficult to give an unbiased evaluation to a product. In this paper, standard machine learning techniques SVM and naive Bayes are incorporated into the domain of online Persian Movie reviews to automatically classify user reviews as positive or negative and performance of these two classifiers is compared with each other in this language. The effects of feature presentations on classification performance are discussed. We find that accuracy is influenced by interaction between the classification models and the feature options. The SVM classifier achieves as well as or better accuracy than naive Bayes in Persian movie. Unigrams are proved better features than bigrams and trigrams in capturing Persian sentiment orientation.

  20. Component Content Soft-Sensor of SVM Based on Ions Color Characteristics

    Zhang Kunpeng

    2012-10-01

    Full Text Available In consideration of different characteristic colors of Ions in the P507-HCL Pr/Nd extraction separation system, ions color image feature H, S, I that closely related to the element component contents are extracted by using image processing method. Principal Component Analysis algorithm is employed to determine statistics mean of H, S, I which has the stronger correlation with element component content and the auxiliary variables are obtained. With the algorithm of support vector machine, a component contents soft-sensor model in Pr/Nd extraction process is established. Finally, simulations and tests verify the rationality and feasibility of the proposed method. The research results provide theoretical foundation for the online measurement of the component content in Pr/Nd countercurrent extraction separation process.

  1. Using LS-SVM based motion recognition for smartphone indoor wireless positioning.

    Pei, Ling; Liu, Jingbin; Guinness, Robert; Chen, Yuwei; Kuusniemi, Heidi; Chen, Ruizhi

    2012-01-01

    The paper presents an indoor navigation solution by combining physical motion recognition with wireless positioning. Twenty-seven simple features are extracted from the built-in accelerometers and magnetometers in a smartphone. Eight common motion states used during indoor navigation are detected by a Least Square-Support Vector Machines (LS-SVM) classification algorithm, e.g., static, standing with hand swinging, normal walking while holding the phone in hand, normal walking with hand swinging, fast walking, U-turning, going up stairs, and going down stairs. The results indicate that the motion states are recognized with an accuracy of up to 95.53% for the test cases employed in this study. A motion recognition assisted wireless positioning approach is applied to determine the position of a mobile user. Field tests show a 1.22 m mean error in "Static Tests" and a 3.53 m in "Stop-Go Tests".

  2. An SVM-Based Solution for Fault Detection in Wind Turbines

    Pedro Santos

    2015-03-01

    Full Text Available Research into fault diagnosis in machines with a wide range of variable loads and speeds, such as wind turbines, is of great industrial interest. Analysis of the power signals emitted by wind turbines for the diagnosis of mechanical faults in their mechanical transmission chain is insufficient. A successful diagnosis requires the inclusion of accelerometers to evaluate vibrations. This work presents a multi-sensory system for fault diagnosis in wind turbines, combined with a data-mining solution for the classification of the operational state of the turbine. The selected sensors are accelerometers, in which vibration signals are processed using angular resampling techniques and electrical, torque and speed measurements. Support vector machines (SVMs are selected for the classification task, including two traditional and two promising new kernels. This multi-sensory system has been validated on a test-bed that simulates the real conditions of wind turbines with two fault typologies: misalignment and imbalance. Comparison of SVM performance with the results of artificial neural networks (ANNs shows that linear kernel SVM outperforms other kernels and ANNs in terms of accuracy, training and tuning times. The suitability and superior performance of linear SVM is also experimentally analyzed, to conclude that this data acquisition technique generates linearly separable datasets.

  3. Using LS-SVM Based Motion Recognition for Smartphone Indoor Wireless Positioning

    Ruizhi Chen

    2012-05-01

    Full Text Available The paper presents an indoor navigation solution by combining physical motion recognition with wireless positioning. Twenty-seven simple features are extracted from the built-in accelerometers and magnetometers in a smartphone. Eight common motion states used during indoor navigation are detected by a Least Square-Support Vector Machines (LS-SVM classification algorithm, e.g., static, standing with hand swinging, normal walking while holding the phone in hand, normal walking with hand swinging, fast walking, U-turning, going up stairs, and going down stairs. The results indicate that the motion states are recognized with an accuracy of up to 95.53% for the test cases employed in this study. A motion recognition assisted wireless positioning approach is applied to determine the position of a mobile user. Field tests show a 1.22 m mean error in “Static Tests” and a 3.53 m in “Stop-Go Tests”.

  4. SVM-based Multiview Face Recognition by Generalization of Discriminant Analysis

    Kisku, Dakshina Ranjan; Sing, Jamuna Kanta; Gupta, Phalguni

    2010-01-01

    Identity verification of authentic persons by their multiview faces is a real valued problem in machine vision. Multiview faces are having difficulties due to non-linear representation in the feature space. This paper illustrates the usability of the generalization of LDA in the form of canonical covariate for face recognition to multiview faces. In the proposed work, the Gabor filter bank is used to extract facial features that characterized by spatial frequency, spatial locality and orientation. Gabor face representation captures substantial amount of variations of the face instances that often occurs due to illumination, pose and facial expression changes. Convolution of Gabor filter bank to face images of rotated profile views produce Gabor faces with high dimensional features vectors. Canonical covariate is then used to Gabor faces to reduce the high dimensional feature spaces into low dimensional subspaces. Finally, support vector machines are trained with canonical sub-spaces that contain reduced set o...

  5. Entropy-Based TOA Estimation and SVM-Based Ranging Error Mitigation in UWB Ranging Systems.

    Yin, Zhendong; Cui, Kai; Wu, Zhilu; Yin, Liang

    2015-05-21

    The major challenges for Ultra-wide Band (UWB) indoor ranging systems are the dense multipath and non-line-of-sight (NLOS) problems of the indoor environment. To precisely estimate the time of arrival (TOA) of the first path (FP) in such a poor environment, a novel approach of entropy-based TOA estimation and support vector machine (SVM) regression-based ranging error mitigation is proposed in this paper. The proposed method can estimate the TOA precisely by measuring the randomness of the received signals and mitigate the ranging error without the recognition of the channel conditions. The entropy is used to measure the randomness of the received signals and the FP can be determined by the decision of the sample which is followed by a great entropy decrease. The SVM regression is employed to perform the ranging-error mitigation by the modeling of the regressor between the characteristics of received signals and the ranging error. The presented numerical simulation results show that the proposed approach achieves significant performance improvements in the CM1 to CM4 channels of the IEEE 802.15.4a standard, as compared to conventional approaches.

  6. SVM-based feature extraction and classification of aflatoxin contaminated corn using fluorescence hyperspectral data

    Support Vector Machine (SVM) was used in the Genetic Algorithms (GA) process to select and classify a subset of hyperspectral image bands. The method was applied to fluorescence hyperspectral data for the detection of aflatoxin contamination in Aspergillus flavus infected single corn kernels. In the...

  7. SVM-PB-Pred: SVM based protein block prediction method using sequence profiles and secondary structures.

    Suresh, V; Parthasarathy, S

    2014-01-01

    We developed a support vector machine based web server called SVM-PB-Pred, to predict the Protein Block for any given amino acid sequence. The input features of SVM-PB-Pred include i) sequence profiles (PSSM) and ii) actual secondary structures (SS) from DSSP method or predicted secondary structures from NPS@ and GOR4 methods. There were three combined input features PSSM+SS(DSSP), PSSM+SS(NPS@) and PSSM+SS(GOR4) used to test and train the SVM models. Similarly, four datasets RS90, DB433, LI1264 and SP1577 were used to develop the SVM models. These four SVM models developed were tested using three different benchmarking tests namely; (i) self consistency, (ii) seven fold cross validation test and (iii) independent case test. The maximum possible prediction accuracy of ~70% was observed in self consistency test for the SVM models of both LI1264 and SP1577 datasets, where PSSM+SS(DSSP) input features was used to test. The prediction accuracies were reduced to ~53% for PSSM+SS(NPS@) and ~43% for PSSM+SS(GOR4) in independent case test, for the SVM models of above two same datasets. Using our method, it is possible to predict the protein block letters for any query protein sequence with ~53% accuracy, when the SP1577 dataset and predicted secondary structure from NPS@ server were used. The SVM-PB-Pred server can be freely accessed through http://bioinfo.bdu.ac.in/~svmpbpred.

  8. SVM-Based CAC System for B-Mode Kidney Ultrasound Images.

    Subramanya, M B; Kumar, Vinod; Mukherjee, Shaktidev; Saini, Manju

    2015-08-01

    The present study proposes a computer-aided classification (CAC) system for three kidney classes, viz. normal, medical renal disease (MRD) and cyst using B-mode ultrasound images. Thirty-five B-mode kidney ultrasound images consisting of 11 normal images, 8 MRD images and 16 cyst images have been used. Regions of interest (ROIs) have been marked by the radiologist from the parenchyma region of the kidney in case of normal and MRD cases and from regions inside lesions for cyst cases. To evaluate the contribution of texture features extracted from de-speckled images for the classification task, original images have been pre-processed by eight de-speckling methods. Six categories of texture features are extracted. One-against-one multi-class support vector machine (SVM) classifier has been used for the present work. Based on overall classification accuracy (OCA), features from ROIs of original images are concatenated with the features from ROIs of pre-processed images. On the basis of OCA, few feature sets are considered for feature selection. Differential evolution feature selection (DEFS) has been used to select optimal features for the classification task. DEFS process is repeated 30 times to obtain 30 subsets. Run-length matrix features from ROIs of images pre-processed by Lee's sigma concatenated with that of enhanced Lee method have resulted in an average accuracy (in %) and standard deviation of 86.3 ± 1.6. The results obtained in the study indicate that the performance of the proposed CAC system is promising, and it can be used by the radiologists in routine clinical practice for the classification of renal diseases.

  9. SVM-based synthetic fingerprint discrimination algorithm and quantitative optimization strategy.

    Suhang Chen

    Full Text Available Synthetic fingerprints are a potential threat to automatic fingerprint identification systems (AFISs. In this paper, we propose an algorithm to discriminate synthetic fingerprints from real ones. First, four typical characteristic factors-the ridge distance features, global gray features, frequency feature and Harris Corner feature-are extracted. Then, a support vector machine (SVM is used to distinguish synthetic fingerprints from real fingerprints. The experiments demonstrate that this method can achieve a recognition accuracy rate of over 98% for two discrete synthetic fingerprint databases as well as a mixed database. Furthermore, a performance factor that can evaluate the SVM's accuracy and efficiency is presented, and a quantitative optimization strategy is established for the first time. After the optimization of our synthetic fingerprint discrimination task, the polynomial kernel with a training sample proportion of 5% is the optimized value when the minimum accuracy requirement is 95%. The radial basis function (RBF kernel with a training sample proportion of 15% is a more suitable choice when the minimum accuracy requirement is 98%.

  10. SVM-based synthetic fingerprint discrimination algorithm and quantitative optimization strategy.

    Chen, Suhang; Chang, Sheng; Huang, Qijun; He, Jin; Wang, Hao; Huang, Qiangui

    2014-01-01

    Synthetic fingerprints are a potential threat to automatic fingerprint identification systems (AFISs). In this paper, we propose an algorithm to discriminate synthetic fingerprints from real ones. First, four typical characteristic factors-the ridge distance features, global gray features, frequency feature and Harris Corner feature-are extracted. Then, a support vector machine (SVM) is used to distinguish synthetic fingerprints from real fingerprints. The experiments demonstrate that this method can achieve a recognition accuracy rate of over 98% for two discrete synthetic fingerprint databases as well as a mixed database. Furthermore, a performance factor that can evaluate the SVM's accuracy and efficiency is presented, and a quantitative optimization strategy is established for the first time. After the optimization of our synthetic fingerprint discrimination task, the polynomial kernel with a training sample proportion of 5% is the optimized value when the minimum accuracy requirement is 95%. The radial basis function (RBF) kernel with a training sample proportion of 15% is a more suitable choice when the minimum accuracy requirement is 98%.

  11. Feature Selection By KDDA For SVM-Based MultiView Face Recognition

    Valiollahzadeh, Seyyed Majid; Nazari, Mohammad

    2008-01-01

    Applications such as face recognition that deal with high-dimensional data need a mapping technique that introduces representation of low-dimensional features with enhanced discriminatory power and a proper classifier, able to classify those complex features. Most of traditional Linear Discriminant Analysis suffer from the disadvantage that their optimality criteria are not directly related to the classification ability of the obtained feature representation. Moreover, their classification accuracy is affected by the "small sample size" problem which is often encountered in FR tasks. In this short paper, we combine nonlinear kernel based mapping of data called KDDA with Support Vector machine classifier to deal with both of the shortcomings in an efficient and cost effective manner. The proposed here method is compared, in terms of classification accuracy, to other commonly used FR methods on UMIST face database. Results indicate that the performance of the proposed method is overall superior to those of trad...

  12. [Application of optimized parameters SVM based on photoacoustic spectroscopy method in fault diagnosis of power transformer].

    Zhang, Yu-xin; Cheng, Zhi-feng; Xu, Zheng-ping; Bai, Jing

    2015-01-01

    In order to solve the problems such as complex operation, consumption for the carrier gas and long test period in traditional power transformer fault diagnosis approach based on dissolved gas analysis (DGA), this paper proposes a new method which is detecting 5 types of characteristic gas content in transformer oil such as CH4, C2H2, C2H4, C2H6 and H2 based on photoacoustic Spectroscopy and C2H2/C2H4, CH4/H2, C2H4/C2H6 three-ratios data are calculated. The support vector machine model was constructed using cross validation method under five support vector machine functions and four kernel functions, heuristic algorithms were used in parameter optimization for penalty factor c and g, which to establish the best SVM model for the highest fault diagnosis accuracy and the fast computing speed. Particles swarm optimization and genetic algorithm two types of heuristic algorithms were comparative studied in this paper for accuracy and speed in optimization. The simulation result shows that SVM model composed of C-SVC, RBF kernel functions and genetic algorithm obtain 97. 5% accuracy in test sample set and 98. 333 3% accuracy in train sample set, and genetic algorithm was about two times faster than particles swarm optimization in computing speed. The methods described in this paper has many advantages such as simple operation, non-contact measurement, no consumption for the carrier gas, long test period, high stability and sensitivity, the result shows that the methods described in this paper can instead of the traditional transformer fault diagnosis by gas chromatography and meets the actual project needs in transformer fault diagnosis.

  13. PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif

    Tang, Shengnan; Li, Tonghua; Cong, Peisheng; Xiong, Wenwei; Wang, Zhiheng; Sun, Jiangming

    2013-01-01

    Knowledge of subcellular localizations (SCLs) of plant proteins relates to their functions and aids in understanding the regulation of biological processes at the cellular level. We present PlantLoc, a highly accurate and fast webserver for predicting the multi-label SCLs of plant proteins. The PlantLoc server has two innovative characters: building localization motif libraries by a recursive method without alignment and Gene Ontology information; and establishing simple architecture for rapi...

  14. Accurate Jones Matrix of the Practical Faraday Rotator

    王林斗; 祝昇翔; 李玉峰; 邢文烈; 魏景芝

    2003-01-01

    The Jones matrix of practical Faraday rotators is often used in the engineering calculation of non-reciprocal optical field. Nevertheless, only the approximate Jones matrix of practical Faraday rotators has been presented by now. Based on the theory of polarized light, this paper presents the accurate Jones matrix of practical Faraday rotators. In addition, an experiment has been carried out to verify the validity of the accurate Jones matrix. This matrix accurately describes the optical characteristics of practical Faraday rotators, including rotation, loss and depolarization of the polarized light. The accurate Jones matrix can be used to obtain the accurate results for the practical Faraday rotator to transform the polarized light, which paves the way for the accurate analysis and calculation of practical Faraday rotators in relevant engineering applications.

  15. Biomimetic Approach for Accurate, Real-Time Aerodynamic Coefficients Project

    National Aeronautics and Space Administration — Aerodynamic and structural reliability and efficiency depends critically on the ability to accurately assess the aerodynamic loads and moments for each lifting...

  16. Speed-of-sound compensated photoacoustic tomography for accurate imaging

    Jose, Jithin; Steenbergen, Wiendelt; Slump, Cornelis H; van Leeuwen, Ton G; Manohar, Srirang

    2012-01-01

    In most photoacoustic (PA) measurements, variations in speed-of-sound (SOS) of the subject are neglected under the assumption of acoustic homogeneity. Biological tissue with spatially heterogeneous SOS cannot be accurately reconstructed under this assumption. We present experimental and image reconstruction methods with which 2-D SOS distributions can be accurately acquired and reconstructed, and with which the SOS map can be used subsequently to reconstruct highly accurate PA tomograms. We begin with a 2-D iterative reconstruction approach in an ultrasound transmission tomography (UTT) setting, which uses ray refracted paths instead of straight ray paths to recover accurate SOS images of the subject. Subsequently, we use the SOS distribution in a new 2-D iterative approach, where refraction of rays originating from PA sources are accounted for in accurately retrieving the distribution of these sources. Both the SOS reconstruction and SOS-compensated PA reconstruction methods utilize the Eikonal equation to m...

  17. Accurate and reliable cancer classification based on probabilistic inference of pathway activity.

    Junjie Su

    Full Text Available With the advent of high-throughput technologies for measuring genome-wide expression profiles, a large number of methods have been proposed for discovering diagnostic markers that can accurately discriminate between different classes of a disease. However, factors such as the small sample size of typical clinical data, the inherent noise in high-throughput measurements, and the heterogeneity across different samples, often make it difficult to find reliable gene markers. To overcome this problem, several studies have proposed the use of pathway-based markers, instead of individual gene markers, for building the classifier. Given a set of known pathways, these methods estimate the activity level of each pathway by summarizing the expression values of its member genes, and use the pathway activities for classification. It has been shown that pathway-based classifiers typically yield more reliable results compared to traditional gene-based classifiers. In this paper, we propose a new classification method based on probabilistic inference of pathway activities. For a given sample, we compute the log-likelihood ratio between different disease phenotypes based on the expression level of each gene. The activity of a given pathway is then inferred by combining the log-likelihood ratios of the constituent genes. We apply the proposed method to the classification of breast cancer metastasis, and show that it achieves higher accuracy and identifies more reproducible pathway markers compared to several existing pathway activity inference methods.

  18. Realization of Quadrature Signal Generator Using Accurate Magnitude Integrator

    Xin, Zhen; Yoon, Changwoo; Zhao, Rende

    2016-01-01

    -signal parameters, espically when a fast resonse is required for usages such as grid synchronization. As a result, the parameters design of the SOGI-QSG becomes complicated. Theoretical analysis shows that it is caused by the inaccurate magnitude-integration characteristic of the SOGI-QSG. To solve this problem......, an Accurate-Magnitude-Integrator based QSG (AMI-QSG) is proposed. The AMI has an accurate magnitude-integration characteristic for the sinusoidal signal, which makes the AMI-QSG possess an accurate First-Order-System (FOS) characteristic in terms of magnitude than the SOGI-QSG. The parameter design process...

  19. Fabricating an Accurate Implant Master Cast: A Technique Report.

    Balshi, Thomas J; Wolfinger, Glenn J; Alfano, Stephen G; Cacovean, Jeannine N; Balshi, Stephen F

    2015-12-01

    The technique for fabricating an accurate implant master cast following the 12-week healing period after Teeth in a Day® dental implant surgery is detailed. The clinical, functional, and esthetic details captured during the final master impression are vital to creating an accurate master cast. This technique uses the properties of the all-acrylic resin interim prosthesis to capture these details. This impression captures the relationship between the remodeled soft tissue and the interim prosthesis. This provides the laboratory technician with an accurate orientation of the implant replicas in the master cast with which a passive fitting restoration can be fabricated.

  20. Highly Accurate Sensor for High-Purity Oxygen Determination Project

    National Aeronautics and Space Administration — In this STTR effort, Los Gatos Research (LGR) and the University of Wisconsin (UW) propose to develop a highly-accurate sensor for high-purity oxygen determination....

  1. Accurate backgrounds to Higgs production at the LHC

    Kauer, N

    2007-01-01

    Corrections of 10-30% for backgrounds to the H --> WW --> l^+l^-\\sla{p}_T search in vector boson and gluon fusion at the LHC are reviewed to make the case for precise and accurate theoretical background predictions.

  2. Multi-objective optimization of inverse planning for accurate radiotherapy

    曹瑞芬; 吴宜灿; 裴曦; 景佳; 李国丽; 程梦云; 李贵; 胡丽琴

    2011-01-01

    The multi-objective optimization of inverse planning based on the Pareto solution set, according to the multi-objective character of inverse planning in accurate radiotherapy, was studied in this paper. Firstly, the clinical requirements of a treatment pl

  3. Controlling Hay Fever Symptoms with Accurate Pollen Counts

    ... counts Share | Controlling Hay Fever Symptoms with Accurate Pollen Counts This article has been reviewed by Thanai ... rhinitis known as hay fever is caused by pollen carried in the air during different times of ...

  4. Digital system accurately controls velocity of electromechanical drive

    Nichols, G. B.

    1965-01-01

    Digital circuit accurately regulates electromechanical drive mechanism velocity. The gain and phase characteristics of digital circuits are relatively unimportant. Control accuracy depends only on the stability of the input signal frequency.

  5. ACCURATE ESTIMATES OF CHARACTERISTIC EXPONENTS FOR SECOND ORDER DIFFERENTIAL EQUATION

    2009-01-01

    In this paper, a second order linear differential equation is considered, and an accurate estimate method of characteristic exponent for it is presented. Finally, we give some examples to verify the feasibility of our result.

  6. Mass spectrometry based protein identification with accurate statistical significance assignment

    Alves, Gelio; Yu, Yi-Kuo

    2014-01-01

    Motivation: Assigning statistical significance accurately has become increasingly important as meta data of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of meta data at any level may propagate to downstream analyses, undermining the validity of scientific conclusions thus drawn. From the perspective of mass spectrometry based proteomics, even though accurate statistics for peptide identification can now be ach...

  7. High-Accurate, Physics-Based Wake Simulation Techniques

    2015-01-27

    physically accurate problem as well as to show that the sensor can account for artificial viscosity where needed but not overload the problem and ”wash out...code) 1/27/2015 Final Technical Report 02/25/10 - 08/31/14 High-Accurate, Physics -Based Wake Simulation Techniques N00014-10-C-0190 Andrew Shelton...code was developed that utilizes the discontinuous Galerkin method to solve the Euler equations while utilizing a modal artificial viscosity sensor

  8. A fluorescence-based quantitative real-time PCR assay for accurate Pocillopora damicornis species identification

    Thomas, Luke; Stat, Michael; Evans, Richard D.; Kennington, W. Jason

    2016-09-01

    Pocillopora damicornis is one of the most extensively studied coral species globally, but high levels of phenotypic plasticity within the genus make species identification based on morphology alone unreliable. As a result, there is a compelling need to develop cheap and time-effective molecular techniques capable of accurately distinguishing P. damicornis from other congeneric species. Here, we develop a fluorescence-based quantitative real-time PCR (qPCR) assay to genotype a single nucleotide polymorphism that accurately distinguishes P. damicornis from other morphologically similar Pocillopora species. We trial the assay across colonies representing multiple Pocillopora species and then apply the assay to screen samples of Pocillopora spp. collected at regional scales along the coastline of Western Australia. This assay offers a cheap and time-effective alternative to Sanger sequencing and has broad applications including studies on gene flow, dispersal, recruitment and physiological thresholds of P. damicornis.

  9. A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

    Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.; Arkin, Adam P.

    2004-12-01

    We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.

  10. Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling

    Boers, Stefan A.; Hays, John P.; Jansen, Ruud

    2017-01-01

    In the last decade, many researchers have embraced 16S rRNA gene sequencing techniques, which has led to a wealth of publications and documented differences in the composition of microbial communities derived from many different ecosystems. However, comparison between different microbiota studies is currently very difficult due to the lack of a standardized 16S rRNA gene sequencing protocol. Here we report on a novel approach employing micelle PCR (micPCR) in combination with an internal calibrator that allows for standardization of microbiota profiles via their absolute abundances. The addition of an internal calibrator allows the researcher to express the resulting operational taxonomic units (OTUs) as a measure of 16S rRNA gene copies by correcting the number of sequences of each individual OTU in a sample for efficiency differences in the NGS process. Additionally, accurate quantification of OTUs obtained from negative extraction control samples allows for the subtraction of contaminating bacterial DNA derived from the laboratory environment or chemicals/reagents used. Using equimolar synthetic microbial community samples and low biomass clinical samples, we demonstrate that the calibrated micPCR/NGS methodology possess a much higher precision and a lower limit of detection compared with traditional PCR/NGS, resulting in more accurate microbiota profiles suitable for multi-study comparison. PMID:28378789

  11. Accurate encoding and decoding by single cells: amplitude versus frequency modulation.

    Gabriele Micali

    2015-06-01

    Full Text Available Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be encoded internally: amplitude modulation (AM, where the absolute concentration of an internal signaling molecule encodes the stimulus, and frequency modulation (FM, where the period between successive bursts represents the stimulus. Although both mechanisms have been observed in biological systems, the question of when it is beneficial for cells to use either AM or FM is largely unanswered. Here, we first consider a simple model for a single receptor (or ion channel, which can either signal continuously whenever a ligand is bound, or produce a burst in signaling molecule upon receptor binding. We find that bursty signaling is more accurate than continuous signaling only for sufficiently fast dynamics. This suggests that modulation based on bursts may be more common in signaling networks than in gene regulation. We then extend our model to multiple receptors, where continuous and bursty signaling are equivalent to AM and FM respectively, finding that AM is always more accurate. This implies that the reason some cells use FM is related to factors other than accuracy, such as the ability to coordinate expression of multiple genes or to implement threshold crossing mechanisms.

  12. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

    Dewey Colin N

    2011-08-01

    Full Text Available Abstract Background RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. Results We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads. On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene. Conclusions RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost

  13. Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory.

    Clune, Jeff; Goldsby, Heather J; Ofria, Charles; Pennock, Robert T

    2011-03-01

    Inclusive fitness theory predicts that natural selection will favour altruist genes that are more accurate in targeting altruism only to copies of themselves. In this paper, we provide evidence from digital evolution in support of this prediction by competing multiple altruist-targeting mechanisms that vary in their accuracy in determining whether a potential target for altruism carries a copy of the altruist gene. We compete altruism-targeting mechanisms based on (i) kinship (kin targeting), (ii) genetic similarity at a level greater than that expected of kin (similarity targeting), and (iii) perfect knowledge of the presence of an altruist gene (green beard targeting). Natural selection always favoured the most accurate targeting mechanism available. Our investigations also revealed that evolution did not increase the altruism level when all green beard altruists used the same phenotypic marker. The green beard altruism levels stably increased only when mutations that changed the altruism level also changed the marker (e.g. beard colour), such that beard colour reliably indicated the altruism level. For kin- and similarity-targeting mechanisms, we found that evolution was able to stably adjust altruism levels. Our results confirm that natural selection favours altruist genes that are increasingly accurate in targeting altruism to only their copies. Our work also emphasizes that the concept of targeting accuracy must include both the presence of an altruist gene and the level of altruism it produces.

  14. A novel PCR-based approach for accurate identification of Vibrio parahaemolyticus

    Ruichao eLi

    2016-01-01

    Full Text Available A PCR-based assay was developed for more accurate identification of Vibrio parahaemolyticus through targeting the blaCARB-17 like element, an intrinsic β-lactamase gene that may also be regarded as a novel species-specific genetic marker of this organism. Phylogenetic analysis showed that blaCARB-17 like genes were more conservative than the tlh, toxR and atpA genes, the genetic markers commonly used as detection targets in identification of V. parahaemolyticus. Our data showed that this blaCARB-17-specific PCR-based detection approach consistently achieved 100% specificity, whereas PCR targeting the tlh, toxR and atpA genes occasionally produced false positive results. Furthermore, a positive result of this test is consistently associated with an intrinsic ampicillin resistance phenotype of the test organism, presumably conferred by the products of blaCARB-17 like genes. We envision that combined analysis of the unique genetic and phenotypic characteristics conferred by blaCARB-17 shall further enhance the detection specificity of this novel yet easy-to-use detection approach to a level superior to the conventional methods used in V. parahaemolyticus detection and identification.

  15. A Novel PCR-Based Approach for Accurate Identification of Vibrio parahaemolyticus.

    Li, Ruichao; Chiou, Jiachi; Chan, Edward Wai-Chi; Chen, Sheng

    2016-01-01

    A PCR-based assay was developed for more accurate identification of Vibrio parahaemolyticus through targeting the bla CARB-17 like element, an intrinsic β-lactamase gene that may also be regarded as a novel species-specific genetic marker of this organism. Homologous analysis showed that bla CARB-17 like genes were more conservative than the tlh, toxR and atpA genes, the genetic markers commonly used as detection targets in identification of V. parahaemolyticus. Our data showed that this bla CARB-17-specific PCR-based detection approach consistently achieved 100% specificity, whereas PCR targeting the tlh and atpA genes occasionally produced false positive results. Furthermore, a positive result of this test is consistently associated with an intrinsic ampicillin resistance phenotype of the test organism, presumably conferred by the products of bla CARB-17 like genes. We envision that combined analysis of the unique genetic and phenotypic characteristics conferred by bla CARB-17 shall further enhance the detection specificity of this novel yet easy-to-use detection approach to a level superior to the conventional methods used in V. parahaemolyticus detection and identification.

  16. UP-TORR: online tool for accurate and Up-to-Date annotation of RNAi Reagents.

    Hu, Yanhui; Roesel, Charles; Flockhart, Ian; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E

    2013-09-01

    RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene. In practice, however, the reagent-gene relationship is complex. Although the sequences of oligonucleotides used to generate most types of RNAi reagents are static, the reference genome and gene annotations are regularly updated. Thus, at the time a researcher chooses an RNAi reagent or analyzes RNAi data, the most current interpretation of the RNAi reagent-gene relationship, as well as related information regarding specificity (e.g., predicted off-target effects), can be different from the original interpretation. Here, we describe a set of strategies and an accompanying online tool, UP-TORR (for Updated Targets of RNAi Reagents; www.flyrnai.org/up-torr), useful for accurate and up-to-date annotation of cell-based and in vivo RNAi reagents. Importantly, UP-TORR automatically synchronizes with gene annotations daily, retrieving the most current information available, and for Drosophila, also synchronizes with the major reagent collections. Thus, UP-TORR allows users to choose the most appropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies.

  17. Nonexposure Accurate Location K-Anonymity Algorithm in LBS

    Jinying Jia

    2014-01-01

    Full Text Available This paper tackles location privacy protection in current location-based services (LBS where mobile users have to report their exact location information to an LBS provider in order to obtain their desired services. Location cloaking has been proposed and well studied to protect user privacy. It blurs the user’s accurate coordinate and replaces it with a well-shaped cloaked region. However, to obtain such an anonymous spatial region (ASR, nearly all existent cloaking algorithms require knowing the accurate locations of all users. Therefore, location cloaking without exposing the user’s accurate location to any party is urgently needed. In this paper, we present such two nonexposure accurate location cloaking algorithms. They are designed for K-anonymity, and cloaking is performed based on the identifications (IDs of the grid areas which were reported by all the users, instead of directly on their accurate coordinates. Experimental results show that our algorithms are more secure than the existent cloaking algorithms, need not have all the users reporting their locations all the time, and can generate smaller ASR.

  18. Nonexposure accurate location K-anonymity algorithm in LBS.

    Jia, Jinying; Zhang, Fengli

    2014-01-01

    This paper tackles location privacy protection in current location-based services (LBS) where mobile users have to report their exact location information to an LBS provider in order to obtain their desired services. Location cloaking has been proposed and well studied to protect user privacy. It blurs the user's accurate coordinate and replaces it with a well-shaped cloaked region. However, to obtain such an anonymous spatial region (ASR), nearly all existent cloaking algorithms require knowing the accurate locations of all users. Therefore, location cloaking without exposing the user's accurate location to any party is urgently needed. In this paper, we present such two nonexposure accurate location cloaking algorithms. They are designed for K-anonymity, and cloaking is performed based on the identifications (IDs) of the grid areas which were reported by all the users, instead of directly on their accurate coordinates. Experimental results show that our algorithms are more secure than the existent cloaking algorithms, need not have all the users reporting their locations all the time, and can generate smaller ASR.

  19. Simple and accurate analytical calculation of shortest path lengths

    Melnik, Sergey

    2016-01-01

    We present an analytical approach to calculating the distribution of shortest paths lengths (also called intervertex distances, or geodesic paths) between nodes in unweighted undirected networks. We obtain very accurate results for synthetic random networks with specified degree distribution (the so-called configuration model networks). Our method allows us to accurately predict the distribution of shortest path lengths on real-world networks using their degree distribution, or joint degree-degree distribution. Compared to some other methods, our approach is simpler and yields more accurate results. In order to obtain the analytical results, we use the analogy between an infection reaching a node in $n$ discrete time steps (i.e., as in the susceptible-infected epidemic model) and that node being at a distance $n$ from the source of the infection.

  20. Accurate level set method for simulations of liquid atomization☆

    Changxiao Shao; Kun Luo; Jianshan Yang; Song Chen; Jianren Fan

    2015-01-01

    Computational fluid dynamics is an efficient numerical approach for spray atomization study, but it is chal enging to accurately capture the gas–liquid interface. In this work, an accurate conservative level set method is intro-duced to accurately track the gas–liquid interfaces in liquid atomization. To validate the capability of this method, binary drop collision and drop impacting on liquid film are investigated. The results are in good agreement with experiment observations. In addition, primary atomization (swirling sheet atomization) is studied using this method. To the swirling sheet atomization, it is found that Rayleigh–Taylor instability in the azimuthal direction causes the primary breakup of liquid sheet and complex vortex structures are clustered around the rim of the liq-uid sheet. The effects of central gas velocity and liquid–gas density ratio on atomization are also investigated. This work lays a solid foundation for further studying the mechanism of spray atomization.

  1. Memory conformity affects inaccurate memories more than accurate memories.

    Wright, Daniel B; Villalba, Daniella K

    2012-01-01

    After controlling for initial confidence, inaccurate memories were shown to be more easily distorted than accurate memories. In two experiments groups of participants viewed 50 stimuli and were then presented with these stimuli plus 50 fillers. During this test phase participants reported their confidence that each stimulus was originally shown. This was followed by computer-generated responses from a bogus participant. After being exposed to this response participants again rated the confidence of their memory. The computer-generated responses systematically distorted participants' responses. Memory distortion depended on initial memory confidence, with uncertain memories being more malleable than confident memories. This effect was moderated by whether the participant's memory was initially accurate or inaccurate. Inaccurate memories were more malleable than accurate memories. The data were consistent with a model describing two types of memory (i.e., recollective and non-recollective memories), which differ in how susceptible these memories are to memory distortion.

  2. Accurate nuclear radii and binding energies from a chiral interaction

    Ekstrom, A; Wendt, K A; Hagen, G; Papenbrock, T; Carlsson, B D; Forssen, C; Hjorth-Jensen, M; Navratil, P; Nazarewicz, W

    2015-01-01

    The accurate reproduction of nuclear radii and binding energies is a long-standing challenge in nuclear theory. To address this problem two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective 3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

  3. Accurate Fiber Length Measurement Using Time-of-Flight Technique

    Terra, Osama; Hussein, Hatem

    2016-06-01

    Fiber artifacts of very well-measured length are required for the calibration of optical time domain reflectometers (OTDR). In this paper accurate length measurement of different fiber lengths using the time-of-flight technique is performed. A setup is proposed to measure accurately lengths from 1 to 40 km at 1,550 and 1,310 nm using high-speed electro-optic modulator and photodetector. This setup offers traceability to the SI unit of time, the second (and hence to meter by definition), by locking the time interval counter to the Global Positioning System (GPS)-disciplined quartz oscillator. Additionally, the length of a recirculating loop artifact is measured and compared with the measurement made for the same fiber by the National Physical Laboratory of United Kingdom (NPL). Finally, a method is proposed to relatively correct the fiber refractive index to allow accurate fiber length measurement.

  4. Highly Accurate Measurement of the Electron Orbital Magnetic Moment

    Awobode, A M

    2015-01-01

    We propose to accurately determine the orbital magnetic moment of the electron by measuring, in a Magneto-Optical or Ion trap, the ratio of the Lande g-factors in two atomic states. From the measurement of (gJ1/gJ2), the quantity A, which depends on the corrections to the electron g-factors can be extracted, if the states are LS coupled. Given that highly accurate values of the correction to the spin g-factor are currently available, accurate values of the correction to the orbital g-factor may also be determined. At present, (-1.8 +/- 0.4) x 10-4 has been determined as a correction to the electron orbital g-factor, by using earlier measurements of the ratio gJ1/gJ2, made on the Indium 2P1/2 and 2P3/2 states.

  5. Extracting Time-Accurate Acceleration Vectors From Nontrivial Accelerometer Arrangements.

    Franck, Jennifer A; Blume, Janet; Crisco, Joseph J; Franck, Christian

    2015-09-01

    Sports-related concussions are of significant concern in many impact sports, and their detection relies on accurate measurements of the head kinematics during impact. Among the most prevalent recording technologies are videography, and more recently, the use of single-axis accelerometers mounted in a helmet, such as the HIT system. Successful extraction of the linear and angular impact accelerations depends on an accurate analysis methodology governed by the equations of motion. Current algorithms are able to estimate the magnitude of acceleration and hit location, but make assumptions about the hit orientation and are often limited in the position and/or orientation of the accelerometers. The newly formulated algorithm presented in this manuscript accurately extracts the full linear and rotational acceleration vectors from a broad arrangement of six single-axis accelerometers directly from the governing set of kinematic equations. The new formulation linearizes the nonlinear centripetal acceleration term with a finite-difference approximation and provides a fast and accurate solution for all six components of acceleration over long time periods (>250 ms). The approximation of the nonlinear centripetal acceleration term provides an accurate computation of the rotational velocity as a function of time and allows for reconstruction of a multiple-impact signal. Furthermore, the algorithm determines the impact location and orientation and can distinguish between glancing, high rotational velocity impacts, or direct impacts through the center of mass. Results are shown for ten simulated impact locations on a headform geometry computed with three different accelerometer configurations in varying degrees of signal noise. Since the algorithm does not require simplifications of the actual impacted geometry, the impact vector, or a specific arrangement of accelerometer orientations, it can be easily applied to many impact investigations in which accurate kinematics need to

  6. Accurate torque-speed performance prediction for brushless dc motors

    Gipper, Patrick D.

    Desirable characteristics of the brushless dc motor (BLDCM) have resulted in their application for electrohydrostatic (EH) and electromechanical (EM) actuation systems. But to effectively apply the BLDCM requires accurate prediction of performance. The minimum necessary performance characteristics are motor torque versus speed, peak and average supply current and efficiency. BLDCM nonlinear simulation software specifically adapted for torque-speed prediction is presented. The capability of the software to quickly and accurately predict performance has been verified on fractional to integral HP motor sizes, and is presented. Additionally, the capability of torque-speed prediction with commutation angle advance is demonstrated.

  7. Method of accurate grinding for single enveloping TI worm

    SUN; Yuehai; ZHENG; Huijiang; BI; Qingzhen; WANG; Shuren

    2005-01-01

    TI worm drive consists of involute helical gear and its enveloping Hourglass worm. Accurate grinding for TI worm is the key manufacture technology for TI worm gearing being popularized and applied. According to the theory of gear mesh, the equations of tooth surface of worm drive are gained, and the equation of the axial section profile of grinding wheel that can accurately grind TI worm is extracted. Simultaneously,the relation of position and motion between TI worm and grinding wheel are expounded.The method for precisely grinding single enveloping TI worm is obtained.

  8. Accurate analysis of planar metamaterials using the RLC theory

    Malureanu, Radu; Lavrinenko, Andrei

    2008-01-01

    In this work we will present an accurate description of metallic pads response using RLC theory. In order to calculate such response we take into account several factors including the mutual inductances, precise formula for determining the capacitance and also the pads’ resistance considering...... the variation of permittivity due to small thicknesses. Even if complex, such strategy gives accurate results and we believe that, after more refinement, can be used to completely calculate a complex metallic structure placed on a substrate in a far faster manner than full simulations programs do....

  9. ArrayExplorer, a program in Visual Basic for robust and accurate filter cDNA array analysis.

    Patriotis, P C; Querec, T D; Gruver, B N; Brown, T R; Patriotis, C

    2001-10-01

    Determining the dynamics in the global regulation of gene expression holds the promise of bringing a better understanding of the processes that govern physiological cell growth regulation and its disruption during the development of disease. The advent for cDNA arrays has created the possibility for the parallel analysis of expression of thousands of genes in a given cell population, simultaneously. The level of expression of a given set of genes within the studied tissue corresponds to the intensity of a labeled cDNA probe synthesized from the studied tissue RNA and bound specifically to the cDNAs of the genes spotted on the array. The accurate extraction of gene expression intensity values is essential for further data analysis and the interpretation of the obtained results. Here, we describe a new array image-processing software developed in Microsoft Visual Basic, the ArrayExplorer, which provides a user-friendly, multiple-window interface and a number of automatic and manual features that facilitate a reliable, robust, and accurate extraction of gene intensity values from filter-array images.

  10. A powerful test of independent assortment that determines genome-wide significance quickly and accurately.

    Stewart, W C L; Hager, V R

    2016-08-01

    In the analysis of DNA sequences on related individuals, most methods strive to incorporate as much information as possible, with little or no attention paid to the issue of statistical significance. For example, a modern workstation can easily handle the computations needed to perform a large-scale genome-wide inheritance-by-descent (IBD) scan, but accurate assessment of the significance of that scan is often hindered by inaccurate approximations and computationally intensive simulation. To address these issues, we developed gLOD-a test of co-segregation that, for large samples, models chromosome-specific IBD statistics as a collection of stationary Gaussian processes. With this simple model, the parametric bootstrap yields an accurate and rapid assessment of significance-the genome-wide corrected P-value. Furthermore, we show that (i) under the null hypothesis, the limiting distribution of the gLOD is the standard Gumbel distribution; (ii) our parametric bootstrap simulator is approximately 40 000 times faster than gene-dropping methods, and it is more powerful than methods that approximate the adjusted P-value; and, (iii) the gLOD has the same statistical power as the widely used maximum Kong and Cox LOD. Thus, our approach gives researchers the ability to determine quickly and accurately the significance of most large-scale IBD scans, which may contain multiple traits, thousands of families and tens of thousands of DNA sequences.

  11. Modeling Battery Behavior for Accurate State-of-Charge Indication

    Pop, V.; Bergveld, H.J.; Veld, op het J.H.G.; Regtien, P.P.L.; Danilov, D.; Notten, P.H.L.

    2006-01-01

    Li-ion is the most commonly used battery chemistry in portable applications nowadays. Accurate state-of-charge (SOC) and remaining run-time indication for portable devices is important for the user's convenience and to prolong the lifetime of batteries. A new SOC indication system, combining the ele

  12. Accurate and Simple Calibration of DLP Projector Systems

    Wilm, Jakob; Olesen, Oline Vinter; Larsen, Rasmus

    2014-01-01

    Much work has been devoted to the calibration of optical cameras, and accurate and simple methods are now available which require only a small number of calibration targets. The problem of obtaining these parameters for light projectors has not been studied as extensively and most current methods...

  13. Speed-of-sound compensated photoacoustic tomography for accurate imaging

    Jose, J.; Willemink, G.H.; Steenbergen, W.; Leeuwen, van A.G.J.M.; Manohar, S.

    2012-01-01

    Purpose: In most photoacoustic (PA) tomographic reconstructions, variations in speed-of-sound (SOS) of the subject are neglected under the assumption of acoustic homogeneity. Biological tissue with spatially heterogeneous SOS cannot be accurately reconstructed under this assumption. The authors pres

  14. BIOACCESSIBILITY TESTS ACCURATELY ESTIMATE BIOAVAILABILITY OF LEAD TO QUAIL

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contami...

  15. Accurate segmentation of dense nanoparticles by partially discrete electron tomography

    Roelandts, T., E-mail: tom.roelandts@ua.ac.be [IBBT-Vision Lab University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Batenburg, K.J. [IBBT-Vision Lab University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Centrum Wiskunde and Informatica, Science Park 123, 1098 XG Amsterdam (Netherlands); Biermans, E. [EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Kuebel, C. [Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Bals, S. [EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Sijbers, J. [IBBT-Vision Lab University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium)

    2012-03-15

    Accurate segmentation of nanoparticles within various matrix materials is a difficult problem in electron tomography. Due to artifacts related to image series acquisition and reconstruction, global thresholding of reconstructions computed by established algorithms, such as weighted backprojection or SIRT, may result in unreliable and subjective segmentations. In this paper, we introduce the Partially Discrete Algebraic Reconstruction Technique (PDART) for computing accurate segmentations of dense nanoparticles of constant composition. The particles are segmented directly by the reconstruction algorithm, while the surrounding regions are reconstructed using continuously varying gray levels. As no properties are assumed for the other compositions of the sample, the technique can be applied to any sample where dense nanoparticles must be segmented, regardless of the surrounding compositions. For both experimental and simulated data, it is shown that PDART yields significantly more accurate segmentations than those obtained by optimal global thresholding of the SIRT reconstruction. -- Highlights: Black-Right-Pointing-Pointer We present a novel reconstruction method for partially discrete electron tomography. Black-Right-Pointing-Pointer It accurately segments dense nanoparticles directly during reconstruction. Black-Right-Pointing-Pointer The gray level to use for the nanoparticles is determined objectively. Black-Right-Pointing-Pointer The method expands the set of samples for which discrete tomography can be applied.

  16. A Simple and Accurate Method for Measuring Enzyme Activity.

    Yip, Din-Yan

    1997-01-01

    Presents methods commonly used for investigating enzyme activity using catalase and presents a new method for measuring catalase activity that is more reliable and accurate. Provides results that are readily reproduced and quantified. Can also be used for investigations of enzyme properties such as the effects of temperature, pH, inhibitors,…

  17. Quantifying Accurate Calorie Estimation Using the "Think Aloud" Method

    Holmstrup, Michael E.; Stearns-Bruening, Kay; Rozelle, Jeffrey

    2013-01-01

    Objective: Clients often have limited time in a nutrition education setting. An improved understanding of the strategies used to accurately estimate calories may help to identify areas of focused instruction to improve nutrition knowledge. Methods: A "Think Aloud" exercise was recorded during the estimation of calories in a standard dinner meal…

  18. $H_{2}^{+}$ ion in strong magnetic field an accurate calculation

    López, J C; Turbiner, A V

    1997-01-01

    Using a unique trial function we perform an accurate calculation of the ground state $1\\sigma_g$ of the hydrogenic molecular ion $H^+_2$ in a constant uniform magnetic field ranging $0-10^{13}$ G. We show that this trial function also makes it possible to study the negative parity ground state $1\\sigma_u$.

  19. Fast, Accurate and Detailed NoC Simulations

    Wolkotte, P.T.; Hölzenspies, P.K.F.; Smit, G.J.M.; Kellenberger, P.

    2007-01-01

    Network-on-Chip (NoC) architectures have a wide variety of parameters that can be adapted to the designer's requirements. Fast exploration of this parameter space is only possible at a high-level and several methods have been proposed. Cycle and bit accurate simulation is necessary when the actual r

  20. Accurate Period Approximation for Any Simple Pendulum Amplitude

    XUE De-Sheng; ZHOU Zhao; GAO Mei-Zhen

    2012-01-01

    Accurate approximate analytical formulae of the pendulum period composed of a few elementary functions for any amplitude are constructed.Based on an approximation of the elliptic integral,two new logarithmic formulae for large amplitude close to 180° are obtained.Considering the trigonometric function modulation results from the dependence of relative error on the amplitude,we realize accurate approximation period expressions for any amplitude between 0 and 180°.A relative error less than 0.02% is achieved for any amplitude.This kind of modulation is also effective for other large-amplitude logarithmic approximation expressions.%Accurate approximate analytical formulae of the pendulum period composed of a few elementary functions for any amplitude are constructed. Based on an approximation of the elliptic integral, two new logarithmic formulae for large amplitude close to 180° are obtained. Considering the trigonometric function modulation results from the dependence of relative error on the amplitude, we realize accurate approximation period expressions for any amplitude between 0 and 180°. A relative error less than 0.02% is achieved for any amplitude. This kind of modulation is also effective for other large-amplitude logarithmic approximation expressions.

  1. On accurate boundary conditions for a shape sensitivity equation method

    Duvigneau, R.; Pelletier, D.

    2006-01-01

    This paper studies the application of the continuous sensitivity equation method (CSEM) for the Navier-Stokes equations in the particular case of shape parameters. Boundary conditions for shape parameters involve flow derivatives at the boundary. Thus, accurate flow gradients are critical to the success of the CSEM. A new approach is presented to extract accurate flow derivatives at the boundary. High order Taylor series expansions are used on layered patches in conjunction with a constrained least-squares procedure to evaluate accurate first and second derivatives of the flow variables at the boundary, required for Dirichlet and Neumann sensitivity boundary conditions. The flow and sensitivity fields are solved using an adaptive finite-element method. The proposed methodology is first verified on a problem with a closed form solution obtained by the Method of Manufactured Solutions. The ability of the proposed method to provide accurate sensitivity fields for realistic problems is then demonstrated. The flow and sensitivity fields for a NACA 0012 airfoil are used for fast evaluation of the nearby flow over an airfoil of different thickness (NACA 0015).

  2. A Self-Instructional Device for Conditioning Accurate Prosody.

    Buiten, Roger; Lane, Harlan

    1965-01-01

    A self-instructional device for conditioning accurate prosody in second-language learning is described in this article. The Speech Auto-Instructional Device (SAID) is electro-mechanical and performs three functions: SAID (1) presents to the student tape-recorded pattern sentences that are considered standards in prosodic performance; (2) processes…

  3. Practical schemes for accurate forces in quantum Monte Carlo

    Moroni, S.; Saccani, S.; Filippi, C.

    2014-01-01

    While the computation of interatomic forces has become a well-established practice within variational Monte Carlo (VMC), the use of the more accurate Fixed-Node Diffusion Monte Carlo (DMC) method is still largely limited to the computation of total energies on structures obtained at a lower level of

  4. Bioaccessibility tests accurately estimate bioavailability of lead to quail

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb, we incorporated Pb-contaminated soils or Pb acetate into diets for Japanese quail (Coturnix japonica), fed the quail for 15 days, and ...

  5. On the importance of having accurate data for astrophysical modelling

    Lique, Francois

    2016-06-01

    The Herschel telescope and the ALMA and NOEMA interferometers have opened new windows of observation for wavelengths ranging from far infrared to sub-millimeter with spatial and spectral resolutions previously unmatched. To make the most of these observations, an accurate knowledge of the physical and chemical processes occurring in the interstellar and circumstellar media is essential.In this presentation, I will discuss what are the current needs of astrophysics in terms of molecular data and I will show that accurate molecular data are crucial for the proper determination of the physical conditions in molecular clouds.First, I will focus on collisional excitation studies that are needed for molecular lines modelling beyond the Local Thermodynamic Equilibrium (LTE) approach. In particular, I will show how new collisional data for the HCN and HNC isomers, two tracers of star forming conditions, have allowed solving the problem of their respective abundance in cold molecular clouds. I will also present the last collisional data that have been computed in order to analyse new highly resolved observations provided by the ALMA interferometer.Then, I will present the calculation of accurate rate constants for the F+H2 → HF+H and Cl+H2 ↔ HCl+H reactions, which have allowed a more accurate determination of the physical conditions in diffuse molecular clouds. I will also present the recent work on the ortho-para-H2 conversion due to hydrogen exchange that allow more accurate determination of the ortho-to-para-H2 ratio in the universe and that imply a significant revision of the cooling mechanism in astrophysical media.

  6. DNA barcode data accurately assign higher spider taxa

    Jonathan A. Coddington

    2016-07-01

    Full Text Available The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%. Accurate assignment of higher taxa (PIdent above which errors totaled less than 5% occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However

  7. Multimodal Spatial Calibration for Accurately Registering EEG Sensor Positions

    Jianhua Zhang

    2014-01-01

    Full Text Available This paper proposes a fast and accurate calibration method to calibrate multiple multimodal sensors using a novel photogrammetry system for fast localization of EEG sensors. The EEG sensors are placed on human head and multimodal sensors are installed around the head to simultaneously obtain all EEG sensor positions. A multiple views’ calibration process is implemented to obtain the transformations of multiple views. We first develop an efficient local repair algorithm to improve the depth map, and then a special calibration body is designed. Based on them, accurate and robust calibration results can be achieved. We evaluate the proposed method by corners of a chessboard calibration plate. Experimental results demonstrate that the proposed method can achieve good performance, which can be further applied to EEG source localization applications on human brain.

  8. Accurate multireference study of Si3 electronic manifold

    Goncalves, Cayo Emilio Monteiro; Braga, Joao Pedro

    2016-01-01

    Since it has been shown that the silicon trimer has a highly multi-reference character, accurate multi-reference configuration interaction calculations are performed to elucidate its electronic manifold. Emphasis is given to the long range part of the potential, aiming to understand the atom-diatom collisions dynamical aspects, to describe conical intersections and important saddle points along the reactive path. Potential energy surface main features analysis are performed for benchmarking, and highly accurate values for structures, vibrational constants and energy gaps are reported, as well as the unpublished spin-orbit coupling magnitude. The results predict that inter-system crossings will play an important role in dynamical simulations, specially in triplet state quenching, making the problem of constructing a precise potential energy surface more complicated and multi-layer dependent. The ground state is predicted to be the singlet one, but since the singlet-triplet gap is rather small (2.448 kJ/mol) bo...

  9. A fast and accurate method for echocardiography strain rate imaging

    Tavakoli, Vahid; Sahba, Nima; Hajebi, Nima; Nambakhsh, Mohammad Saleh

    2009-02-01

    Recently Strain and strain rate imaging have proved their superiority with respect to classical motion estimation methods in myocardial evaluation as a novel technique for quantitative analysis of myocardial function. Here in this paper, we propose a novel strain rate imaging algorithm using a new optical flow technique which is more rapid and accurate than the previous correlation-based methods. The new method presumes a spatiotemporal constancy of intensity and Magnitude of the image. Moreover the method makes use of the spline moment in a multiresolution approach. Moreover cardiac central point is obtained using a combination of center of mass and endocardial tracking. It is proved that the proposed method helps overcome the intensity variations of ultrasound texture while preserving the ability of motion estimation technique for different motions and orientations. Evaluation is performed on simulated, phantom (a contractile rubber balloon) and real sequences and proves that this technique is more accurate and faster than the previous methods.

  10. Accurate speed and slip measurement of induction motors

    Ho, S.Y.S.; Langman, R. [Tasmania Univ., Hobart, TAS (Australia)

    1996-03-01

    Two alternative hardware circuits, for the accurate measurement of low slip in cage induction motors, are discussed. Both circuits compare the periods of the fundamental of the supply frequency and pulses from a shaft-connected toothed-wheel. The better of the two achieves accuracy to 0.5 percent of slip over the range 0.1 to 0.005, or better than 0.001 percent of speed over the range. This method is considered useful for slip measurement of motors supplied by either constant frequency mains of variable speed controllers with PMW waveforms. It is demonstrated that accurate slip measurement supports the conclusions of work previously done on the detection of broken rotor bars. (author). 1 tab., 6 figs., 13 refs.

  11. Accurate analysis of arbitrarily-shaped helical groove waveguide

    Liu Hong-Tao; Wei Yan-Yu; Gong Yu-Bin; Yue Ling-Na; Wang Wen-Xiang

    2006-01-01

    This paper presents a theory on accurately analysing the dispersion relation and the interaction impedance of electromagnetic waves propagating through a helical groove waveguide with arbitrary groove shape, in which the complex groove profile is synthesized by a series of rectangular steps. By introducing the influence of high-order evanescent modes on the connection of any two neighbouring steps by an equivalent susceptance under a modified admittance matching condition, the assumption of the neglecting discontinuity capacitance in previously published analysis is avoided, and the accurate dispersion equation is obtained by means of a combination of field-matching method and admittancematching technique. The validity of this theory is proved by comparison between the measurements and the numerical calculations for two kinds of helical groove waveguides with different groove shapes.

  12. An Accurate Link Correlation Estimator for Improving Wireless Protocol Performance

    Zhiwei Zhao

    2015-02-01

    Full Text Available Wireless link correlation has shown significant impact on the performance of various sensor network protocols. Many works have been devoted to exploiting link correlation for protocol improvements. However, the effectiveness of these designs heavily relies on the accuracy of link correlation measurement. In this paper, we investigate state-of-the-art link correlation measurement and analyze the limitations of existing works. We then propose a novel lightweight and accurate link correlation estimation (LACE approach based on the reasoning of link correlation formation. LACE combines both long-term and short-term link behaviors for link correlation estimation. We implement LACE as a stand-alone interface in TinyOS and incorporate it into both routing and flooding protocols. Simulation and testbed results show that LACE: (1 achieves more accurate and lightweight link correlation measurements than the state-of-the-art work; and (2 greatly improves the performance of protocols exploiting link correlation.

  13. Accurate measurement of the helical twisting power of chiral dopants

    Kosa, Tamas; Bodnar, Volodymyr; Taheri, Bahman; Palffy-Muhoray, Peter

    2002-03-01

    We propose a method for the accurate determination of the helical twisting power (HTP) of chiral dopants. In the usual Cano-wedge method, the wedge angle is determined from the far-field separation of laser beams reflected from the windows of the test cell. Here we propose to use an optical fiber based spectrometer to accurately measure the cell thickness. Knowing the cell thickness at the positions of the disclination lines allows determination of the HTP. We show that this extension of the Cano-wedge method greatly increases the accuracy with which the HTP is determined. We show the usefulness of this method by determining the HTP of ZLI811 in a variety of hosts with negative dielectric anisotropy.

  14. Efficient and Accurate Robustness Estimation for Large Complex Networks

    Wandelt, Sebastian

    2016-01-01

    Robustness estimation is critical for the design and maintenance of resilient networks, one of the global challenges of the 21st century. Existing studies exploit network metrics to generate attack strategies, which simulate intentional attacks in a network, and compute a metric-induced robustness estimation. While some metrics are easy to compute, e.g. degree centrality, other, more accurate, metrics require considerable computation efforts, e.g. betweennes centrality. We propose a new algorithm for estimating the robustness of a network in sub-quadratic time, i.e., significantly faster than betweenness centrality. Experiments on real-world networks and random networks show that our algorithm estimates the robustness of networks close to or even better than betweenness centrality, while being orders of magnitudes faster. Our work contributes towards scalable, yet accurate methods for robustness estimation of large complex networks.

  15. Accurate parameter estimation for unbalanced three-phase system.

    Chen, Yuan; So, Hing Cheung

    2014-01-01

    Smart grid is an intelligent power generation and control console in modern electricity networks, where the unbalanced three-phase power system is the commonly used model. Here, parameter estimation for this system is addressed. After converting the three-phase waveforms into a pair of orthogonal signals via the α β-transformation, the nonlinear least squares (NLS) estimator is developed for accurately finding the frequency, phase, and voltage parameters. The estimator is realized by the Newton-Raphson scheme, whose global convergence is studied in this paper. Computer simulations show that the mean square error performance of NLS method can attain the Cramér-Rao lower bound. Moreover, our proposal provides more accurate frequency estimation when compared with the complex least mean square (CLMS) and augmented CLMS.

  16. Symmetric Uniformly Accurate Gauss-Runge-Kutta Method

    Dauda G. YAKUBU

    2007-08-01

    Full Text Available Symmetric methods are particularly attractive for solving stiff ordinary differential equations. In this paper by the selection of Gauss-points for both interpolation and collocation, we derive high order symmetric single-step Gauss-Runge-Kutta collocation method for accurate solution of ordinary differential equations. The resulting symmetric method with continuous coefficients is evaluated for the proposed block method for accurate solution of ordinary differential equations. More interestingly, the block method is self-starting with adequate absolute stability interval that is capable of producing simultaneously dense approximation to the solution of ordinary differential equations at a block of points. The use of this method leads to a maximal gain in efficiency as well as in minimal function evaluation per step.

  17. Library preparation for highly accurate population sequencing of RNA viruses

    Acevedo, Ashley; Andino, Raul

    2015-01-01

    Circular resequencing (CirSeq) is a novel technique for efficient and highly accurate next-generation sequencing (NGS) of RNA virus populations. The foundation of this approach is the circularization of fragmented viral RNAs, which are then redundantly encoded into tandem repeats by ‘rolling-circle’ reverse transcription. When sequenced, the redundant copies within each read are aligned to derive a consensus sequence of their initial RNA template. This process yields sequencing data with error rates far below the variant frequencies observed for RNA viruses, facilitating ultra-rare variant detection and accurate measurement of low-frequency variants. Although library preparation takes ~5 d, the high-quality data generated by CirSeq simplifies downstream data analysis, making this approach substantially more tractable for experimentalists. PMID:24967624

  18. FIXED-WING MICRO AERIAL VEHICLE FOR ACCURATE CORRIDOR MAPPING

    M. Rehak

    2015-08-01

    Full Text Available In this study we present a Micro Aerial Vehicle (MAV equipped with precise position and attitude sensors that together with a pre-calibrated camera enables accurate corridor mapping. The design of the platform is based on widely available model components to which we integrate an open-source autopilot, customized mass-market camera and navigation sensors. We adapt the concepts of system calibration from larger mapping platforms to MAV and evaluate them practically for their achievable accuracy. We present case studies for accurate mapping without ground control points: first for a block configuration, later for a narrow corridor. We evaluate the mapping accuracy with respect to checkpoints and digital terrain model. We show that while it is possible to achieve pixel (3-5 cm mapping accuracy in both cases, precise aerial position control is sufficient for block configuration, the precise position and attitude control is required for corridor mapping.

  19. The FLUKA code: An accurate simulation tool for particle therapy

    Battistoni, Giuseppe; Böhlen, Till T; Cerutti, Francesco; Chin, Mary Pik Wai; Dos Santos Augusto, Ricardo M; Ferrari, Alfredo; Garcia Ortega, Pablo; Kozlowska, Wioletta S; Magro, Giuseppe; Mairani, Andrea; Parodi, Katia; Sala, Paola R; Schoofs, Philippe; Tessonnier, Thomas; Vlachoudis, Vasilis

    2016-01-01

    Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models capable of handling all components of the expected radiation field. This becomes extremely important for correctly performing not only physical but also biologically-based dose calculations, especially in cases where ions heavier than protons are involved. In addition, accurate prediction of emerging secondary radiation is of utmost importance in innovative areas of research aiming at in-vivo treatment verification. This contribution will address the recent developments of the FLUKA MC code and its practical applications in this field. Refinements of the FLUKA nuclear models in the therapeutic energy interval lead to an improved description of the mixed radiation field as shown in the presented benchmarks against experimental data with bot...

  20. Novel multi-beam radiometers for accurate ocean surveillance

    Cappellin, C.; Pontoppidan, K.; Nielsen, P. H.

    2014-01-01

    Novel antenna architectures for real aperture multi-beam radiometers providing high resolution and high sensitivity for accurate sea surface temperature (SST) and ocean vector wind (OVW) measurements are investigated. On the basis of the radiometer requirements set for future SST/OVW missions, co......, conical scanners and push-broom antennas are compared. The comparison will cover reflector optics and focal plane array configuration....

  1. Accurate Insertion Loss Measurements of the Juno Patch Array Antennas

    Chamberlain, Neil; Chen, Jacqueline; Hodges, Richard; Demas, John

    2010-01-01

    This paper describes two independent methods for estimating the insertion loss of patch array antennas that were developed for the Juno Microwave Radiometer instrument. One method is based principally on pattern measurements while the other method is based solely on network analyzer measurements. The methods are accurate to within 0.1 dB for the measured antennas and show good agreement (to within 0.1dB) of separate radiometric measurements.

  2. The highly accurate anteriolateral portal for injecting the knee

    Chavez-Chiang Colbert E

    2011-03-01

    Full Text Available Abstract Background The extended knee lateral midpatellar portal for intraarticular injection of the knee is accurate but is not practical for all patients. We hypothesized that a modified anteriolateral portal where the synovial membrane of the medial femoral condyle is the target would be highly accurate and effective for intraarticular injection of the knee. Methods 83 subjects with non-effusive osteoarthritis of the knee were randomized to intraarticular injection using the modified anteriolateral bent knee versus the standard lateral midpatellar portal. After hydrodissection of the synovial membrane with lidocaine using a mechanical syringe (reciprocating procedure device, 80 mg of triamcinolone acetonide were injected into the knee with a 2.0-in (5.1-cm 21-gauge needle. Baseline pain, procedural pain, and pain at outcome (2 weeks and 6 months were determined with the 10 cm Visual Analogue Pain Score (VAS. The accuracy of needle placement was determined by sonographic imaging. Results The lateral midpatellar and anteriolateral portals resulted in equivalent clinical outcomes including procedural pain (VAS midpatellar: 4.6 ± 3.1 cm; anteriolateral: 4.8 ± 3.2 cm; p = 0.77, pain at outcome (VAS midpatellar: 2.6 ± 2.8 cm; anteriolateral: 1.7 ± 2.3 cm; p = 0.11, responders (midpatellar: 45%; anteriolateral: 56%; p = 0.33, duration of therapeutic effect (midpatellar: 3.9 ± 2.4 months; anteriolateral: 4.1 ± 2.2 months; p = 0.69, and time to next procedure (midpatellar: 7.3 ± 3.3 months; anteriolateral: 7.7 ± 3.7 months; p = 0.71. The anteriolateral portal was 97% accurate by real-time ultrasound imaging. Conclusion The modified anteriolateral bent knee portal is an effective, accurate, and equivalent alternative to the standard lateral midpatellar portal for intraarticular injection of the knee. Trial Registration ClinicalTrials.gov: NCT00651625

  3. Ultra accurate collaborative information filtering via directed user similarity

    Guo, Qiang; Song, Wen-Jun; Liu, Jian-Guo

    2014-01-01

    A key challenge of the collaborative filtering (CF) information filtering is how to obtain the reliable and accurate results with the help of peers' recommendation. Since the similarities from small-degree users to large-degree users would be larger than the ones opposite direction, the large-degree users' selections are recommended extensively by the traditional second-order CF algorithms. By considering the users' similarity direction and the second-order correlations to depress the influen...

  4. Accurate quantum state estimation via "Keeping the experimentalist honest"

    Blume-Kohout, R; Blume-Kohout, Robin; Hayden, Patrick

    2006-01-01

    In this article, we derive a unique procedure for quantum state estimation from a simple, self-evident principle: an experimentalist's estimate of the quantum state generated by an apparatus should be constrained by honesty. A skeptical observer should subject the estimate to a test that guarantees that a self-interested experimentalist will report the true state as accurately as possible. We also find a non-asymptotic, operational interpretation of the quantum relative entropy function.

  5. Accurate Method for Determining Adhesion of Cantilever Beams

    Michalske, T.A.; de Boer, M.P.

    1999-01-08

    Using surface micromachined samples, we demonstrate the accurate measurement of cantilever beam adhesion by using test structures which are adhered over long attachment lengths. We show that this configuration has a deep energy well, such that a fracture equilibrium is easily reached. When compared to the commonly used method of determining the shortest attached beam, the present method is much less sensitive to variations in surface topography or to details of capillary drying.

  6. Accurate and Simple Calibration of DLP Projector Systems

    Wilm, Jakob; Olesen, Oline Vinter; Larsen, Rasmus

    2014-01-01

    Much work has been devoted to the calibration of optical cameras, and accurate and simple methods are now available which require only a small number of calibration targets. The problem of obtaining these parameters for light projectors has not been studied as extensively and most current methods require a camera and involve feature extraction from a known projected pattern. In this work we present a novel calibration technique for DLP Projector systems based on phase shifting profilometry pr...

  7. Interactive Isogeometric Volume Visualization with Pixel-Accurate Geometry

    Fuchs, Franz G.; Hjelmervik, Jon M.

    2014-01-01

    A recent development, called isogeometric analysis, provides a unified approach for design, analysis and optimization of functional products in industry. Traditional volume rendering methods for inspecting the results from the numerical simulations cannot be applied directly to isogeometric models. We present a novel approach for interactive visualization of isogeometric analysis results, ensuring correct, i.e., pixel-accurate geometry of the volume including its bounding surfaces. The entire...

  8. A highly accurate method to solve Fisher’s equation

    Mehdi Bastani; Davod Khojasteh Salkuyeh

    2012-03-01

    In this study, we present a new and very accurate numerical method to approximate the Fisher’s-type equations. Firstly, the spatial derivative in the proposed equation is approximated by a sixth-order compact finite difference (CFD6) scheme. Secondly, we solve the obtained system of differential equations using a third-order total variation diminishing Runge–Kutta (TVD-RK3) scheme. Numerical examples are given to illustrate the efficiency of the proposed method.

  9. Accurate genome relative abundance estimation based on shotgun metagenomic reads.

    Li C Xia

    Full Text Available Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates. We have developed a unified probabilistic framework (named GRAMMy by explicitly modeling read assignment ambiguities, genome size biases and read distributions along the genomes. Maximum likelihood method is employed to compute Genome Relative Abundance of microbial communities using the Mixture Model theory (GRAMMy. GRAMMy has been demonstrated to give estimates that are accurate and robust across both simulated and real read benchmark datasets. We applied GRAMMy to a collection of 34 metagenomic read sets from four metagenomics projects and identified 99 frequent species (minimally 0.5% abundant in at least 50% of the data-sets in the human gut samples. Our results show substantial improvements over previous studies, such as adjusting the over-estimated abundance for Bacteroides species for human gut samples, by providing a new reference-based strategy for metagenomic sample comparisons. GRAMMy can be used flexibly with many read assignment tools (mapping, alignment or composition-based even with low-sensitivity mapping results from huge short-read datasets. It will be increasingly useful as an accurate and robust tool for abundance estimation with the growing size of read sets and the expanding database of reference genomes.

  10. Accurate and simple calibration of DLP projector systems

    Wilm, Jakob; Olesen, Oline V.; Larsen, Rasmus

    2014-03-01

    Much work has been devoted to the calibration of optical cameras, and accurate and simple methods are now available which require only a small number of calibration targets. The problem of obtaining these parameters for light projectors has not been studied as extensively and most current methods require a camera and involve feature extraction from a known projected pattern. In this work we present a novel calibration technique for DLP Projector systems based on phase shifting profilometry projection onto a printed calibration target. In contrast to most current methods, the one presented here does not rely on an initial camera calibration, and so does not carry over the error into projector calibration. A radial interpolation scheme is used to convert features coordinates into projector space, thereby allowing for a very accurate procedure. This allows for highly accurate determination of parameters including lens distortion. Our implementation acquires printed planar calibration scenes in less than 1s. This makes our method both fast and convenient. We evaluate our method in terms of reprojection errors and structured light image reconstruction quality.

  11. Accurate thermoelastic tensor and acoustic velocities of NaCl

    Marcondes, Michel L., E-mail: michel@if.usp.br [Physics Institute, University of Sao Paulo, Sao Paulo, 05508-090 (Brazil); Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455 (United States); Shukla, Gaurav, E-mail: shukla@physics.umn.edu [School of Physics and Astronomy, University of Minnesota, Minneapolis, 55455 (United States); Minnesota supercomputer Institute, University of Minnesota, Minneapolis, 55455 (United States); Silveira, Pedro da [Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455 (United States); Wentzcovitch, Renata M., E-mail: wentz002@umn.edu [Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455 (United States); Minnesota supercomputer Institute, University of Minnesota, Minneapolis, 55455 (United States)

    2015-12-15

    Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor by using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.

  12. An accurate metric for the spacetime around neutron stars

    Pappas, George

    2016-01-01

    The problem of having an accurate description of the spacetime around neutron stars is of great astrophysical interest. For astrophysical applications, one needs to have a metric that captures all the properties of the spacetime around a neutron star. Furthermore, an accurate appropriately parameterised metric, i.e., a metric that is given in terms of parameters that are directly related to the physical structure of the neutron star, could be used to solve the inverse problem, which is to infer the properties of the structure of a neutron star from astrophysical observations. In this work we present such an approximate stationary and axisymmetric metric for the exterior of neutron stars, which is constructed using the Ernst formalism and is parameterised by the relativistic multipole moments of the central object. This metric is given in terms of an expansion on the Weyl-Papapetrou coordinates with the multipole moments as free parameters and is shown to be extremely accurate in capturing the physical propert...

  13. [Spectroscopy technique and ruminant methane emissions accurate inspecting].

    Shang, Zhan-Huan; Guo, Xu-Sheng; Long, Rui-Jun

    2009-03-01

    The increase in atmospheric CH4 concentration, on the one hand through the radiation process, will directly cause climate change, and on the other hand, cause a lot of changes in atmospheric chemical processes, indirectly causing climate change. The rapid growth of atmospheric methane has gained attention of governments and scientists. All countries in the world now deal with global climate change as an important task of reducing emissions of greenhouse gases, but the need for monitoring the concentration of methane gas, in particular precision monitoring, can be scientifically formulated to provide a scientific basis for emission reduction measures. So far, CH4 gas emissions of different animal production systems have received extensive research. The methane emission by ruminant reported in the literature is only estimation. This is due to the various factors that affect the methane production in ruminant, there are various variables associated with the techniques for measuring methane production, the techniques currently developed to measure methane are unable to accurately determine the dynamics of methane emission by ruminant, and therefore there is an urgent need to develop an accurate method for this purpose. Currently, spectroscopy technique has been used and is relatively a more accurate and reliable method. Various spectroscopy techniques such as modified infrared spectroscopy methane measuring system, laser and near-infrared sensory system are able to achieve the objective of determining the dynamic methane emission by both domestic and grazing ruminant. Therefore spectroscopy technique is an important methane measuring technique, and contributes to proposing reduction methods of methane.

  14. Gene finding in novel genomes

    Korf Ian

    2004-05-01

    Full Text Available Abstract Background Computational gene prediction continues to be an important problem, especially for genomes with little experimental data. Results I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate. Conclusion Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

  15. Overview of BioCreative II gene normalization

    A.A. Morgan (Alexander); Z. Lu (Zhongbing); S.X. Wang; A.M. Cohen (Aaron); J. Fluck (Juliane); P. Ruch (Patrick); A. Divoli (Anna); K. Fundel (Katrin); R. Leaman (Robert); J. Hakenberg (Jörg); C.W. Sun; H.H. Liu (Hong); R. Torres (Rafael); M. Krauthammer (Michael); W.W. Lau (William); C.N. Hsu; M.J. Schuemie (Martijn); L. Hirschman (Lynette)

    2008-01-01

    textabstractBackground: The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the human expert; genes are often described

  16. A simplified and accurate detection of the genetically modified wheat MON71800 with one calibrator plasmid.

    Kim, Jae-Hwan; Park, Saet-Byul; Roh, Hyo-Jeong; Park, Sunghoon; Shin, Min-Ki; Moon, Gui Im; Hong, Jin-Hwan; Kim, Hae-Yeong

    2015-06-01

    With the increasing number of genetically modified (GM) events, unauthorized GMO releases into the food market have increased dramatically, and many countries have developed detection tools for them. This study described the qualitative and quantitative detection methods of unauthorized the GM wheat MON71800 with a reference plasmid (pGEM-M71800). The wheat acetyl-CoA carboxylase (acc) gene was used as the endogenous gene. The plasmid pGEM-M71800, which contains both the acc gene and the event-specific target MON71800, was constructed as a positive control for the qualitative and quantitative analyses. The limit of detection in the qualitative PCR assay was approximately 10 copies. In the quantitative PCR assay, the standard deviation and relative standard deviation repeatability values ranged from 0.06 to 0.25 and from 0.23% to 1.12%, respectively. This study supplies a powerful and very simple but accurate detection strategy for unauthorized GM wheat MON71800 that utilizes a single calibrator plasmid.

  17. The FLUKA Code: An Accurate Simulation Tool for Particle Therapy.

    Battistoni, Giuseppe; Bauer, Julia; Boehlen, Till T; Cerutti, Francesco; Chin, Mary P W; Dos Santos Augusto, Ricardo; Ferrari, Alfredo; Ortega, Pablo G; Kozłowska, Wioletta; Magro, Giuseppe; Mairani, Andrea; Parodi, Katia; Sala, Paola R; Schoofs, Philippe; Tessonnier, Thomas; Vlachoudis, Vasilis

    2016-01-01

    Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models capable of handling all components of the expected radiation field. This becomes extremely important for correctly performing not only physical but also biologically based dose calculations, especially in cases where ions heavier than protons are involved. In addition, accurate prediction of emerging secondary radiation is of utmost importance in innovative areas of research aiming at in vivo treatment verification. This contribution will address the recent developments of the FLUKA MC code and its practical applications in this field. Refinements of the FLUKA nuclear models in the therapeutic energy interval lead to an improved description of the mixed radiation field as shown in the presented benchmarks against experimental data with both (4)He and (12)C ion beams. Accurate description of ionization energy losses and of particle scattering and interactions lead to the excellent agreement of calculated depth-dose profiles with those measured at leading European hadron therapy centers, both with proton and ion beams. In order to support the application of FLUKA in hospital-based environments, Flair, the FLUKA graphical interface, has been enhanced with the capability of translating CT DICOM images into voxel-based computational phantoms in a fast and well-structured way. The interface is capable of importing also radiotherapy treatment data described in DICOM RT standard. In addition, the interface is equipped with an intuitive PET scanner geometry generator and automatic recording of coincidence events. Clinically, similar cases will be presented both in terms of absorbed dose and biological dose calculations describing the various available features.

  18. Accurate LAI retrieval method based on PROBA/CHRIS data

    W. Fan

    2009-11-01

    Full Text Available Leaf area index (LAI is one of the key structural variables in terrestrial vegetation ecosystems. Remote sensing offers a chance to derive LAI in regional scales accurately. Variations of background, atmospheric conditions and the anisotropy of canopy reflectance are three factors that can strongly restrain the accuracy of retrieved LAI. Based on the hybrid canopy reflectance model, a new hyperspectral directional second derivative method (DSD is proposed in this paper. This method can estimate LAI accurately through analyzing the canopy anisotropy. The effect of the background can also be effectively removed. So the inversion precision and the dynamic range can be improved remarkably, which has been proved by numerical simulations. As the derivative method is very sensitive to the random noise, we put forward an innovative filtering approach, by which the data can be de-noised in spectral and spatial dimensions synchronously. It shows that the filtering method can remove the random noise effectively; therefore, the method can be performed to the remotely sensed hyperspectral image. The study region is situated in Zhangye, Gansu Province, China; the hyperspectral and multi-angular image of the study region has been acquired from Compact High-Resolution Imaging Spectrometer/Project for On-Board Autonomy (CHRIS/PROBA, on 4 and 14 June 2008. After the pre-processing procedures, the DSD method was applied, and the retrieve LAI was validated by the ground truth of 11 sites. It shows that by applying innovative filtering method, the new LAI inversion method is accurate and effective.

  19. Accurate Programming: Thinking about programs in terms of properties

    Walid Taha

    2011-09-01

    Full Text Available Accurate programming is a practical approach to producing high quality programs. It combines ideas from test-automation, test-driven development, agile programming, and other state of the art software development methods. In addition to building on approaches that have proven effective in practice, it emphasizes concepts that help programmers sharpen their understanding of both the problems they are solving and the solutions they come up with. This is achieved by encouraging programmers to think about programs in terms of properties.

  20. Accurate emulators for large-scale computer experiments

    Haaland, Ben; 10.1214/11-AOS929

    2012-01-01

    Large-scale computer experiments are becoming increasingly important in science. A multi-step procedure is introduced to statisticians for modeling such experiments, which builds an accurate interpolator in multiple steps. In practice, the procedure shows substantial improvements in overall accuracy, but its theoretical properties are not well established. We introduce the terms nominal and numeric error and decompose the overall error of an interpolator into nominal and numeric portions. Bounds on the numeric and nominal error are developed to show theoretically that substantial gains in overall accuracy can be attained with the multi-step approach.

  1. Accurate studies on dissociation energies of diatomic molecules

    SUN; WeiGuo; FAN; QunChao

    2007-01-01

    The molecular dissociation energies of some electronic states of hydride and N2 molecules were studied using a parameter-free analytical formula suggested in this study and the algebraic method (AM) proposed recently. The results show that the accurate AM dissociation energies DeAM agree excellently with experimental dissociation energies Deexpt, and that the dissociation energy of an electronic state such as the 23△g state of 7Li2 whose experimental value is not available can be predicted using the new formula.

  2. An Accurate Technique for Calculation of Radiation From Printed Reflectarrays

    Zhou, Min; Sorensen, Stig B.; Jorgensen, Erik

    2011-01-01

    The accuracy of various techniques for calculating the radiation from printed reflectarrays is examined, and an improved technique based on the equivalent currents approach is proposed. The equivalent currents are found from a continuous plane wave spectrum calculated by use of the spectral dyadic...... Green's function. This ensures a correct relation between the equivalent electric and magnetic currents and thus allows an accurate calculation of the radiation over the entire far-field sphere. A comparison to DTU-ESA Facility measurements of a reference offset reflectarray designed and manufactured...

  3. Accurate Excited State Geometries within Reduced Subspace TDDFT/TDA.

    Robinson, David

    2014-12-09

    A method for the calculation of TDDFT/TDA excited state geometries within a reduced subspace of Kohn-Sham orbitals has been implemented and tested. Accurate geometries are found for all of the fluorophore-like molecules tested, with at most all valence occupied orbitals and half of the virtual orbitals included but for some molecules even fewer orbitals. Efficiency gains of between 15 and 30% are found for essentially the same level of accuracy as a standard TDDFT/TDA excited state geometry optimization calculation.

  4. Accurate strand-specific quantification of viral RNA.

    Nicole E Plaskon

    Full Text Available The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR assays are increasingly being used for this purpose, but the accuracy of these assays depends on the assumption that the amount of cDNA measured during the quantitative PCR (qPCR step accurately reflects amounts of a specific viral RNA strand present in the RT reaction. To specifically test this assumption, we developed multiple ssqPCR assays for the positive-strand RNA virus o'nyong-nyong (ONNV that were based upon the most prevalent ssqPCR assay design types in the literature. We then compared various parameters of the ONNV-specific assays. We found that an assay employing standard unmodified virus-specific primers failed to discern the difference between cDNAs generated from virus specific primers and those generated through false priming. Further, we were unable to accurately measure levels of ONNV (- strand RNA with this assay when higher levels of cDNA generated from the (+ strand were present. Taken together, these results suggest that assays of this type do not accurately quantify levels of the anti-genomic strand present during RNA virus infectious cycles. However, an assay permitting the use of a tag-specific primer was able to distinguish cDNAs transcribed from ONNV (- strand RNA from other cDNAs present, thus allowing accurate quantification of the anti-genomic strand. We also report the sensitivities of two different detection strategies and chemistries, SYBR(R Green and DNA hydrolysis probes, used with our tagged ONNV-specific ssqPCR assays. Finally, we describe development, design and validation of ssqPCR assays for chikungunya virus (CHIKV, the recent cause of large outbreaks of disease in the Indian Ocean

  5. Accurate measurement of ultrasonic velocity by eliminating the diffraction effect

    WEI Tingcun

    2003-01-01

    The accurate measurement method of ultrasonic velocity by the pulse interferencemethod with eliminating the diffraction effect has been investigated in VHF range experimen-tally. Two silicate glasses were taken as the specimens, their frequency dependences of longitu-dinal velocities were measured in the frequency range 50-350 MHz, and the phase advances ofultrasonic signals caused by diffraction effect were calculated using A. O. Williams' theoreticalexpression. For the frequency dependences of longitudinal velocities, the measurement resultswere in good agreement with the simulation ones in which the phase advances were included.It has been shown that the velocity error due to diffraction effect can be corrected very well bythis method.

  6. A novel simple and accurate flatness measurement method

    Thang, H L

    2011-01-01

    Flatness measurement of a surface plate is an intensive and old research topic. However ISO definition related and other measurement methods seem uneasy in measuring and/ or complicated in data analysis. Especially in reality, the mentioned methods don't take a clear and straightforward care on the inclining angle which is always included in any given flatness measurement. In this report a novel simple and accurate flatness measurement method was introduced to overcome this prevailing feature in the available methods. The mathematical modeling for this method was also presented making the underlying nature of the method transparent. The applying examples show consistent results.

  7. Fourth order accurate compact scheme with group velocity control (GVC)

    2001-01-01

    For solving complex flow field with multi-scale structure higher order accurate schemes are preferred. Among high order schemes the compact schemes have higher resolving efficiency. When the compact and upwind compact schemes are used to solve aerodynamic problems there are numerical oscillations near the shocks. The reason of oscillation production is because of non-uniform group velocity of wave packets in numerical solutions. For improvement of resolution of the shock a parameter function is introduced in compact scheme to control the group velocity. The newly developed method is simple. It has higher accuracy and less stencil of grid points.

  8. Rapid and Accurate Idea Transfer: Presenting Ideas with Concept Maps

    2008-07-30

    questions from the Pre-test were included in the Post-test. I. At the end of the day, people in the camps take home about __ taka to feed their families. 2...teachers are not paid regularly. Tuition fees for different classes are 40 to 80 taka (Bangladesh currency) 27 per month which is very high for the...October 26, 2002. 27 In April 2005, exchange rate, one $ = 60 taka . 44 Rapid and Accurate Idea Transfer: CDRL (DI-MIS-807 11 A, 00012 1) Presenting

  9. Calibration Techniques for Accurate Measurements by Underwater Camera Systems

    Mark Shortis

    2015-12-01

    Full Text Available Calibration of a camera system is essential to ensure that image measurements result in accurate estimates of locations and dimensions within the object space. In the underwater environment, the calibration must implicitly or explicitly model and compensate for the refractive effects of waterproof housings and the water medium. This paper reviews the different approaches to the calibration of underwater camera systems in theoretical and practical terms. The accuracy, reliability, validation and stability of underwater camera system calibration are also discussed. Samples of results from published reports are provided to demonstrate the range of possible accuracies for the measurements produced by underwater camera systems.

  10. Calibration Techniques for Accurate Measurements by Underwater Camera Systems.

    Shortis, Mark

    2015-12-07

    Calibration of a camera system is essential to ensure that image measurements result in accurate estimates of locations and dimensions within the object space. In the underwater environment, the calibration must implicitly or explicitly model and compensate for the refractive effects of waterproof housings and the water medium. This paper reviews the different approaches to the calibration of underwater camera systems in theoretical and practical terms. The accuracy, reliability, validation and stability of underwater camera system calibration are also discussed. Samples of results from published reports are provided to demonstrate the range of possible accuracies for the measurements produced by underwater camera systems.

  11. Immunoglobulin genes

    Honjo, T. (Kyoto Univ. (Japan)); Alt, F.W. (Columbia Univ., Dobbs Ferry, NY (USA). Hudson Labs.); Rabbitts, T.H. (Medical Research Council, Cambridge (UK))

    1989-01-01

    This book reports on the structure, function, and expression of the genes encoding antibodies in normal and neoplastic cells. Topics covered are: B Cells; Organization and rearrangement of immunoglobin genes; Immunoglobin genes in disease; Immunoglobin gene expression; and Immunoglobin-related genes.

  12. Accurate Prediction of Phase Transitions in Compressed Sensing via a Connection to Minimax Denoising

    Donoho, David; Montanari, Andrea

    2011-01-01

    Compressed sensing posits that, within limits, one can undersample a sparse signal and yet reconstruct it accurately. Knowing the precise limits to such undersampling is important both for theory and practice. We present a formula precisely delineating the allowable degree of of undersampling of generalized sparse objects. The formula applies to Approximate Message Passing (AMP) algorithms for compressed sensing, which are here generalized to employ denoising operators besides the traditional scalar shrinkers (soft thresholding, positive soft thresholding and capping). This paper gives several examples including scalar shrinkers not derivable from convex optimization -- the firm shrinkage nonlinearity and the minimax} nonlinearity -- and also nonscalar denoisers -- block thresholding (both block soft and block James-Stein), monotone regression, and total variation minimization. Let the variables \\epsilon = k/N and \\delta = n/N denote the generalized sparsity and undersampling fractions for sampling the k-gene...

  13. Accurate Runout Measurement for HDD Spinning Motors and Disks

    Jiang, Quan; Bi, Chao; Lin, Song

    As hard disk drive (HDD) areal density increases, its track width becomes smaller and smaller and so is non-repeatable runout. HDD industry needs more accurate and better resolution runout measurements of spinning spindle motors and media platters in both axial and radial directions. This paper introduces a new system how to precisely measure the runout of HDD spinning disks and motors through synchronously acquiring the rotor position signal and the displacements in axial or radial directions. In order to minimize the synchronizing error between the rotor position and the displacement signal, a high resolution counter is adopted instead of the conventional phase-lock loop method. With Laser Doppler Vibrometer and proper signal processing, the proposed runout system can precisely measure the runout of the HDD spinning disks and motors with 1 nm resolution and 0.2% accuracy with a proper sampling rate. It can provide an effective and accurate means to measure the runout of high areal density HDDs, in particular the next generation HDDs, such as, pattern media HDDs and HAMR HDDs.

  14. Simple and accurate optical height sensor for wafer inspection systems

    Shimura, Kei; Nakai, Naoya; Taniguchi, Koichi; Itoh, Masahide

    2016-02-01

    An accurate method for measuring the wafer surface height is required for wafer inspection systems to adjust the focus of inspection optics quickly and precisely. A method for projecting a laser spot onto the wafer surface obliquely and for detecting its image displacement using a one-dimensional position-sensitive detector is known, and a variety of methods have been proposed for improving the accuracy by compensating the measurement error due to the surface patterns. We have developed a simple and accurate method in which an image of a reticle with eight slits is projected on the wafer surface and its reflected image is detected using an image sensor. The surface height is calculated by averaging the coordinates of the images of the slits in both the two directions in the captured image. Pattern-related measurement error was reduced by applying the coordinates averaging to the multiple-slit-projection method. Accuracy of better than 0.35 μm was achieved for a patterned wafer at the reference height and ±0.1 mm from the reference height in a simple configuration.

  15. Quality metric for accurate overlay control in <20nm nodes

    Klein, Dana; Amit, Eran; Cohen, Guy; Amir, Nuriel; Har-Zvi, Michael; Huang, Chin-Chou Kevin; Karur-Shanmugam, Ramkumar; Pierson, Bill; Kato, Cindy; Kurita, Hiroyuki

    2013-04-01

    The semiconductor industry is moving toward 20nm nodes and below. As the Overlay (OVL) budget is getting tighter at these advanced nodes, the importance in the accuracy in each nanometer of OVL error is critical. When process owners select OVL targets and methods for their process, they must do it wisely; otherwise the reported OVL could be inaccurate, resulting in yield loss. The same problem can occur when the target sampling map is chosen incorrectly, consisting of asymmetric targets that will cause biased correctable terms and a corrupted wafer. Total measurement uncertainty (TMU) is the main parameter that process owners use when choosing an OVL target per layer. Going towards the 20nm nodes and below, TMU will not be enough for accurate OVL control. KLA-Tencor has introduced a quality score named `Qmerit' for its imaging based OVL (IBO) targets, which is obtained on the-fly for each OVL measurement point in X & Y. This Qmerit score will enable the process owners to select compatible targets which provide accurate OVL values for their process and thereby improve their yield. Together with K-T Analyzer's ability to detect the symmetric targets across the wafer and within the field, the Archer tools will continue to provide an independent, reliable measurement of OVL error into the next advanced nodes, enabling fabs to manufacture devices that meet their tight OVL error budgets.

  16. Cerebral fat embolism: Use of MR spectroscopy for accurate diagnosis

    Laxmi Kokatnur

    2015-01-01

    Full Text Available Cerebral fat embolism (CFE is an uncommon but serious complication following orthopedic procedures. It usually presents with altered mental status, and can be a part of fat embolism syndrome (FES if associated with cutaneous and respiratory manifestations. Because of the presence of other common factors affecting the mental status, particularly in the postoperative period, the diagnosis of CFE can be challenging. Magnetic resonance imaging (MRI of brain typically shows multiple lesions distributed predominantly in the subcortical region, which appear as hyperintense lesions on T2 and diffusion weighted images. Although the location offers a clue, the MRI findings are not specific for CFE. Watershed infarcts, hypoxic encephalopathy, disseminated infections, demyelinating disorders, diffuse axonal injury can also show similar changes on MRI of brain. The presence of fat in these hyperintense lesions, identified by MR spectroscopy as raised lipid peaks will help in accurate diagnosis of CFE. Normal brain tissue or conditions producing similar MRI changes will not show any lipid peak on MR spectroscopy. We present a case of CFE initially misdiagnosed as brain stem stroke based on clinical presentation and cranial computed tomography (CT scan, and later, MR spectroscopy elucidated the accurate diagnosis.

  17. Accurate Multisteps Traffic Flow Prediction Based on SVM

    Zhang Mingheng

    2013-01-01

    Full Text Available Accurate traffic flow prediction is prerequisite and important for realizing intelligent traffic control and guidance, and it is also the objective requirement for intelligent traffic management. Due to the strong nonlinear, stochastic, time-varying characteristics of urban transport system, artificial intelligence methods such as support vector machine (SVM are now receiving more and more attentions in this research field. Compared with the traditional single-step prediction method, the multisteps prediction has the ability that can predict the traffic state trends over a certain period in the future. From the perspective of dynamic decision, it is far important than the current traffic condition obtained. Thus, in this paper, an accurate multi-steps traffic flow prediction model based on SVM was proposed. In which, the input vectors were comprised of actual traffic volume and four different types of input vectors were compared to verify their prediction performance with each other. Finally, the model was verified with actual data in the empirical analysis phase and the test results showed that the proposed SVM model had a good ability for traffic flow prediction and the SVM-HPT model outperformed the other three models for prediction.

  18. Accurate location estimation of moving object In Wireless Sensor network

    Vinay Bhaskar Semwal

    2011-12-01

    Full Text Available One of the central issues in wirless sensor networks is track the location, of moving object which have overhead of saving data, an accurate estimation of the target location of object with energy constraint .We do not have any mechanism which control and maintain data .The wireless communication bandwidth is also very limited. Some field which is using this technique are flood and typhoon detection, forest fire detection, temperature and humidity and ones we have these information use these information back to a central air conditioning and ventilation.In this research paper, we propose protocol based on the prediction and adaptive based algorithm which is using less sensor node reduced by an accurate estimation of the target location. We had shown that our tracking method performs well in terms of energy saving regardless of mobility pattern of the mobile target. We extends the life time of network with less sensor node. Once a new object is detected, a mobile agent will be initiated to track the roaming path of the object.

  19. Accurate Interatomic Force Fields via Machine Learning with Covariant Kernels

    Glielmo, Aldo; De Vita, Alessandro

    2016-01-01

    We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian Process (GP) Regression. This is based on matrix-valued kernel functions, to which we impose that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such "covariant" GP kernels can be obtained by integration over the elements of the rotation group SO(d) for the relevant dimensionality d. Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni and Fe crystalline...

  20. The economic value of accurate wind power forecasting to utilities

    Watson, S.J. [Rutherford Appleton Lab., Oxfordshire (United Kingdom); Giebel, G.; Joensen, A. [Risoe National Lab., Dept. of Wind Energy and Atmospheric Physics, Roskilde (Denmark)

    1999-03-01

    With increasing penetrations of wind power, the need for accurate forecasting is becoming ever more important. Wind power is by its very nature intermittent. For utility schedulers this presents its own problems particularly when the penetration of wind power capacity in a grid reaches a significant level (>20%). However, using accurate forecasts of wind power at wind farm sites, schedulers are able to plan the operation of conventional power capacity to accommodate the fluctuating demands of consumers and wind farm output. The results of a study to assess the value of forecasting at several potential wind farm sites in the UK and in the US state of Iowa using the Reading University/Rutherford Appleton Laboratory National Grid Model (NGM) are presented. The results are assessed for different types of wind power forecasting, namely: persistence, optimised numerical weather prediction or perfect forecasting. In particular, it will shown how the NGM has been used to assess the value of numerical weather prediction forecasts from the Danish Meteorological Institute model, HIRLAM, and the US Nested Grid Model, which have been `site tailored` by the use of the linearized flow model WA{sup s}P and by various Model output Statistics (MOS) and autoregressive techniques. (au)

  1. More-Accurate Model of Flows in Rocket Injectors

    Hosangadi, Ashvin; Chenoweth, James; Brinckman, Kevin; Dash, Sanford

    2011-01-01

    An improved computational model for simulating flows in liquid-propellant injectors in rocket engines has been developed. Models like this one are needed for predicting fluxes of heat in, and performances of, the engines. An important part of predicting performance is predicting fluctuations of temperature, fluctuations of concentrations of chemical species, and effects of turbulence on diffusion of heat and chemical species. Customarily, diffusion effects are represented by parameters known in the art as the Prandtl and Schmidt numbers. Prior formulations include ad hoc assumptions of constant values of these parameters, but these assumptions and, hence, the formulations, are inaccurate for complex flows. In the improved model, these parameters are neither constant nor specified in advance: instead, they are variables obtained as part of the solution. Consequently, this model represents the effects of turbulence on diffusion of heat and chemical species more accurately than prior formulations do, and may enable more-accurate prediction of mixing and flows of heat in rocket-engine combustion chambers. The model has been implemented within CRUNCH CFD, a proprietary computational fluid dynamics (CFD) computer program, and has been tested within that program. The model could also be implemented within other CFD programs.

  2. Ultra-accurate collaborative information filtering via directed user similarity

    Guo, Q.; Song, W.-J.; Liu, J.-G.

    2014-07-01

    A key challenge of the collaborative filtering (CF) information filtering is how to obtain the reliable and accurate results with the help of peers' recommendation. Since the similarities from small-degree users to large-degree users would be larger than the ones in opposite direction, the large-degree users' selections are recommended extensively by the traditional second-order CF algorithms. By considering the users' similarity direction and the second-order correlations to depress the influence of mainstream preferences, we present the directed second-order CF (HDCF) algorithm specifically to address the challenge of accuracy and diversity of the CF algorithm. The numerical results for two benchmark data sets, MovieLens and Netflix, show that the accuracy of the new algorithm outperforms the state-of-the-art CF algorithms. Comparing with the CF algorithm based on random walks proposed by Liu et al. (Int. J. Mod. Phys. C, 20 (2009) 285) the average ranking score could reach 0.0767 and 0.0402, which is enhanced by 27.3% and 19.1% for MovieLens and Netflix, respectively. In addition, the diversity, precision and recall are also enhanced greatly. Without relying on any context-specific information, tuning the similarity direction of CF algorithms could obtain accurate and diverse recommendations. This work suggests that the user similarity direction is an important factor to improve the personalized recommendation performance.

  3. Towards an accurate determination of the age of the Universe

    Jiménez, R

    1998-01-01

    In the past 40 years a considerable effort has been focused in determining the age of the Universe at zero redshift using several stellar clocks. In this review I will describe the best theoretical methods to determine the age of the oldest Galactic Globular Clusters (GC). I will also argue that a more accurate age determination may come from passively evolving high-redshift ellipticals. In particular, I will review two new methods to determine the age of GC. These two methods are more accurate than the classical isochrone fitting technique. The first method is based on the morphology of the horizontal branch and is independent of the distance modulus of the globular cluster. The second method uses a careful binning of the stellar luminosity function which determines simultaneously the distance and age of the GC. It is found that the oldest GCs have an age of $13.5 \\pm 2$ Gyr. The absolute minimum age for the oldest GCs is 10.5 Gyr and the maximum is 16.0 Gyr (with 99% confidence). Therefore, an Einstein-De S...

  4. Learning fast accurate movements requires intact frontostriatal circuits

    Britne eShabbott

    2013-11-01

    Full Text Available The basal ganglia are known to play a crucial role in movement execution, but their importance for motor skill learning remains unclear. Obstacles to our understanding include the lack of a universally accepted definition of motor skill learning (definition confound, and difficulties in distinguishing learning deficits from execution impairments (performance confound. We studied how healthy subjects and subjects with a basal ganglia disorder learn fast accurate reaching movements, and we addressed the definition and performance confounds by: 1 focusing on an operationally defined core element of motor skill learning (speed-accuracy learning, and 2 using normal variation in initial performance to separate movement execution impairment from motor learning abnormalities. We measured motor skill learning learning as performance improvement in a reaching task with a speed-accuracy trade-off. We compared the performance of subjects with Huntington’s disease (HD, a neurodegenerative basal ganglia disorder, to that of premanifest carriers of the HD mutation and of control subjects. The initial movements of HD subjects were less skilled (slower and/or less accurate than those of control subjects. To factor out these differences in initial execution, we modeled the relationship between learning and baseline performance in control subjects. Subjects with HD exhibited a clear learning impairment that was not explained by differences in initial performance. These results support a role for the basal ganglia in both movement execution and motor skill learning.

  5. Accurate measurement of streamwise vortices using dual-plane PIV

    Waldman, Rye M.; Breuer, Kenneth S.

    2012-11-01

    Low Reynolds number aerodynamic experiments with flapping animals (such as bats and small birds) are of particular interest due to their application to micro air vehicles which operate in a similar parameter space. Previous PIV wake measurements described the structures left by bats and birds and provided insight into the time history of their aerodynamic force generation; however, these studies have faced difficulty drawing quantitative conclusions based on said measurements. The highly three-dimensional and unsteady nature of the flows associated with flapping flight are major challenges for accurate measurements. The challenge of animal flight measurements is finding small flow features in a large field of view at high speed with limited laser energy and camera resolution. Cross-stream measurement is further complicated by the predominately out-of-plane flow that requires thick laser sheets and short inter-frame times, which increase noise and measurement uncertainty. Choosing appropriate experimental parameters requires compromise between the spatial and temporal resolution and the dynamic range of the measurement. To explore these challenges, we do a case study on the wake of a fixed wing. The fixed model simplifies the experiment and allows direct measurements of the aerodynamic forces via load cell. We present a detailed analysis of the wake measurements, discuss the criteria for making accurate measurements, and present a solution for making quantitative aerodynamic load measurements behind free-flyers.

  6. Accurate and precise zinc isotope ratio measurements in urban aerosols.

    Gioia, Simone; Weiss, Dominik; Coles, Barry; Arnold, Tim; Babinski, Marly

    2008-12-15

    We developed an analytical method and constrained procedural boundary conditions that enable accurate and precise Zn isotope ratio measurements in urban aerosols. We also demonstrate the potential of this new isotope system for air pollutant source tracing. The procedural blank is around 5 ng and significantly lower than published methods due to a tailored ion chromatographic separation. Accurate mass bias correction using external correction with Cu is limited to Zn sample content of approximately 50 ng due to the combined effect of blank contribution of Cu and Zn from the ion exchange procedure and the need to maintain a Cu/Zn ratio of approximately 1. Mass bias is corrected for by applying the common analyte internal standardization method approach. Comparison with other mass bias correction methods demonstrates the accuracy of the method. The average precision of delta(66)Zn determinations in aerosols is around 0.05 per thousand per atomic mass unit. The method was tested on aerosols collected in Sao Paulo City, Brazil. The measurements reveal significant variations in delta(66)Zn(Imperial) ranging between -0.96 and -0.37 per thousand in coarse and between -1.04 and 0.02 per thousand in fine particular matter. This variability suggests that Zn isotopic compositions distinguish atmospheric sources. The isotopic light signature suggests traffic as the main source. We present further delta(66)Zn(Imperial) data for the standard reference material NIST SRM 2783 (delta(66)Zn(Imperial) = 0.26 +/- 0.10 per thousand).

  7. Novel dispersion tolerant interferometry method for accurate measurements of displacement

    Bradu, Adrian; Maria, Michael; Leick, Lasse; Podoleanu, Adrian G.

    2015-05-01

    We demonstrate that the recently proposed master-slave interferometry method is able to provide true dispersion free depth profiles in a spectrometer-based set-up that can be used for accurate displacement measurements in sensing and optical coherence tomography. The proposed technique is based on correlating the channelled spectra produced by the linear camera in the spectrometer with previously recorded masks. As such technique is not based on Fourier transformations (FT), it does not require any resampling of data and is immune to any amounts of dispersion left unbalanced in the system. In order to prove the tolerance of technique to dispersion, different lengths of optical fiber are used in the interferometer to introduce dispersion and it is demonstrated that neither the sensitivity profile versus optical path difference (OPD) nor the depth resolution are affected. In opposition, it is shown that the classical FT based methods using calibrated data provide less accurate optical path length measurements and exhibit a quicker decays of sensitivity with OPD.

  8. An Analytic Method for Measuring Accurate Fundamental Frequency Components

    Nam, Soon Ryul; Park Jong Keun [Seoul National University, Seoul(Korea); Kang, Sang Hee [Myongji University, Seoul (Korea)

    2002-04-01

    This paper proposes an analytic method for measuring the accurate fundamental frequency component of a fault current signal distorted with a DC-offset, a characteristic frequency component, and harmonics. The proposed algorithm is composed of four stages: sine filer, linear filter, Prony's method, and measurement. The sine filter and the linear filter eliminate harmonics and the fundamental frequency component, respectively. Then Prony's method is used to estimate the parameters of the DC-offset and the characteristic frequency component. Finally, the fundamental frequency component is measured by compensating the sine-filtered signal with the estimated parameters. The performance evaluation of the proposed method is presented for a-phase to ground faults on a 345 kV 200 km overhead transmission line. The EMTP is used to generate fault current signals under different fault locations and fault inception angles. It is shown that the analytic method accurately measures the fundamental frequency component regardless of the characteristic frequency component as well as the DC-offset.(author). 19 refs., 4 figs., 4 tabs.

  9. Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

    Antonielli, Livio; Sessitsch, Angela

    2016-04-01

    Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

  10. In vitro transcription accurately predicts lac repressor phenotype in vivo in Escherichia coli

    Matthew Almond Sochor

    2014-07-01

    Full Text Available A multitude of studies have looked at the in vivo and in vitro behavior of the lac repressor binding to DNA and effector molecules in order to study transcriptional repression, however these studies are not always reconcilable. Here we use in vitro transcription to directly mimic the in vivo system in order to build a self consistent set of experiments to directly compare in vivo and in vitro genetic repression. A thermodynamic model of the lac repressor binding to operator DNA and effector is used to link DNA occupancy to either normalized in vitro mRNA product or normalized in vivo fluorescence of a regulated gene, YFP. An accurate measurement of repressor, DNA and effector concentrations were made both in vivo and in vitro allowing for direct modeling of the entire thermodynamic equilibrium. In vivo repression profiles are accurately predicted from the given in vitro parameters when molecular crowding is considered. Interestingly, our measured repressor–operator DNA affinity differs significantly from previous in vitro measurements. The literature values are unable to replicate in vivo binding data. We therefore conclude that the repressor-DNA affinity is much weaker than previously thought. This finding would suggest that in vitro techniques that are specifically designed to mimic the in vivo process may be necessary to replicate the native system.

  11. Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

    Kevin R Ramkissoon

    Full Text Available The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

  12. Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

    Ramkissoon, Kevin R; Miller, Jennifer K; Ojha, Sunil; Watson, Douglas S; Bomar, Martha G; Galande, Amit K; Shearer, Alexander G

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

  13. The KFM, A Homemade Yet Accurate and Dependable Fallout Meter

    Kearny, C.H.

    2001-11-20

    The KFM is a homemade fallout meter that can be made using only materials, tools, and skills found in millions of American homes. It is an accurate and dependable electroscope-capacitor. The KFM, in conjunction with its attached table and a watch, is designed for use as a rate meter. Its attached table relates observed differences in the separations of its two leaves (before and after exposures at the listed time intervals) to the dose rates during exposures of these time intervals. In this manner dose rates from 30 mR/hr up to 43 R/hr can be determined with an accuracy of {+-}25%. A KFM can be charged with any one of the three expedient electrostatic charging devices described. Due to the use of anhydrite (made by heating gypsum from wallboard) inside a KFM and the expedient ''dry-bucket'' in which it can be charged when the air is very humid, this instrument always can be charged and used to obtain accurate measurements of gamma radiation no matter how high the relative humidity. The heart of this report is the step-by-step illustrated instructions for making and using a KFM. These instructions have been improved after each successive field test. The majority of the untrained test families, adequately motivated by cash bonuses offered for success and guided only by these written instructions, have succeeded in making and using a KFM. NOTE: ''The KFM, A Homemade Yet Accurate and Dependable Fallout Meter'', was published by Oak Ridge National Laboratory report in1979. Some of the materials originally suggested for suspending the leaves of the Kearny Fallout Meter (KFM) are no longer available. Because of changes in the manufacturing process, other materials (e.g., sewing thread, unwaxed dental floss) may not have the insulating capability to work properly. Oak Ridge National Laboratory has not tested any of the suggestions provided in the preface of the report, but they have been used by other groups. When using these

  14. Accurate complex scaling of three dimensional numerical potentials.

    Cerioni, Alessandro; Genovese, Luigi; Duchemin, Ivan; Deutsch, Thierry

    2013-05-28

    The complex scaling method, which consists in continuing spatial coordinates into the complex plane, is a well-established method that allows to compute resonant eigenfunctions of the time-independent Schrödinger operator. Whenever it is desirable to apply the complex scaling to investigate resonances in physical systems defined on numerical discrete grids, the most direct approach relies on the application of a similarity transformation to the original, unscaled Hamiltonian. We show that such an approach can be conveniently implemented in the Daubechies wavelet basis set, featuring a very promising level of generality, high accuracy, and no need for artificial convergence parameters. Complex scaling of three dimensional numerical potentials can be efficiently and accurately performed. By carrying out an illustrative resonant state computation in the case of a one-dimensional model potential, we then show that our wavelet-based approach may disclose new exciting opportunities in the field of computational non-Hermitian quantum mechanics.

  15. GLIMPSE: Accurate 3D weak lensing reconstructions using sparsity

    Leonard, Adrienne; Starck, Jean-Luc

    2013-01-01

    We present GLIMPSE - Gravitational Lensing Inversion and MaPping with Sparse Estimators - a new algorithm to generate density reconstructions in three dimensions from photometric weak lensing measurements. This is an extension of earlier work in one dimension aimed at applying compressive sensing theory to the inversion of gravitational lensing measurements to recover 3D density maps. Using the assumption that the density can be represented sparsely in our chosen basis - 2D transverse wavelets and 1D line of sight dirac functions - we show that clusters of galaxies can be identified and accurately localised and characterised using this method. Throughout, we use simulated data consistent with the quality currently attainable in large surveys. We present a thorough statistical analysis of the errors and biases in both the redshifts of detected structures and their amplitudes. The GLIMPSE method is able to produce reconstructions at significantly higher resolution than the input data; in this paper we show reco...

  16. Fast and accurate determination of modularity and its effect size

    Treviño, Santiago; Del Genio, Charo I; Bassler, Kevin E

    2014-01-01

    We present a fast spectral algorithm for community detection in complex networks. Our method searches for the partition with the maximum value of the modularity via the interplay of several refinement steps that include both agglomeration and division. We validate the accuracy of the algorithm by applying it to several real-world benchmark networks. On all these, our algorithm performs as well or better than any other known polynomial scheme. This allows us to extensively study the modularity distribution in ensembles of Erd\\H{o}s-R\\'enyi networks, producing theoretical predictions for means and variances inclusive of finite-size corrections. Our work provides a way to accurately estimate the effect size of modularity, providing a $z$-score measure of it and enabling a more informative comparison of networks with different numbers of nodes and links.

  17. Methods for Accurate Free Flight Measurement of Drag Coefficients

    Courtney, Elya; Courtney, Michael

    2015-01-01

    This paper describes experimental methods for free flight measurement of drag coefficients to an accuracy of approximately 1%. There are two main methods of determining free flight drag coefficients, or equivalent ballistic coefficients: 1) measuring near and far velocities over a known distance and 2) measuring a near velocity and time of flight over a known distance. Atmospheric conditions must also be known and nearly constant over the flight path. A number of tradeoffs are important when designing experiments to accurately determine drag coefficients. The flight distance must be large enough so that the projectile's loss of velocity is significant compared with its initial velocity and much larger than the uncertainty in the near and/or far velocity measurements. On the other hand, since drag coefficients and ballistic coefficients both depend on velocity, the change in velocity over the flight path should be small enough that the average drag coefficient over the path (which is what is really determined)...

  18. An Integrative Approach to Accurate Vehicle Logo Detection

    Hao Pan

    2013-01-01

    required for many applications in intelligent transportation systems and automatic surveillance. The task is challenging considering the small target of logos and the wide range of variability in shape, color, and illumination. A fast and reliable vehicle logo detection approach is proposed following visual attention mechanism from the human vision. Two prelogo detection steps, that is, vehicle region detection and a small RoI segmentation, rapidly focalize a small logo target. An enhanced Adaboost algorithm, together with two types of features of Haar and HOG, is proposed to detect vehicles. An RoI that covers logos is segmented based on our prior knowledge about the logos’ position relative to license plates, which can be accurately localized from frontal vehicle images. A two-stage cascade classier proceeds with the segmented RoI, using a hybrid of Gentle Adaboost and Support Vector Machine (SVM, resulting in precise logo positioning. Extensive experiments were conducted to verify the efficiency of the proposed scheme.

  19. Accurate Parallel Algorithm for Adini Nonconforming Finite Element

    罗平; 周爱辉

    2003-01-01

    Multi-parameter asymptotic expansions are interesting since they justify the use of multi-parameter extrapolation which can be implemented in parallel and are well studied in many papers for the conforming finite element methods. For the nonconforming finite element methods, however, the work of the multi-parameter asymptotic expansions and extrapolation have seldom been found in the literature. This paper considers the solution of the biharmonic equation using Adini nonconforming finite elements and reports new results for the multi-parameter asymptotic expansions and extrapolation. The Adini nonconforming finite element solution of the biharmonic equation is shown to have a multi-parameter asymptotic error expansion and extrapolation. This expansion and a multi-parameter extrapolation technique were used to develop an accurate approximation parallel algorithm for the biharmonic equation. Finally, numerical results have verified the extrapolation theory.

  20. Accurate Performance Analysis of Opportunistic Decode-and-Forward Relaying

    Tourki, Kamel; Alouni, Mohamed-Slim

    2011-01-01

    In this paper, we investigate an opportunistic relaying scheme where the selected relay assists the source-destination (direct) communication. In our study, we consider a regenerative opportunistic relaying scheme in which the direct path can be considered unusable, and takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We first derive statistics based on exact probability density function (PDF) of each hop. Then, the PDFs are used to determine accurate closed form expressions for end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation. Furthermore, we evaluate the asymptotical performance analysis and the diversity order is deduced. Finally, we validate our analysis by showing that performance simulation results coincide with our analytical results over different network architectures.

  1. Spectropolarimetrically accurate magnetohydrostatic sunspot model for forward modelling in helioseismology

    Przybylski, D; Cally, P S

    2015-01-01

    We present a technique to construct a spectropolarimetrically accurate magneto-hydrostatic model of a large-scale solar magnetic field concentration, mimicking a sunspot. Using the constructed model we perform a simulation of acoustic wave propagation, conversion and absorption in the solar interior and photosphere with the sunspot embedded into it. With the $6173\\mathrm{\\AA}$ magnetically sensitive photospheric absorption line of neutral iron, we calculate observable quantities such as continuum intensities, Doppler velocities, as well as full Stokes vector for the simulation at various positions at the solar disk, and analyse the influence of non-locality of radiative transport in the solar photosphere on helioseismic measurements. Bisector shapes were used to perform multi-height observations. The differences in acoustic power at different heights within the line formation region at different positions at the solar disk were simulated and characterised. An increase in acoustic power in the simulated observ...

  2. Inverter Modeling For Accurate Energy Predictions Of Tracking HCPV Installations

    Bowman, J.; Jensen, S.; McDonald, Mark

    2010-10-01

    High efficiency high concentration photovoltaic (HCPV) solar plants of megawatt scale are now operational, and opportunities for expanded adoption are plentiful. However, effective bidding for sites requires reliable prediction of energy production. HCPV module nameplate power is rated for specific test conditions; however, instantaneous HCPV power varies due to site specific irradiance and operating temperature, and is degraded by soiling, protective stowing, shading, and electrical connectivity. These factors interact with the selection of equipment typically supplied by third parties, e.g., wire gauge and inverters. We describe a time sequence model accurately accounting for these effects that predicts annual energy production, with specific reference to the impact of the inverter on energy output and interactions between system-level design decisions and the inverter. We will also show two examples, based on an actual field design, of inverter efficiency calculations and the interaction between string arrangements and inverter selection.

  3. Accurate derivative evaluation for any Grad–Shafranov solver

    Ricketson, L.F. [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Cerfon, A.J., E-mail: cerfon@cims.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Rachh, M. [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Freidberg, J.P. [Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

    2016-01-15

    We present a numerical scheme that can be combined with any fixed boundary finite element based Poisson or Grad–Shafranov solver to compute the first and second partial derivatives of the solution to these equations with the same order of convergence as the solution itself. At the heart of our scheme is an efficient and accurate computation of the Dirichlet to Neumann map through the evaluation of a singular volume integral and the solution to a Fredholm integral equation of the second kind. Our numerical method is particularly useful for magnetic confinement fusion simulations, since it allows the evaluation of quantities such as the magnetic field, the parallel current density and the magnetic curvature with much higher accuracy than has been previously feasible on the affordable coarse grids that are usually implemented.

  4. A fast and accurate FPGA based QRS detection system.

    Shukla, Ashish; Macchiarulo, Luca

    2008-01-01

    An accurate Field Programmable Gate Array (FPGA) based ECG Analysis system is described in this paper. The design, based on a popular software based QRS detection algorithm, calculates the threshold value for the next peak detection cycle, from the median of eight previously detected peaks. The hardware design has accuracy in excess of 96% in detecting the beats correctly when tested with a subset of five 30 minute data records obtained from the MIT-BIH Arrhythmia database. The design, implemented using a proprietary design tool (System Generator), is an extension of our previous work and uses 76% resources available in a small-sized FPGA device (Xilinx Spartan xc3s500), has a higher detection accuracy as compared to our previous design and takes almost half the analysis time in comparison to software based approach.

  5. Accurate platelet counting in an insidious case of pseudothrombocytopenia.

    Lombarts, A J; Zijlstra, J J; Peters, R H; Thomasson, C G; Franck, P F

    1999-01-01

    Anticoagulant-induced aggregation of platelets leads to pseudothrombocytopenia. Blood cell counters generally trigger alarms to alert the user. We describe an insidious case of pseudothrombocytopenia, where the complete absence of Coulter counter alarms both in ethylenediaminetetraacetic acid blood and in citrate or acid citrate dextrose blood samples was compounded by the fact that the massive aggregates were exclusively found at the edges of the blood smear. Non-recognition of pseudothrombocytopenia can have serious diagnostic and therapeutic consequences. While the anti-aggregant mixture citrate-theophylline-adenosine-dipyridamole completely failed in preventing pseudothrombocytopenia, addition of iloprost to anticoagulants only partially prevented the aggregation. Only the prior addition of gentamicin to any anticoagulant used resulted in a complete prevention of pseudothrombocytopenia and enabled to count accurately the platelets.

  6. Accurate Calculation of Fringe Fields in the LHC Main Dipoles

    Kurz, S; Siegel, N

    2000-01-01

    The ROXIE program developed at CERN for the design and optimization of the superconducting LHC magnets has been recently extended in a collaboration with the University of Stuttgart, Germany, with a field computation method based on the coupling between the boundary element (BEM) and the finite element (FEM) technique. This avoids the meshing of the coils and the air regions, and avoids the artificial far field boundary conditions. The method is therefore specially suited for the accurate calculation of fields in the superconducting magnets in which the field is dominated by the coil. We will present the fringe field calculations in both 2d and 3d geometries to evaluate the effect of connections and the cryostat on the field quality and the flux density to which auxiliary bus-bars are exposed.

  7. Interactive Isogeometric Volume Visualization with Pixel-Accurate Geometry.

    Fuchs, Franz G; Hjelmervik, Jon M

    2016-02-01

    A recent development, called isogeometric analysis, provides a unified approach for design, analysis and optimization of functional products in industry. Traditional volume rendering methods for inspecting the results from the numerical simulations cannot be applied directly to isogeometric models. We present a novel approach for interactive visualization of isogeometric analysis results, ensuring correct, i.e., pixel-accurate geometry of the volume including its bounding surfaces. The entire OpenGL pipeline is used in a multi-stage algorithm leveraging techniques from surface rendering, order-independent transparency, as well as theory and numerical methods for ordinary differential equations. We showcase the efficiency of our approach on different models relevant to industry, ranging from quality inspection of the parametrization of the geometry, to stress analysis in linear elasticity, to visualization of computational fluid dynamics results.

  8. Accurate Enthalpies of Formation of Astromolecules: Energy, Stability and Abundance

    Etim, Emmanuel E

    2016-01-01

    Accurate enthalpies of formation are reported for known and potential astromolecules using high level ab initio quantum chemical calculations. A total of 130 molecules comprising of 31 isomeric groups and 24 cyanide/isocyanide pairs with atoms ranging from 3 to 12 have been considered. The results show an interesting, surprisingly not well explored, relationship between energy, stability and abundance (ESA) existing among these molecules. Among the isomeric species, isomers with lower enthalpies of formation are more easily observed in the interstellar medium compared to their counterparts with higher enthalpies of formation. Available data in literature confirm the high abundance of the most stable isomer over other isomers in the different groups considered. Potential for interstellar hydrogen bonding accounts for the few exceptions observed. Thus, in general, it suffices to say that the interstellar abundances of related species are directly proportional to their stabilities. The immediate consequences of ...

  9. Accurate performance analysis of opportunistic decode-and-forward relaying

    Tourki, Kamel

    2011-07-01

    In this paper, we investigate an opportunistic relaying scheme where the selected relay assists the source-destination (direct) communication. In our study, we consider a regenerative opportunistic relaying scheme in which the direct path may be considered unusable, and the destination may use a selection combining technique. We first derive the exact statistics of each hop, in terms of probability density function (PDF). Then, the PDFs are used to determine accurate closed form expressions for end-to-end outage probability for a transmission rate R. Furthermore, we evaluate the asymptotical performance analysis and the diversity order is deduced. Finally, we validate our analysis by showing that performance simulation results coincide with our analytical results over different network architectures. © 2011 IEEE.

  10. Second-Order Accurate Projective Integrators for Multiscale Problems

    Lee, S L; Gear, C W

    2005-05-27

    We introduce new projective versions of second-order accurate Runge-Kutta and Adams-Bashforth methods, and demonstrate their use as outer integrators in solving stiff differential systems. An important outcome is that the new outer integrators, when combined with an inner telescopic projective integrator, can result in fully explicit methods with adaptive outer step size selection and solution accuracy comparable to those obtained by implicit integrators. If the stiff differential equations are not directly available, our formulations and stability analysis are general enough to allow the combined outer-inner projective integrators to be applied to black-box legacy codes or perform a coarse-grained time integration of microscopic systems to evolve macroscopic behavior, for example.

  11. CLOMP: Accurately Characterizing OpenMP Application Overheads

    Bronevetsky, G; Gyllenhaal, J; de Supinski, B

    2008-02-11

    Despite its ease of use, OpenMP has failed to gain widespread use on large scale systems, largely due to its failure to deliver sufficient performance. Our experience indicates that the cost of initiating OpenMP regions is simply too high for the desired OpenMP usage scenario of many applications. In this paper, we introduce CLOMP, a new benchmark to characterize this aspect of OpenMP implementations accurately. CLOMP complements the existing EPCC benchmark suite to provide simple, easy to understand measurements of OpenMP overheads in the context of application usage scenarios. Our results for several OpenMP implementations demonstrate that CLOMP identifies the amount of work required to compensate for the overheads observed with EPCC. Further, we show that CLOMP also captures limitations for OpenMP parallelization on NUMA systems.

  12. Fast and spectrally accurate summation of 2-periodic Stokes potentials

    Lindbo, Dag

    2011-01-01

    We derive a Ewald decomposition for the Stokeslet in planar periodicity and a novel PME-type O(N log N) method for the fast evaluation of the resulting sums. The decomposition is the natural 2P counterpart to the classical 3P decomposition by Hasimoto, and is given in an explicit form not found in the literature. Truncation error estimates are provided to aid in selecting parameters. The fast, PME-type, method appears to be the first fast method for computing Stokeslet Ewald sums in planar periodicity, and has three attractive properties: it is spectrally accurate; it uses the minimal amount of memory that a gridded Ewald method can use; and provides clarity regarding numerical errors and how to choose parameters. Analytical and numerical results are give to support this. We explore the practicalities of the proposed method, and survey the computational issues involved in applying it to 2-periodic boundary integral Stokes problems.

  13. Accurate mass measurements on neutron-deficient krypton isotopes

    Rodríguez, D; Äystö, J; Beck, D

    2006-01-01

    The masses of $^{72–78,80,82,86}$Kr were measured directly with the ISOLTRAP Penning trap mass spectrometer at ISOLDE/CERN. For all these nuclides, the measurements yielded mass uncertainties below 10 keV. The ISOLTRAP mass values for $^{72–75}$Kr being more precise than the previous results obtained by means of other techniques, and thus completely determine the new values in the Atomic-Mass Evaluation. Besides the interest of these masses for nuclear astrophysics, nuclear structure studies, and Standard Model tests, these results constitute a valuable and accurate input to improve mass models. In this paper, we present the mass measurements and discuss the mass evaluation for these Kr isotopes.

  14. Accurate bond dissociation energies (D 0) for FHF- isotopologues

    Stein, Christopher; Oswald, Rainer; Sebald, Peter; Botschwina, Peter; Stoll, Hermann; Peterson, Kirk A.

    2013-09-01

    Accurate bond dissociation energies (D 0) are determined for three isotopologues of the bifluoride ion (FHF-). While the zero-point vibrational contributions are taken from our previous work (P. Sebald, A. Bargholz, R. Oswald, C. Stein, P. Botschwina, J. Phys. Chem. A, DOI: 10.1021/jp3123677), the equilibrium dissociation energy (D e ) of the reaction ? was obtained by a composite method including frozen-core (fc) CCSD(T) calculations with basis sets up to cardinal number n = 7 followed by extrapolation to the complete basis set limit. Smaller terms beyond fc-CCSD(T) cancel each other almost completely. The D 0 values of FHF-, FDF-, and FTF- are predicted to be 15,176, 15,191, and 15,198 cm-1, respectively, with an uncertainty of ca. 15 cm-1.

  15. Accurate mass measurements on neutron-deficient krypton isotopes

    Rodriguez, D. [GSI, Planckstrasse 1, 64291 Darmstadt (Germany)]. E-mail: rodriguez@lpccaen.in2p3.fr; Audi, G. [CSNSM-IN2P3-CNRS, 91405 Orsay-Campus(France); Aystoe, J. [University of Jyvaeskylae, Department of Physics, P.O. Box 35, 40351 Jyvaeskylae (Finland); Beck, D. [GSI, Planckstrasse 1, 64291 Darmstadt (Germany); Blaum, K. [GSI, Planckstrasse 1, 64291 Darmstadt (Germany); Institute of Physics, University of Mainz, Staudingerweg 7, 55128 Mainz (Germany); Bollen, G. [NSCL, Michigan State University, East Lansing, MI 48824-1321 (United States); Herfurth, F. [GSI, Planckstrasse 1, 64291 Darmstadt (Germany); Jokinen, A. [University of Jyvaeskylae, Department of Physics, P.O. Box 35, 40351 Jyvaeskylae (Finland); Kellerbauer, A. [CERN, Division EP, 1211 Geneva 23 (Switzerland); Kluge, H.-J. [GSI, Planckstrasse 1, 64291 Darmstadt (Germany); University of Heidelberg, 69120 Heidelberg (Germany); Kolhinen, V.S. [University of Jyvaeskylae, Department of Physics, P.O. Box 35, 40351 Jyvaeskylae (Finland); Oinonen, M. [Helsinki Institute of Physics, P.O. Box 64, 00014 University of Helsinki (Finland); Sauvan, E. [Institute of Physics, University of Mainz, Staudingerweg 7, 55128 Mainz (Germany); Schwarz, S. [NSCL, Michigan State University, East Lansing, MI 48824-1321 (United States)

    2006-04-17

    The masses of {sup 72-78,80,82,86}Kr were measured directly with the ISOLTRAP Penning trap mass spectrometer at ISOLDE/CERN. For all these nuclides, the measurements yielded mass uncertainties below 10 keV. The ISOLTRAP mass values for {sup 72-75}Kr outweighed previous results obtained by means of other techniques, and thus completely determine the new values in the Atomic-Mass Evaluation. Besides the interest of these masses for nuclear astrophysics, nuclear structure studies, and Standard Model tests, these results constitute a valuable and accurate input to improve mass models. In this paper, we present the mass measurements and discuss the mass evaluation for these Kr isotopes.

  16. Redundancy-Free, Accurate Analytical Center Machine for Classification

    ZHENGFanzi; QIUZhengding; LengYonggang; YueJianhai

    2005-01-01

    Analytical center machine (ACM) has remarkable generalization performance based on analytical center of version space and outperforms SVM. From the analysis of geometry of machine learning and principle of ACM, it is showed that some training patterns are redundant to the definition of version space. Redundant patterns push ACM classifier away from analytical center of the prime version space so that the generalization performance degrades, at the same time redundant patterns slow down the classifier and reduce the efficiency of storage. Thus, an incremental algorithm is proposed to remove redundant patterns and embed into the frame of ACM that yields a Redundancy free accurate-Analytical center machine (RFA-ACM) for classification. Experiments with Heart, Thyroid, Banana datasets demonstrate the validity of RFA-ACM.

  17. Accurate Element of Compressive Bar considering the Effect of Displacement

    Lifeng Tang

    2015-01-01

    Full Text Available By constructing the compressive bar element and developing the stiffness matrix, most issues about the compressive bar can be solved. In this paper, based on second derivative to the equilibrium differential governing equations, the displacement shape functions are got. And then the finite element formula of compressive bar element is developed by using the potential energy principle and analytical shape function. Based on the total potential energy variation principle, the static and geometrical stiffness matrices are proposed, in which the large deformation of compressive bar is considered. To verify the accurate and validity of the analytical trial function element proposed in this paper, a number of the numerical examples are presented. Comparisons show that the proposed element has high calculation efficiency and rapid speed of convergence.

  18. Accurate finite difference methods for time-harmonic wave propagation

    Harari, Isaac; Turkel, Eli

    1994-01-01

    Finite difference methods for solving problems of time-harmonic acoustics are developed and analyzed. Multidimensional inhomogeneous problems with variable, possibly discontinuous, coefficients are considered, accounting for the effects of employing nonuniform grids. A weighted-average representation is less sensitive to transition in wave resolution (due to variable wave numbers or nonuniform grids) than the standard pointwise representation. Further enhancement in method performance is obtained by basing the stencils on generalizations of Pade approximation, or generalized definitions of the derivative, reducing spurious dispersion, anisotropy and reflection, and by improving the representation of source terms. The resulting schemes have fourth-order accurate local truncation error on uniform grids and third order in the nonuniform case. Guidelines for discretization pertaining to grid orientation and resolution are presented.

  19. Accurate and efficient maximal ball algorithm for pore network extraction

    Arand, Frederick; Hesser, Jürgen

    2017-04-01

    The maximal ball (MB) algorithm is a well established method for the morphological analysis of porous media. It extracts a network of pores and throats from volumetric data. This paper describes structural modifications to the algorithm, while the basic concepts are preserved. Substantial improvements to accuracy and efficiency are achieved as follows: First, all calculations are performed on a subvoxel accurate distance field, and no approximations to discretize balls are made. Second, data structures are simplified to keep memory usage low and improve algorithmic speed. Third, small and reasonable adjustments increase speed significantly. In volumes with high porosity, memory usage is improved compared to classic MB algorithms. Furthermore, processing is accelerated more than three times. Finally, the modified MB algorithm is verified by extracting several network properties from reference as well as real data sets. Runtimes are measured and compared to literature.

  20. Machine Learning of Accurate Energy-Conserving Molecular Force Fields

    Chmiela, Stefan; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert

    2016-01-01

    Using conservation of energy -- a fundamental property of closed classical and quantum mechanical systems -- we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/{\\AA} for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations...

  1. Efficient and Accurate Indoor Localization Using Landmark Graphs

    Gu, F.; Kealy, A.; Khoshelham, K.; Shang, J.

    2016-06-01

    Indoor localization is important for a variety of applications such as location-based services, mobile social networks, and emergency response. Fusing spatial information is an effective way to achieve accurate indoor localization with little or with no need for extra hardware. However, existing indoor localization methods that make use of spatial information are either too computationally expensive or too sensitive to the completeness of landmark detection. In this paper, we solve this problem by using the proposed landmark graph. The landmark graph is a directed graph where nodes are landmarks (e.g., doors, staircases, and turns) and edges are accessible paths with heading information. We compared the proposed method with two common Dead Reckoning (DR)-based methods (namely, Compass + Accelerometer + Landmarks and Gyroscope + Accelerometer + Landmarks) by a series of experiments. Experimental results show that the proposed method can achieve 73% accuracy with a positioning error less than 2.5 meters, which outperforms the other two DR-based methods.

  2. An accurate solver for forward and inverse transport

    Monard, François; Bal, Guillaume

    2010-07-01

    This paper presents a robust and accurate way to solve steady-state linear transport (radiative transfer) equations numerically. Our main objective is to address the inverse transport problem, in which the optical parameters of a domain of interest are reconstructed from measurements performed at the domain's boundary. This inverse problem has important applications in medical and geophysical imaging, and more generally in any field involving high frequency waves or particles propagating in scattering environments. Stable solutions of the inverse transport problem require that the singularities of the measurement operator, which maps the optical parameters to the available measurements, be captured with sufficient accuracy. This in turn requires that the free propagation of particles be calculated with care, which is a difficult problem on a Cartesian grid. A standard discrete ordinates method is used for the direction of propagation of the particles. Our methodology to address spatial discretization is based on rotating the computational domain so that each direction of propagation is always aligned with one of the grid axes. Rotations are performed in the Fourier domain to achieve spectral accuracy. The numerical dispersion of the propagating particles is therefore minimal. As a result, the ballistic and single scattering components of the transport solution are calculated robustly and accurately. Physical blurring effects, such as small angular diffusion, are also incorporated into the numerical tool. Forward and inverse calculations performed in a two-dimensional setting exemplify the capabilities of the method. Although the methodology might not be the fastest way to solve transport equations, its physical accuracy provides us with a numerical tool to assess what can and cannot be reconstructed in inverse transport theory.

  3. Accurate skin dose measurements using radiochromic film in clinical applications.

    Devic, S; Seuntjens, J; Abdel-Rahman, W; Evans, M; Olivares, M; Podgorsak, E B; Vuong, Té; Soares, Christopher G

    2006-04-01

    Megavoltage x-ray beams exhibit the well-known phenomena of dose buildup within the first few millimeters of the incident phantom surface, or the skin. Results of the surface dose measurements, however, depend vastly on the measurement technique employed. Our goal in this study was to determine a correction procedure in order to obtain an accurate skin dose estimate at the clinically relevant depth based on radiochromic film measurements. To illustrate this correction, we have used as a reference point a depth of 70 micron. We used the new GAFCHROMIC dosimetry films (HS, XR-T, and EBT) that have effective points of measurement at depths slightly larger than 70 micron. In addition to films, we also used an Attix parallel-plate chamber and a home-built extrapolation chamber to cover tissue-equivalent depths in the range from 4 micron to 1 mm of water-equivalent depth. Our measurements suggest that within the first millimeter of the skin region, the PDD for a 6 MV photon beam and field size of 10 x 10 cm2 increases from 14% to 43%. For the three GAFCHROMIC dosimetry film models, the 6 MV beam entrance skin dose measurement corrections due to their effective point of measurement are as follows: 15% for the EBT, 15% for the HS, and 16% for the XR-T model GAFCHROMIC films. The correction factors for the exit skin dose due to the build-down region are negligible. There is a small field size dependence for the entrance skin dose correction factor when using the EBT GAFCHROMIC film model. Finally, a procedure that uses EBT model GAFCHROMIC film for an accurate measurement of the skin dose in a parallel-opposed pair 6 MV photon beam arrangement is described.

  4. Influence of pansharpening techniques in obtaining accurate vegetation thematic maps

    Ibarrola-Ulzurrun, Edurne; Gonzalo-Martin, Consuelo; Marcello-Ruiz, Javier

    2016-10-01

    In last decades, there have been a decline in natural resources, becoming important to develop reliable methodologies for their management. The appearance of very high resolution sensors has offered a practical and cost-effective means for a good environmental management. In this context, improvements are needed for obtaining higher quality of the information available in order to get reliable classified images. Thus, pansharpening enhances the spatial resolution of the multispectral band by incorporating information from the panchromatic image. The main goal in the study is to implement pixel and object-based classification techniques applied to the fused imagery using different pansharpening algorithms and the evaluation of thematic maps generated that serve to obtain accurate information for the conservation of natural resources. A vulnerable heterogenic ecosystem from Canary Islands (Spain) was chosen, Teide National Park, and Worldview-2 high resolution imagery was employed. The classes considered of interest were set by the National Park conservation managers. 7 pansharpening techniques (GS, FIHS, HCS, MTF based, Wavelet `à trous' and Weighted Wavelet `à trous' through Fractal Dimension Maps) were chosen in order to improve the data quality with the goal to analyze the vegetation classes. Next, different classification algorithms were applied at pixel-based and object-based approach, moreover, an accuracy assessment of the different thematic maps obtained were performed. The highest classification accuracy was obtained applying Support Vector Machine classifier at object-based approach in the Weighted Wavelet `à trous' through Fractal Dimension Maps fused image. Finally, highlight the difficulty of the classification in Teide ecosystem due to the heterogeneity and the small size of the species. Thus, it is important to obtain accurate thematic maps for further studies in the management and conservation of natural resources.

  5. Accurate, fully-automated NMR spectral profiling for metabolomics.

    Siamak Ravanbakhsh

    Full Text Available Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid, BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF, defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error, in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of

  6. An accurate and portable solid state neutron rem meter

    Oakes, T.M. [Nuclear Science and Engineering Institute, University of Missouri, Columbia, MO (United States); Bellinger, S.L. [Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS (United States); Miller, W.H. [Nuclear Science and Engineering Institute, University of Missouri, Columbia, MO (United States); Missouri University Research Reactor, Columbia, MO (United States); Myers, E.R. [Department of Physics, University of Missouri, Kansas City, MO (United States); Fronk, R.G.; Cooper, B.W [Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS (United States); Sobering, T.J. [Electronics Design Laboratory, Kansas State University, KS (United States); Scott, P.R. [Department of Physics, University of Missouri, Kansas City, MO (United States); Ugorowski, P.; McGregor, D.S; Shultis, J.K. [Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS (United States); Caruso, A.N., E-mail: carusoan@umkc.edu [Department of Physics, University of Missouri, Kansas City, MO (United States)

    2013-08-11

    Accurately resolving the ambient neutron dose equivalent spanning the thermal to 15 MeV energy range with a single configuration and lightweight instrument is desirable. This paper presents the design of a portable, high intrinsic efficiency, and accurate neutron rem meter whose energy-dependent response is electronically adjusted to a chosen neutron dose equivalent standard. The instrument may be classified as a moderating type neutron spectrometer, based on an adaptation to the classical Bonner sphere and position sensitive long counter, which, simultaneously counts thermalized neutrons by high thermal efficiency solid state neutron detectors. The use of multiple detectors and moderator arranged along an axis of symmetry (e.g., long axis of a cylinder) with known neutron-slowing properties allows for the construction of a linear combination of responses that approximate the ambient neutron dose equivalent. Variations on the detector configuration are investigated via Monte Carlo N-Particle simulations to minimize the total instrument mass while maintaining acceptable response accuracy—a dose error less than 15% for bare {sup 252}Cf, bare AmBe, an epi-thermal and mixed monoenergetic sources is found at less than 4.5 kg moderator mass in all studied cases. A comparison of the energy dependent dose equivalent response and resultant energy dependent dose equivalent error of the present dosimeter to commercially-available portable rem meters and the prior art are presented. Finally, the present design is assessed by comparison of the simulated output resulting from applications of several known neutron sources and dose rates.

  7. HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors

    Sun Yanni

    2011-05-01

    Full Text Available Abstract Background Protein domain classification is an important step in metagenomic annotation. The state-of-the-art method for protein domain classification is profile HMM-based alignment. However, the relatively high rates of insertions and deletions in homopolymer regions of pyrosequencing reads create frameshifts, causing conventional profile HMM alignment tools to generate alignments with marginal scores. This makes error-containing gene fragments unclassifiable with conventional tools. Thus, there is a need for an accurate domain classification tool that can detect and correct sequencing errors. Results We introduce HMM-FRAME, a protein domain classification tool based on an augmented Viterbi algorithm that can incorporate error models from different sequencing platforms. HMM-FRAME corrects sequencing errors and classifies putative gene fragments into domain families. It achieved high error detection sensitivity and specificity in a data set with annotated errors. We applied HMM-FRAME in Targeted Metagenomics and a published metagenomic data set. The results showed that our tool can correct frameshifts in error-containing sequences, generate much longer alignments with significantly smaller E-values, and classify more sequences into their native families. Conclusions HMM-FRAME provides a complementary protein domain classification tool to conventional profile HMM-based methods for data sets containing frameshifts. Its current implementation is best used for small-scale metagenomic data sets. The source code of HMM-FRAME can be downloaded at http://www.cse.msu.edu/~zhangy72/hmmframe/ and at https://sourceforge.net/projects/hmm-frame/.

  8. Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin

    Michael B. Doud

    2016-06-01

    Full Text Available Influenza genes evolve mostly via point mutations, and so knowing the effect of every amino-acid mutation provides information about evolutionary paths available to the virus. We and others have combined high-throughput mutagenesis with deep sequencing to estimate the effects of large numbers of mutations to influenza genes. However, these measurements have suffered from substantial experimental noise due to a variety of technical problems, the most prominent of which is bottlenecking during the generation of mutant viruses from plasmids. Here we describe advances that ameliorate these problems, enabling us to measure with greatly improved accuracy and reproducibility the effects of all amino-acid mutations to an H1 influenza hemagglutinin on viral replication in cell culture. The largest improvements come from using a helper virus to reduce bottlenecks when generating viruses from plasmids. Our measurements confirm at much higher resolution the results of previous studies suggesting that antigenic sites on the globular head of hemagglutinin are highly tolerant of mutations. We also show that other regions of hemagglutinin—including the stalk epitopes targeted by broadly neutralizing antibodies—have a much lower inherent capacity to tolerate point mutations. The ability to accurately measure the effects of all influenza mutations should enhance efforts to understand and predict viral evolution.

  9. SVM-based multimodal classification of activities of daily living in Health Smart Homes: sensors, algorithms, and first experimental results.

    Fleury, Anthony; Vacher, Michel; Noury, Norbert

    2010-03-01

    By 2050, about one third of the French population will be over 65. Our laboratory's current research focuses on the monitoring of elderly people at home, to detect a loss of autonomy as early as possible. Our aim is to quantify criteria such as the international activities of daily living (ADL) or the French Autonomie Gerontologie Groupes Iso-Ressources (AGGIR) scales, by automatically classifying the different ADL performed by the subject during the day. A Health Smart Home is used for this. Our Health Smart Home includes, in a real flat, infrared presence sensors (location), door contacts (to control the use of some facilities), temperature and hygrometry sensor in the bathroom, and microphones (sound classification and speech recognition). A wearable kinematic sensor also informs postural transitions (using pattern recognition) and walk periods (frequency analysis). This data collected from the various sensors are then used to classify each temporal frame into one of the ADL that was previously acquired (seven activities: hygiene, toilet use, eating, resting, sleeping, communication, and dressing/undressing). This is done using support vector machines. We performed a 1-h experimentation with 13 young and healthy subjects to determine the models of the different activities, and then we tested the classification algorithm (cross validation) with real data.

  10. On the Use of Time–Frequency Reassignment and SVM-Based Classifier for Audio Surveillance Applications

    Souli S. Sameh

    2014-11-01

    Full Text Available In this paper, we propose a robust environmental sound spectrogram classification approach. Its purpose is surveillance and security applications based on the reassignment method and log-Gabor filters. Besides, the reassignment method is applied to the spectrogram to improve the readability of the time-frequency representation, and to assure a better localization of the signal components. Our approach includes three methods. In the first two methods, the reassigned spectrograms are passed through appropriate log-Gabor filter banks and the outputs are averaged and underwent an optimal feature selection procedure based on a mutual information criterion. The third method uses the same steps but applied only to three patches extracted from each reassigned spectrogram. The proposed approach is tested on a large database consists of 1000 sounds belonging to ten classes. The recognition is based on Multiclass Support Vector Machines.

  11. Classification of Convective and Stratiform Cells in Meteorological Radar Images Using SVM Based on a Textural Analysis

    Abdenasser Djafri; Boualem Haddad

    2014-01-01

    This contribution deals with the discrimination between stratiform and convective cells in meteorological radar images. This study is based on a textural analysis of the latter and their classification using a support vector machine (SVM). First, we apply different textural parameters such as energy, entropy, inertia, and local homogeneity. Through this experience, we identify the different textural features of both the stratiform and convective cells. Then, we use an SVM to find the best discriminating parameter between the two types of clouds. The main goal of this work is to better apply the Palmer and Marshall Z-R relations specific to each type of precipitation.

  12. Detection of subsurface metallic utilities by means of a SAP technique: Comparing MUSIC- and SVM-based approaches

    Meschino, Simone; Pajewski, Lara; Pastorino, Matteo; Randazzo, Andrea; Schettini, Giuseppe

    2013-10-01

    The identification of buried cables, pipes, conduits, and other cylindrical utilities is a very important task in civil engineering. In the last years, several methods have been proposed in the literature for tackling this problem. Most commonly employed approaches are based on the use of Ground Penetrating Radars, i.e., they extract the needed information about the unknown scenario starting from the electromagnetic field collected by a set of antennas. In the present paper, a statistical method, based on the use of smart antenna techniques, is used for the localization of a single buried object. In particular, two efficient algorithms for the estimation of the directions of arrival of the electromagnetic waves scattered by the targets, namely the MUltiple SIgnal Classification and the Support Vector Regression, are considered and their performances are compared.

  13. SVM-BASED MULTI-AGENT NEGOTIATION PARTNER SELECTION%基于SVM的多Agent协商伙伴选择

    谷琦松; 刘胜全

    2012-01-01

    According to the interactive features of Multi-agent negotiation problem, SVM (Support Vector Machine) classification method is involved in to study the Agent' s negotiation history information, extract samples from the Agent' s negotiation history information to train SVM, and combine the simulated negotiation process with one's decision-making information to predict possible results when negotiating with a particular partner and the corresponding negotiation revenue. Thus, depending on the Agent's self-interest principle, the most appropriate negotiation partner is selected. Finally, the effectiveness and superiority of the method presented in this paper are verified through simulation experiments.%根据多Agent协商问题的交互特点,引入SVM(Support Vector Machine)分类方法对Agent的协商历史信息进行学习,从Agent的协商历史信息中提取样本来训练SVM,结合模拟协商过程和己方的决策信息,预测与特定伙伴协商时可能出现的结果以及相应的协商收益,根据Agent的自利性原则,选择最合适的协商伙伴.最后,通过仿真实验验证了所提出方法的有效性和优越性.

  14. DTC-SVM Based on PI Torque and PI Flux Controllers to Achieve High Performance of Induction Motor

    Hassan Farhan Rashag

    2014-01-01

    Full Text Available The fundamental idea of direct torque control of induction machines is investigated in order to emphasize the property produced by a given voltage vector on stator flux and torque variations. The proposed control system is based on Space Vector Modulation (SVM of electrical machines, Improvement model reference adaptive system, real time of stator resistance and estimation of stator flux. The purpose of this control is to minimize electromagnetic torque and flux ripple and minimizing distortion of stator current. In this proposed method, PI torque and PI flux controller are designed to achieve estimated torque and flux with good tracking and fast response with reference torque and there is no steady state error. In addition, design of PI torque and PI flux controller are used to optimize voltages in d-q reference frame that applied to SVM. The simulation Results of proposed DTC-SVM have complete excellent performance in steady and transient states as compared with classical DTC-SVM.

  15. Full-polarization radar remote sensing and data mining for tropical crops mapping: a successful SVM-based classification model

    Denize, J.; Corgne, S.; Todoroff, P.; LE Mezo, L.

    2015-12-01

    In Reunion, a tropical island of 2,512 km², 700 km east of Madagascar in the Indian Ocean, constrained by a rugged relief, agricultural sectors are competing in highly fragmented agricultural land constituted by heterogeneous farming systems from corporate to small-scale farming. Policymakers, planners and institutions are in dire need of reliable and updated land use references. Actually conventional land use mapping methods are inefficient under the tropic with frequent cloud cover and loosely synchronous vegetative cycles of the crops due to a constant temperature. This study aims to provide an appropriate method for the identification and mapping of tropical crops by remote sensing. For this purpose, we assess the potential of polarimetric SAR imagery associated with associated with machine learning algorithms. The method has been developed and tested on a study area of 25*25 km thanks to 6 RADARSAT-2 images in 2014 in full-polarization. A set of radar indicators (backscatter coefficient, bands ratios, indices, polarimetric decompositions (Freeman-Durden, Van zyl, Yamaguchi, Cloude and Pottier, Krogager), texture, etc.) was calculated from the coherency matrix. A random forest procedure allowed the selection of the most important variables on each images to reduce the dimension of the dataset and the processing time. Support Vector Machines (SVM), allowed the classification of these indicators based on a learning database created from field observations in 2013. The method shows an overall accuracy of 88% with a Kappa index of 0.82 for the identification of four major crops.

  16. A COMPARISON STUDY OF DIFFERENT KERNEL FUNCTIONS FOR SVM-BASED CLASSIFICATION OF MULTI-TEMPORAL POLARIMETRY SAR DATA

    B. Yekkehkhany

    2014-10-01

    Full Text Available In this paper, a framework is developed based on Support Vector Machines (SVM for crop classification using polarimetric features extracted from multi-temporal Synthetic Aperture Radar (SAR imageries. The multi-temporal integration of data not only improves the overall retrieval accuracy but also provides more reliable estimates with respect to single-date data. Several kernel functions are employed and compared in this study for mapping the input space to higher Hilbert dimension space. These kernel functions include linear, polynomials and Radial Based Function (RBF. The method is applied to several UAVSAR L-band SAR images acquired over an agricultural area near Winnipeg, Manitoba, Canada. In this research, the temporal alpha features of H/A/α decomposition method are used in classification. The experimental tests show an SVM classifier with RBF kernel for three dates of data increases the Overall Accuracy (OA to up to 3% in comparison to using linear kernel function, and up to 1% in comparison to a 3rd degree polynomial kernel function.

  17. PLS-LS-SVM based modeling of ATR-IR as a robust method in detection and qualification of alprazolam

    Parhizkar, Elahehnaz; Ghazali, Mohammad; Ahmadi, Fatemeh; Sakhteman, Amirhossein

    2017-02-01

    According to the United States pharmacopeia (USP), Gold standard technique for Alprazolam determination in dosage forms is HPLC, an expensive and time-consuming method that is not easy to approach. In this study chemometrics assisted ATR-IR was introduced as an alternative method that produce similar results in fewer time and energy consumed manner. Fifty-eight samples containing different concentrations of commercial alprazolam were evaluated by HPLC and ATR-IR method. A preprocessing approach was applied to convert raw data obtained from ATR-IR spectra to normal matrix. Finally, a relationship between alprazolam concentrations achieved by HPLC and ATR-IR data was established using PLS-LS-SVM (partial least squares least squares support vector machines). Consequently, validity of the method was verified to yield a model with low error values (root mean square error of cross validation equal to 0.98). The model was able to predict about 99% of the samples according to R2 of prediction set. Response permutation test was also applied to affirm that the model was not assessed by chance correlations. At conclusion, ATR-IR can be a reliable method in manufacturing process in detection and qualification of alprazolam content.

  18. SVM-based CAD system for early detection of the Alzheimer's disease using kernel PCA and LDA.

    López, M M; Ramírez, J; Górriz, J M; Alvarez, I; Salas-Gonzalez, D; Segovia, F; Chaves, R

    2009-10-30

    Single-photon emission tomography (SPECT) imaging has been widely used to guide clinicians in the early Alzheimer's disease (AD) diagnosis challenge. However, AD detection still relies on subjective steps carried out by clinicians, which entail in some way subjectivity to the final diagnosis. In this work, kernel principal component analysis (PCA) and linear discriminant analysis (LDA) are applied on functional images as dimension reduction and feature extraction techniques, which are subsequently used to train a supervised support vector machine (SVM) classifier. The complete methodology provides a kernel-based computer-aided diagnosis (CAD) system capable to distinguish AD from normal subjects with 92.31% accuracy rate for a SPECT database consisting of 91 patients. The proposed methodology outperforms voxels-as-features (VAF) that was considered as baseline approach, which yields 80.22% for the same SPECT database.

  19. SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula.

    Emily S W Wong

    Full Text Available Spider neurotoxins are commonly used as pharmacological tools and are a popular source of novel compounds with therapeutic and agrochemical potential. Since venom peptides are inherently toxic, the host spider must employ strategies to avoid adverse effects prior to venom use. It is partly for this reason that most spider toxins encode a protective proregion that upon enzymatic cleavage is excised from the mature peptide. In order to identify the mature toxin sequence directly from toxin transcripts, without resorting to protein sequencing, the propeptide cleavage site in the toxin precursor must be predicted bioinformatically. We evaluated different machine learning strategies (support vector machines, hidden Markov model and decision tree and developed an algorithm (SpiderP for prediction of propeptide cleavage sites in spider toxins. Our strategy uses a support vector machine (SVM framework that combines both local and global sequence information. Our method is superior or comparable to current tools for prediction of propeptide sequences in spider toxins. Evaluation of the SVM method on an independent test set of known toxin sequences yielded 96% sensitivity and 100% specificity. Furthermore, we sequenced five novel peptides (not used to train the final predictor from the venom of the Australian tarantula Selenotypus plumipes to test the accuracy of the predictor and found 80% sensitivity and 99.6% 8-mer specificity. Finally, we used the predictor together with homology information to predict and characterize seven groups of novel toxins from the deeply sequenced venom gland transcriptome of S. plumipes, which revealed structural complexity and innovations in the evolution of the toxins. The precursor prediction tool (SpiderP is freely available on ArachnoServer (http://www.arachnoserver.org/spiderP.html, a web portal to a comprehensive relational database of spider toxins. All training data, test data, and scripts used are available from the SpiderP website.

  20. Analysis of inteins in the Candida parapsilosis complex for simple and accurate species identification.

    Prandini, Tâmara Heloísa Rocha; Theodoro, Raquel Cordeiro; Bruder-Nascimento, Ariane C M O; Scheel, Christina M; Bagagli, Eduardo

    2013-09-01

    Inteins are coding sequences that are transcribed and translated with flanking sequences and then are excised by an autocatalytic process. There are two types of inteins in fungi, mini-inteins and full-length inteins, both of which present a splicing domain containing well-conserved amino acid sequences. Full-length inteins also present a homing endonuclease domain that makes the intein a mobile genetic element. These parasitic genetic elements are located in highly conserved genes and may allow for the differentiation of closely related species of the Candida parapsilosis (psilosis) complex. The correct identification of the three psilosis complex species C. parapsilosis, Candida metapsilosis, and Candida orthopsilosis is very important in the clinical setting for improving antifungal therapy and patient care. In this work, we analyzed inteins that are present in the vacuolar ATPase gene VMA and in the threonyl-tRNA synthetase gene ThrRS in 85 strains of the Candida psilosis complex (46 C. parapsilosis, 17 C. metapsilosis, and 22 C. orthopsilosis). Here, we describe an accessible and accurate technique based on a single PCR that is able to differentiate the psilosis complex based on the VMA intein. Although the ThrRS intein does not distinguish the three species of the psilosis complex by PCR product size, it can differentiate them by sequencing and phylogenetic analysis. Furthermore, this intein is unusually present as both mini- and full-length forms in C. orthopsilosis. Additional population studies should be performed to address whether this represents a common intraspecific variability or the presence of subspecies within C. orthopsilosis.

  1. Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics

    Cecilia Noecker

    2015-03-01

    Full Text Available Upon infection of a new host, human immunodeficiency virus (HIV replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV. First, we found that the mode of virus production by infected cells (budding vs. bursting has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral

  2. Automatic classification and accurate size measurement of blank mask defects

    Bhamidipati, Samir; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

    2015-07-01

    A blank mask and its preparation stages, such as cleaning or resist coating, play an important role in the eventual yield obtained by using it. Blank mask defects' impact analysis directly depends on the amount of available information such as the number of defects observed, their accurate locations and sizes. Mask usability qualification at the start of the preparation process, is crudely based on number of defects. Similarly, defect information such as size is sought to estimate eventual defect printability on the wafer. Tracking of defect characteristics, specifically size and shape, across multiple stages, can further be indicative of process related information such as cleaning or coating process efficiencies. At the first level, inspection machines address the requirement of defect characterization by detecting and reporting relevant defect information. The analysis of this information though is still largely a manual process. With advancing technology nodes and reducing half-pitch sizes, a large number of defects are observed; and the detailed knowledge associated, make manual defect review process an arduous task, in addition to adding sensitivity to human errors. Cases where defect information reported by inspection machine is not sufficient, mask shops rely on other tools. Use of CDSEM tools is one such option. However, these additional steps translate into increased costs. Calibre NxDAT based MDPAutoClassify tool provides an automated software alternative to the manual defect review process. Working on defect images generated by inspection machines, the tool extracts and reports additional information such as defect location, useful for defect avoidance[4][5]; defect size, useful in estimating defect printability; and, defect nature e.g. particle, scratch, resist void, etc., useful for process monitoring. The tool makes use of smart and elaborate post-processing algorithms to achieve this. Their elaborateness is a consequence of the variety and

  3. A spectroscopic transfer standard for accurate atmospheric CO measurements

    Nwaboh, Javis A.; Li, Gang; Serdyukov, Anton; Werhahn, Olav; Ebert, Volker

    2016-04-01

    Atmospheric carbon monoxide (CO) is a precursor of essential climate variables and has an indirect effect for enhancing global warming. Accurate and reliable measurements of atmospheric CO concentration are becoming indispensable. WMO-GAW reports states a compatibility goal of ±2 ppb for atmospheric CO concentration measurements. Therefore, the EMRP-HIGHGAS (European metrology research program - high-impact greenhouse gases) project aims at developing spectroscopic transfer standards for CO concentration measurements to meet this goal. A spectroscopic transfer standard would provide results that are directly traceable to the SI, can be very useful for calibration of devices operating in the field, and could complement classical gas standards in the field where calibration gas mixtures in bottles often are not accurate, available or stable enough [1][2]. Here, we present our new direct tunable diode laser absorption spectroscopy (dTDLAS) sensor capable of performing absolute ("calibration free") CO concentration measurements, and being operated as a spectroscopic transfer standard. To achieve the compatibility goal stated by WMO for CO concentration measurements and ensure the traceability of the final concentration results, traceable spectral line data especially line intensities with appropriate uncertainties are needed. Therefore, we utilize our new high-resolution Fourier-transform infrared (FTIR) spectroscopy CO line data for the 2-0 band, with significantly reduced uncertainties, for the dTDLAS data evaluation. Further, we demonstrate the capability of our sensor for atmospheric CO measurements, discuss uncertainty calculation following the guide to the expression of uncertainty in measurement (GUM) principles and show that CO concentrations derived using the sensor, based on the TILSAM (traceable infrared laser spectroscopic amount fraction measurement) method, are in excellent agreement with gravimetric values. Acknowledgement Parts of this work have been

  4. Accurate in-line CD metrology for nanometer semiconductor manufacturing

    Perng, Baw-Ching; Shieh, Jyu-Horng; Jang, S.-M.; Liang, M.-S.; Huang, Renee; Chen, Li-Chien; Hwang, Ruey-Lian; Hsu, Joe; Fong, David

    2006-03-01

    The need for absolute accuracy is increasing as semiconductor-manufacturing technologies advance to sub-65nm nodes, since device sizes are reducing to sub-50nm but offsets ranging from 5nm to 20nm are often encountered. While TEM is well-recognized as the most accurate CD metrology, direct comparison between the TEM data and in-line CD data might be misleading sometimes due to different statistical sampling and interferences from sidewall roughness. In this work we explore the capability of CD-AFM as an accurate in-line CD reference metrology. Being a member of scanning profiling metrology, CD-AFM has the advantages of avoiding e-beam damage and minimum sample damage induced CD changes, in addition to the capability of more statistical sampling than typical cross section metrologies. While AFM has already gained its reputation on the accuracy of depth measurement, not much data was reported on the accuracy of CD-AFM for CD measurement. Our main focus here is to prove the accuracy of CD-AFM and show its measuring capability for semiconductor related materials and patterns. In addition to the typical precision check, we spent an intensive effort on examining the bias performance of this CD metrology, which is defined as the difference between CD-AFM data and the best-known CD value of the prepared samples. We first examine line edge roughness (LER) behavior for line patterns of various materials, including polysilicon, photoresist, and a porous low k material. Based on the LER characteristics of each patterning, a method is proposed to reduce its influence on CD measurement. Application of our method to a VLSI nanoCD standard is then performed, and agreement of less than 1nm bias is achieved between the CD-AFM data and the standard's value. With very careful sample preparations and TEM tool calibration, we also obtained excellent correlation between CD-AFM and TEM for poly-CDs ranging from 70nm to 400nm. CD measurements of poly ADI and low k trenches are also

  5. Accurate, low-cost 3D-models of gullies

    Onnen, Nils; Gronz, Oliver; Ries, Johannes B.; Brings, Christine

    2015-04-01

    Soil erosion is a widespread problem in arid and semi-arid areas. The most severe form is the gully erosion. They often cut into agricultural farmland and can make a certain area completely unproductive. To understand the development and processes inside and around gullies, we calculated detailed 3D-models of gullies in the Souss Valley in South Morocco. Near Taroudant, we had four study areas with five gullies different in size, volume and activity. By using a Canon HF G30 Camcorder, we made varying series of Full HD videos with 25fps. Afterwards, we used the method Structure from Motion (SfM) to create the models. To generate accurate models maintaining feasible runtimes, it is necessary to select around 1500-1700 images from the video, while the overlap of neighboring images should be at least 80%. In addition, it is very important to avoid selecting photos that are blurry or out of focus. Nearby pixels of a blurry image tend to have similar color values. That is why we used a MATLAB script to compare the derivatives of the images. The higher the sum of the derivative, the sharper an image of similar objects. MATLAB subdivides the video into image intervals. From each interval, the image with the highest sum is selected. E.g.: 20min. video at 25fps equals 30.000 single images. The program now inspects the first 20 images, saves the sharpest and moves on to the next 20 images etc. Using this algorithm, we selected 1500 images for our modeling. With VisualSFM, we calculated features and the matches between all images and produced a point cloud. Then, MeshLab has been used to build a surface out of it using the Poisson surface reconstruction approach. Afterwards we are able to calculate the size and the volume of the gullies. It is also possible to determine soil erosion rates, if we compare the data with old recordings. The final step would be the combination of the terrestrial data with the data from our aerial photography. So far, the method works well and we

  6. How accurate are our assumptions about our students' background knowledge?

    Rovick, A A; Michael, J A; Modell, H I; Bruce, D S; Horwitz, B; Adamson, T; Richardson, D R; Silverthorn, D U; Whitescarver, S A

    1999-06-01

    Teachers establish prerequisites that students must meet before they are permitted to enter their courses. It is expected that having these prerequisites will provide students with the knowledge and skills they will need to successfully learn the course content. Also, the material that the students are expected to have previously learned need not be included in a course. We wanted to determine how accurate instructors' understanding of their students background knowledge actually was. To do this, we wrote a set of multiple-choice questions that could be used to test students' knowledge of concepts deemed to be essential for learning respiratory physiology. Instructors then selected 10 of these questions to be used as a prerequisite knowledge test. The instructors also predicted the performance they expected from the students on each of the questions they had selected. The resulting tests were administered in the first week of each of seven courses. The results of this study demonstrate that instructors are poor judges of what beginning students know. Instructors tended to both underestimate and overestimate students' knowledge by large margins on individual questions. Although on the average they tended to underestimate students' factual knowledge, they overestimated the students' abilities to apply this knowledge. Hence, the validity of decisions that instructors make, predicated on the basis of their students having the prerequisite knowledge that they expect, is open to question.

  7. Accurate Completion of Medical Report on Diagnosing Death.

    Savić, Slobodan; Alempijević, Djordje; Andjelić, Sladjana

    2015-01-01

    Diagnosing death and issuing a Death Diagnosing Form (DDF) represents an activity that carries a great deal of public responsibility for medical professionals of the Emergency Medical Services (EMS) and is perpetually exposed to the control of the general public. Diagnosing death is necessary so as to confirm true, to exclude apparent death and consequentially to avoid burying a person alive, i.e. apparently dead. These expert-methodological guidelines based on the most up-to-date and medically based evidence have the goal of helping the physicians of the EMS in accurately filling out a medical report on diagnosing death. If the outcome of applied cardiopulmonary resuscitation measures is negative or when the person is found dead, the physician is under obligation to diagnose death and correctly fill out the DDF. It is also recommended to perform electrocardiography (EKG) and record asystole in at least two leads. In the process of diagnostics and treatment, it is a moral obligation of each Belgrade EMS physician to apply all available achievements and knowledge of modern medicine acquired from extensive international studies, which have been indeed the major theoretical basis for the creation of these expert-methodological guidelines. Those acting differently do so in accordance with their conscience and risk professional, and even criminal sanctions.

  8. Concurrent and Accurate Short Read Mapping on Multicore Processors.

    Martínez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina, Sergio; Castillo, Maribel; Dopazo, Joaquín; Quintana-Ortí, Enrique S

    2015-01-01

    We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.

  9. Faster and More Accurate Sequence Alignment with SNAP

    Zaharia, Matei; Curtis, Kristal; Fox, Armando; Patterson, David; Shenker, Scott; Stoica, Ion; Karp, Richard M; Sittler, Taylor

    2011-01-01

    We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST's. However, SNAP greatly reduces the number and cost of local alignment checks performed through several measures: it uses longer seeds to reduce the false positive locations considered, leverages larger memory capacities to speed index lookup, and excludes most candidate locations without fully computing their edit distance to the read. The result is an algorithm that scales well for reads from one hundred to thousands of bases long and provides a rich error model that can match classes of mutations (e.g., longer indels) that today's fast aligners ignore. We calculate that SNAP can align a dataset with 30x coverage of a human genome in le...

  10. Progress in Fast, Accurate Multi-scale Climate Simulations

    Collins, William D [Lawrence Berkeley National Laboratory (LBNL); Johansen, Hans [Lawrence Berkeley National Laboratory (LBNL); Evans, Katherine J [ORNL; Woodward, Carol S. [Lawrence Livermore National Laboratory (LLNL); Caldwell, Peter [Lawrence Livermore National Laboratory (LLNL)

    2015-01-01

    We present a survey of physical and computational techniques that have the potential to con- tribute to the next generation of high-fidelity, multi-scale climate simulations. Examples of the climate science problems that can be investigated with more depth include the capture of remote forcings of localized hydrological extreme events, an accurate representation of cloud features over a range of spatial and temporal scales, and parallel, large ensembles of simulations to more effectively explore model sensitivities and uncertainties. Numerical techniques, such as adaptive mesh refinement, implicit time integration, and separate treatment of fast physical time scales are enabling improved accuracy and fidelity in simulation of dynamics and allow more complete representations of climate features at the global scale. At the same time, part- nerships with computer science teams have focused on taking advantage of evolving computer architectures, such as many-core processors and GPUs, so that these approaches which were previously considered prohibitively costly have become both more efficient and scalable. In combination, progress in these three critical areas is poised to transform climate modeling in the coming decades.

  11. Accurate multipixel phase measurement with classical-light interferometry

    Singh, Mandeep; Khare, Kedar; Jha, Anand Kumar; Prabhakar, Shashi; Singh, R. P.

    2015-02-01

    We demonstrate accurate phase measurement from experimental low photon level interferograms using a constrained optimization method that takes into account the expected redundancy in the unknown phase function. This approach is shown to have significant noise advantage over traditional methods, such as balanced homodyning or phase shifting, that treat individual pixels in the interference data as independent of each other. Our interference experiments comparing the optimization method with the traditional phase-shifting method show that when the same photon resources are used, the optimization method provides phase recoveries with tighter error bars. In particular, rms phase error performance of the optimization method for low photon number data (10 photons per pixel) shows a >5 × noise gain over the phase-shifting method. In our experiments where a laser light source is used for illumination, the results imply phase measurement with an accuracy better than the conventional single-pixel-based shot-noise limit that assumes independent phases at individual pixels. The constrained optimization approach presented here is independent of the nature of the light source and may further enhance the accuracy of phase detection when a nonclassical-light source is used.

  12. Accurate estimators of correlation functions in Fourier space

    Sefusatti, E.; Crocce, M.; Scoccimarro, R.; Couchman, H. M. P.

    2016-08-01

    Efficient estimators of Fourier-space statistics for large number of objects rely on fast Fourier transforms (FFTs), which are affected by aliasing from unresolved small-scale modes due to the finite FFT grid. Aliasing takes the form of a sum over images, each of them corresponding to the Fourier content displaced by increasing multiples of the sampling frequency of the grid. These spurious contributions limit the accuracy in the estimation of Fourier-space statistics, and are typically ameliorated by simultaneously increasing grid size and discarding high-frequency modes. This results in inefficient estimates for e.g. the power spectrum when desired systematic biases are well under per cent level. We show that using interlaced grids removes odd images, which include the dominant contribution to aliasing. In addition, we discuss the choice of interpolation kernel used to define density perturbations on the FFT grid and demonstrate that using higher order interpolation kernels than the standard Cloud-In-Cell algorithm results in significant reduction of the remaining images. We show that combining fourth-order interpolation with interlacing gives very accurate Fourier amplitudes and phases of density perturbations. This results in power spectrum and bispectrum estimates that have systematic biases below 0.01 per cent all the way to the Nyquist frequency of the grid, thus maximizing the use of unbiased Fourier coefficients for a given grid size and greatly reducing systematics for applications to large cosmological data sets.

  13. Accurate measurement method for tube's endpoints based on machine vision

    Liu, Shaoli; Jin, Peng; Liu, Jianhua; Wang, Xiao; Sun, Peng

    2017-01-01

    Tubes are used widely in aerospace vehicles, and their accurate assembly can directly affect the assembling reliability and the quality of products. It is important to measure the processed tube's endpoints and then fix any geometric errors correspondingly. However, the traditional tube inspection method is time-consuming and complex operations. Therefore, a new measurement method for a tube's endpoints based on machine vision is proposed. First, reflected light on tube's surface can be removed by using photometric linearization. Then, based on the optimization model for the tube's endpoint measurements and the principle of stereo matching, the global coordinates and the relative distance of the tube's endpoint are obtained. To confirm the feasibility, 11 tubes are processed to remove the reflected light and then the endpoint's positions of tubes are measured. The experiment results show that the measurement repeatability accuracy is 0.167 mm, and the absolute accuracy is 0.328 mm. The measurement takes less than 1 min. The proposed method based on machine vision can measure the tube's endpoints without any surface treatment or any tools and can realize on line measurement.

  14. Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET)

    Namias, R.; Donnelly Kehoe, P.; D'Amato, J. P.; Nagel, J.

    2015-12-01

    The removal of non-brain regions in neuroimaging is a critical task to perform a favorable preprocessing. The skull-stripping depends on different factors including the noise level in the image, the anatomy of the subject being scanned and the acquisition sequence. For these and other reasons, an ideal brain extraction method should be fast, accurate, user friendly, open-source and knowledge based (to allow for the interaction with the algorithm in case the expected outcome is not being obtained), producing stable results and making it possible to automate the process for large datasets. There are already a large number of validated tools to perform this task but none of them meets the desired characteristics. In this paper we introduced an open source brain extraction tool (OSBET), composed of four steps using simple well-known operations such as: optimal thresholding, binary morphology, labeling and geometrical analysis that aims to assemble all the desired features. We present an experiment comparing OSBET with other six state-of-the-art techniques against a publicly available dataset consisting of 40 T1-weighted 3D scans and their corresponding manually segmented images. OSBET gave both: a short duration with an excellent accuracy, getting the best Dice Coefficient metric. Further validation should be performed, for instance, in unhealthy population, to generalize its usage for clinical purposes.

  15. AUTOMATED, HIGHLY ACCURATE VERIFICATION OF RELAP5-3D

    George L Mesina; David Aumiller; Francis Buschman

    2014-07-01

    Computer programs that analyze light water reactor safety solve complex systems of governing, closure and special process equations to model the underlying physics. In addition, these programs incorporate many other features and are quite large. RELAP5-3D[1] has over 300,000 lines of coding for physics, input, output, data management, user-interaction, and post-processing. For software quality assurance, the code must be verified and validated before being released to users. Verification ensures that a program is built right by checking that it meets its design specifications. Recently, there has been an increased importance on the development of automated verification processes that compare coding against its documented algorithms and equations and compares its calculations against analytical solutions and the method of manufactured solutions[2]. For the first time, the ability exists to ensure that the data transfer operations associated with timestep advancement/repeating and writing/reading a solution to a file have no unintended consequences. To ensure that the code performs as intended over its extensive list of applications, an automated and highly accurate verification method has been modified and applied to RELAP5-3D. Furthermore, mathematical analysis of the adequacy of the checks used in the comparisons is provided.

  16. An accurate {delta}f method for neoclassical transport calculation

    Wang, W.X.; Nakajima, N.; Murakami, S.; Okamoto, M. [National Inst. for Fusion Science, Toki, Gifu (Japan)

    1999-03-01

    A {delta}f method, solving drift kinetic equation, for neoclassical transport calculation is presented in detail. It is demonstrated that valid results essentially rely on the correct evaluation of marker density g in weight calculation. A general and accurate weighting scheme is developed without using some assumed g in weight equation for advancing particle weights, unlike the previous schemes. This scheme employs an additional weight function to directly solve g from its kinetic equation using the idea of {delta}f method. Therefore the severe constraint that the real marker distribution must be consistent with the initially assumed g during a simulation is relaxed. An improved like-particle collision scheme is presented. By performing compensation for momentum, energy and particle losses arising from numerical errors, the conservations of all the three quantities are greatly improved during collisions. Ion neoclassical transport due to self-collisions is examined under finite banana case as well as zero banana limit. A solution with zero particle and zero energy flux (in case of no temperature gradient) over whole poloidal section is obtained. With the improvement in both like-particle collision scheme and weighting scheme, the {delta}f simulation shows a significantly upgraded performance for neoclassical transport study. (author)

  17. Accurate estimation of third-order moments from turbulence measurements

    J. J. Podesta

    2009-02-01

    Full Text Available Politano and Pouquet's law, a generalization of Kolmogorov's four-fifths law to incompressible MHD, makes it possible to measure the energy cascade rate in incompressible MHD turbulence by means of third-order moments. In hydrodynamics, accurate measurement of third-order moments requires large amounts of data because the probability distributions of velocity-differences are nearly symmetric and the third-order moments are relatively small. Measurements of the energy cascade rate in solar wind turbulence have recently been performed for the first time, but without careful consideration of the accuracy or statistical uncertainty of the required third-order moments. This paper investigates the statistical convergence of third-order moments as a function of the sample size N. It is shown that the accuracy of the third-moment <(δ v||3> depends on the number of correlation lengths spanned by the data set and a method of estimating the statistical uncertainty of the third-moment is developed. The technique is illustrated using both wind tunnel data and solar wind data.

  18. A highly accurate ab initio potential energy surface for methane

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2016-09-01

    A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of 12CH4 reproduced with a root-mean-square error of 0.70 cm-1. The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

  19. How complete and accurate is meningococcal disease notification?

    Breen, E; Ghebrehewet, S; Regan, M; Thomson, A P J

    2004-12-01

    Effective public health control of meningococcal disease (meningococcal meningitis and septicaemia) is dependent on complete, accurate and speedy notification. Using capture-recapture techniques this study assesses the completeness, accuracy and timeliness of meningococcal notification in a health authority. The completeness of meningococcal disease notification was 94.8% (95% confidence interval 93.2% to 96.2%); 91.2% of cases in 2001 were notified within 24 hours of diagnosis, but 28.0% of notifications in 2001 were false positives. Clinical staff need to be aware of the public health implications of a notification of meningococcal disease, and of failure of, or delay in notification. Incomplete or delayed notification not only leads to inaccurate data collection but also means that important public health measures may not be taken. A clinical diagnosis of meningococcal disease should be carefully considered between the clinician and the consultant in communicable disease control (CCDC). Otherwise, prophylaxis may be given unnecessarily, disease incidence inflated, and the benefits of control measures underestimated. Consultants in communicable disease control (CCDCs), in conjunction with clinical staff, should de-notify meningococcal disease if the diagnosis changes.

  20. Accurate stereochemistry for two related 22,26-epiminocholestene derivatives

    Vega-Baez, José Luis; Sandoval-Ramírez, Jesús; Meza-Reyes, Socorro; Montiel-Smith, Sara; Gómez-Calvario, Victor [Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, San Manuel, 72000 Puebla, Pue. (Mexico); Bernès, Sylvain, E-mail: sylvain-bernes@hotmail.com [DEP Facultad de Ciencias Químicas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570 Monterrey, NL (Mexico); Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, San Manuel, 72000 Puebla, Pue. (Mexico)

    2008-04-01

    Regioselective opening of ring E of solasodine under various conditions afforded (25R)-22,26-epimino@@cholesta-5,22(N)-di@@ene-3β,16β-diyl diacetate (previously known as 3,16-diacetyl pseudosolasodine B), C{sub 31}H{sub 47}NO{sub 4}, or (22S,25R)-16β-hydr@@oxy-22,26-epimino@@cholesta-5-en-3β-yl acetate (a derivative of the naturally occurring alkaloid oblonginine), C{sub 29}H{sub 47}NO{sub 3}. In both cases, the reactions are carried out with retention of chirality at the C16, C20 and C25 stereogenic centers, which are found to be S, S and R, respectively. Although pseudosolasodine was synthesized 50 years ago, these accurate assignments clarify some controversial points about the actual stereochemistry for these alkaloids. This is of particular importance in the case of oblonginine, since this compound is currently under consideration for the treatment of aphasia arising from apoplexy; the present study defines a diastereoisomerically pure compound for pharmacological studies.

  1. Subvoxel accurate graph search using non-Euclidean graph space.

    Michael D Abràmoff

    Full Text Available Graph search is attractive for the quantitative analysis of volumetric medical images, and especially for layered tissues, because it allows globally optimal solutions in low-order polynomial time. However, because nodes of graphs typically encode evenly distributed voxels of the volume with arcs connecting orthogonally sampled voxels in Euclidean space, segmentation cannot achieve greater precision than a single unit, i.e. the distance between two adjoining nodes, and partial volume effects are ignored. We generalize the graph to non-Euclidean space by allowing non-equidistant spacing between nodes, so that subvoxel accurate segmentation is achievable. Because the number of nodes and edges in the graph remains the same, running time and memory use are similar, while all the advantages of graph search, including global optimality and computational efficiency, are retained. A deformation field calculated from the volume data adaptively changes regional node density so that node density varies with the inverse of the expected cost. We validated our approach using optical coherence tomography (OCT images of the retina and 3-D MR of the arterial wall, and achieved statistically significant increased accuracy. Our approach allows improved accuracy in volume data acquired with the same hardware, and also, preserved accuracy with lower resolution, more cost-effective, image acquisition equipment. The method is not limited to any specific imaging modality and readily extensible to higher dimensions.

  2. HIPPI: highly accurate protein family classification with ensembles of HMMs

    Nam-phuong Nguyen

    2016-11-01

    Full Text Available Abstract Background Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics. Results We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification. HIPPI uses a novel technique to represent a multiple sequence alignment for a given protein family or superfamily by an ensemble of profile hidden Markov models computed using HMMER. An evaluation of HIPPI on the Pfam database shows that HIPPI has better overall precision and recall than blastp, HMMER, and pipelines based on HHsearch, and maintains good accuracy even for fragmentary query sequences and for protein families with low average pairwise sequence identity, both conditions where other methods degrade in accuracy. Conclusion HIPPI provides accurate protein family identification and is robust to difficult model conditions. Our results, combined with observations from previous studies, show that ensembles of profile Hidden Markov models can better represent multiple sequence alignments than a single profile Hidden Markov model, and thus can improve downstream analyses for various bioinformatic tasks. Further research is needed to determine the best practices for building the ensemble of profile Hidden Markov models. HIPPI is available on GitHub at https://github.com/smirarab/sepp .

  3. Data fusion for accurate microscopic rough surface metrology.

    Chen, Yuhang

    2016-06-01

    Data fusion for rough surface measurement and evaluation was analyzed on simulated datasets, one with higher density (HD) but lower accuracy and the other with lower density (LD) but higher accuracy. Experimental verifications were then performed on laser scanning microscopy (LSM) and atomic force microscopy (AFM) characterizations of surface areal roughness artifacts. The results demonstrated that the fusion based on Gaussian process models is effective and robust under different measurement biases and noise strengths. All the amplitude, height distribution, and spatial characteristics of the original sample structure can be precisely recovered, with better metrological performance than any individual measurements. As for the influencing factors, the HD noise has a relatively weaker effect as compared with the LD noise. Furthermore, to enable an accurate fusion, the ratio of LD sampling interval to surface autocorrelation length should be smaller than a critical threshold. In general, data fusion is capable of enhancing the nanometrology of rough surfaces by combining efficient LSM measurement and down-sampled fast AFM scan. The accuracy, resolution, spatial coverage and efficiency can all be significantly improved. It is thus expected to have potential applications in development of hybrid microscopy and in surface metrology.

  4. CLOMP: Accurately Characterizing OpenMP Application Overheads

    Bronevetsky, G; Gyllenhaal, J; de Supinski, B R

    2008-11-10

    Despite its ease of use, OpenMP has failed to gain widespread use on large scale systems, largely due to its failure to deliver sufficient performance. Our experience indicates that the cost of initiating OpenMP regions is simply too high for the desired OpenMP usage scenario of many applications. In this paper, we introduce CLOMP, a new benchmark to characterize this aspect of OpenMP implementations accurately. CLOMP complements the existing EPCC benchmark suite to provide simple, easy to understand measurements of OpenMP overheads in the context of application usage scenarios. Our results for several OpenMP implementations demonstrate that CLOMP identifies the amount of work required to compensate for the overheads observed with EPCC.We also show that CLOMP also captures limitations for OpenMP parallelization on SMT and NUMA systems. Finally, CLOMPI, our MPI extension of CLOMP, demonstrates which aspects of OpenMP interact poorly with MPI when MPI helper threads cannot run on the NIC.

  5. Accurate measurement method for tube's endpoints based on machine vision

    Liu, Shaoli; Jin, Peng; Liu, Jianhua; Wang, Xiao; Sun, Peng

    2016-08-01

    Tubes are used widely in aerospace vehicles, and their accurate assembly can directly affect the assembling reliability and the quality of products. It is important to measure the processed tube's endpoints and then fix any geometric errors correspondingly. However, the traditional tube inspection method is time-consuming and complex operations. Therefore, a new measurement method for a tube's endpoints based on machine vision is proposed. First, reflected light on tube's surface can be removed by using photometric linearization. Then, based on the optimization model for the tube's endpoint measurements and the principle of stereo matching, the global coordinates and the relative distance of the tube's endpoint are obtained. To confirm the feasibility, 11 tubes are processed to remove the reflected light and then the endpoint's positions of tubes are measured. The experiment results show that the measurement repeatability accuracy is 0.167 mm, and the absolute accuracy is 0.328 mm. The measurement takes less than 1 min. The proposed method based on machine vision can measure the tube's endpoints without any surface treatment or any tools and can realize on line measurement.

  6. Accurate ionization potential of semiconductors from efficient density functional calculations

    Ye, Lin-Hui

    2016-07-01

    Despite its huge successes in total-energy-related applications, the Kohn-Sham scheme of density functional theory cannot get reliable single-particle excitation energies for solids. In particular, it has not been able to calculate the ionization potential (IP), one of the most important material parameters, for semiconductors. We illustrate that an approximate exact-exchange optimized effective potential (EXX-OEP), the Becke-Johnson exchange, can be used to largely solve this long-standing problem. For a group of 17 semiconductors, we have obtained the IPs to an accuracy similar to that of the much more sophisticated G W approximation (GWA), with the computational cost of only local-density approximation/generalized gradient approximation. The EXX-OEP, therefore, is likely as useful for solids as for finite systems. For solid surfaces, the asymptotic behavior of the vx c has effects similar to those of finite systems which, when neglected, typically cause the semiconductor IPs to be underestimated. This may partially explain why standard GWA systematically underestimates the IPs and why using the same GWA procedures has not been able to get an accurate IP and band gap at the same time.

  7. Accurate measurement of streamwise vortices in low speed aerodynamic flows

    Waldman, Rye M.; Kudo, Jun; Breuer, Kenneth S.

    2010-11-01

    Low Reynolds number experiments with flapping animals (such as bats and small birds) are of current interest in understanding biological flight mechanics, and due to their application to Micro Air Vehicles (MAVs) which operate in a similar parameter space. Previous PIV wake measurements have described the structures left by bats and birds, and provided insight to the time history of their aerodynamic force generation; however, these studies have faced difficulty drawing quantitative conclusions due to significant experimental challenges associated with the highly three-dimensional and unsteady nature of the flows, and the low wake velocities associated with lifting bodies that only weigh a few grams. This requires the high-speed resolution of small flow features in a large field of view using limited laser energy and finite camera resolution. Cross-stream measurements are further complicated by the high out-of-plane flow which requires thick laser sheets and short interframe times. To quantify and address these challenges we present data from a model study on the wake behind a fixed wing at conditions comparable to those found in biological flight. We present a detailed analysis of the PIV wake measurements, discuss the criteria necessary for accurate measurements, and present a new dual-plane PIV configuration to resolve these issues.

  8. Accurate Complex Systems Design: Integrating Serious Games with Petri Nets

    Kirsten Sinclair

    2016-03-01

    Full Text Available Difficulty understanding the large number of interactions involved in complex systems makes their successful engineering a problem. Petri Nets are one graphical modelling technique used to describe and check proposed designs of complex systems thoroughly. While automatic analysis capabilities of Petri Nets are useful, their visual form is less so, particularly for communicating the design they represent. In engineering projects, this can lead to a gap in communications between people with different areas of expertise, negatively impacting achieving accurate designs.In contrast, although capable of representing a variety of real and imaginary objects effectively, behaviour of serious games can only be analysed manually through interactive simulation. This paper examines combining the complementary strengths of Petri Nets and serious games. The novel contribution of this work is a serious game prototype of a complex system design that has been checked thoroughly. Underpinned by Petri Net analysis, the serious game can be used as a high-level interface to communicate and refine the design.Improvement of a complex system design is demonstrated by applying the integration to a proof-of-concept case study.   

  9. Accurate measurement of RF exposure from emerging wireless communication systems

    Letertre, Thierry; Monebhurrun, Vikass; Toffano, Zeno

    2013-04-01

    Isotropic broadband probes or spectrum analyzers (SAs) may be used for the measurement of rapidly varying electromagnetic fields generated by emerging wireless communication systems. In this paper this problematic is investigated by comparing the responses measured by two different isotropic broadband probes typically used to perform electric field (E-field) evaluations. The broadband probes are submitted to signals with variable duty cycles (DC) and crest factors (CF) either with or without Orthogonal Frequency Division Multiplexing (OFDM) modulation but with the same root-mean-square (RMS) power. The two probes do not provide accurate enough results for deterministic signals such as Worldwide Interoperability for Microwave Access (WIMAX) or Long Term Evolution (LTE) as well as for non-deterministic signals such as Wireless Fidelity (WiFi). The legacy measurement protocols should be adapted to cope for the emerging wireless communication technologies based on the OFDM modulation scheme. This is not easily achieved except when the statistics of the RF emission are well known. In this case the measurement errors are shown to be systematic and a correction factor or calibration can be applied to obtain a good approximation of the total RMS power.

  10. Accurate measurement of liquid transport through nanoscale conduits

    Alibakhshi, Mohammad Amin; Xie, Quan; Li, Yinxiao; Duan, Chuanhua

    2016-01-01

    Nanoscale liquid transport governs the behaviour of a wide range of nanofluidic systems, yet remains poorly characterized and understood due to the enormous hydraulic resistance associated with the nanoconfinement and the resulting minuscule flow rates in such systems. To overcome this problem, here we present a new measurement technique based on capillary flow and a novel hybrid nanochannel design and use it to measure water transport through single 2-D hydrophilic silica nanochannels with heights down to 7 nm. Our results show that silica nanochannels exhibit increased mass flow resistance compared to the classical hydrodynamics prediction. This difference increases with decreasing channel height and reaches 45% in the case of 7 nm nanochannels. This resistance increase is attributed to the formation of a 7-angstrom-thick stagnant hydration layer on the hydrophilic surfaces. By avoiding use of any pressure and flow sensors or any theoretical estimations the hybrid nanochannel scheme enables facile and precise flow measurement through single nanochannels, nanotubes, or nanoporous media and opens the prospect for accurate characterization of both hydrophilic and hydrophobic nanofluidic systems. PMID:27112404

  11. An Accurate Projector Calibration Method Based on Polynomial Distortion Representation

    Miao Liu

    2015-10-01

    Full Text Available In structure light measurement systems or 3D printing systems, the errors caused by optical distortion of a digital projector always affect the precision performance and cannot be ignored. Existing methods to calibrate the projection distortion rely on calibration plate and photogrammetry, so the calibration performance is largely affected by the quality of the plate and the imaging system. This paper proposes a new projector calibration approach that makes use of photodiodes to directly detect the light emitted from a digital projector. By analyzing the output sequence of the photoelectric module, the pixel coordinates can be accurately obtained by the curve fitting method. A polynomial distortion representation is employed to reduce the residuals of the traditional distortion representation model. Experimental results and performance evaluation show that the proposed calibration method is able to avoid most of the disadvantages in traditional methods and achieves a higher accuracy. This proposed method is also practically applicable to evaluate the geometric optical performance of other optical projection system.

  12. Accurate determination of segmented X-ray detector geometry.

    Yefanov, Oleksandr; Mariani, Valerio; Gati, Cornelius; White, Thomas A; Chapman, Henry N; Barty, Anton

    2015-11-02

    Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical for many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. We show that the refined detector geometry greatly improves the results of experiments.

  13. Study of accurate volume measurement system for plutonium nitrate solution

    Hosoma, T. [Power Reactor and Nuclear Fuel Development Corp., Tokai, Ibaraki (Japan). Tokai Works

    1998-12-01

    It is important for effective safeguarding of nuclear materials to establish a technique for accurate volume measurement of plutonium nitrate solution in accountancy tank. The volume of the solution can be estimated by two differential pressures between three dip-tubes, in which the air is purged by an compressor. One of the differential pressure corresponds to the density of the solution, and another corresponds to the surface level of the solution in the tank. The measurement of the differential pressure contains many uncertain errors, such as precision of pressure transducer, fluctuation of back-pressure, generation of bubbles at the front of the dip-tubes, non-uniformity of temperature and density of the solution, pressure drop in the dip-tube, and so on. The various excess pressures at the volume measurement are discussed and corrected by a reasonable method. High precision-differential pressure measurement system is developed with a quartz oscillation type transducer which converts a differential pressure to a digital signal. The developed system is used for inspection by the government and IAEA. (M. Suetake)

  14. Accurate energy model for WSN node and its optimal design

    Kan Baoqiang; Cai Li; Zhu Hongsong; Xu Yongjun

    2008-01-01

    With the development of CMOS and MEMS technologies, the implementation of a large number of wireless distributed micro-sensors that can be easily and rapidly deployed to form highly redundant, self-configuring, and ad hoc sensor networks. To facilitate ease of deployment, these sensors operate on battery for extended periods of time. A particular challenge in maintaining extended battery lifetime lies in achieving communications with low power. For better understanding of the design tradeoffs of wireless sensor network (WSN), a more accurate energy model for wireless sensor node is proposed, and an optimal design method of energy efficient wireless sensor node is described as well. Different from power models ever shown which assume the power cost of each component in WSN node is constant, the new one takes into account the energy dissipation of circuits in practical physical layer. It shows that there are some parameters, such as data rate, carrier frequency, bandwidth, Tsw, etc, which have a significant effect on the WSN node energy consumption per useful bit (EPUB). For a given quality specification, how energy consumption can be reduced by adjusting one or more of these parameters is shown.

  15. Accurate and efficient waveforms for compact binaries on eccentric orbits

    Huerta, E A; McWilliams, Sean T; O'Shaughnessy, Richard; Yunes, Nicolas

    2014-01-01

    Compact binaries that emit gravitational waves in the sensitivity band of ground-based detectors can have non-negligible eccentricities just prior to merger, depending on the formation scenario. We develop a purely analytic, frequency-domain model for gravitational waves emitted by compact binaries on orbits with small eccentricity, which reduces to the quasi-circular post-Newtonian approximant TaylorF2 at zero eccentricity and to the post-circular approximation of Yunes et al. (2009) at small eccentricity. Our model uses a spectral approximation to the (post-Newtonian) Kepler problem to model the orbital phase as a function of frequency, accounting for eccentricity effects up to ${\\cal{O}}(e^8)$ at each post-Newtonian order. Our approach accurately reproduces an alternative time-domain eccentric waveform model for eccentricities $e\\in [0, 0.4]$ and binaries with total mass less than 12 solar masses. As an application, we evaluate the signal amplitude that eccentric binaries produce in different networks of e...

  16. A Distributed Weighted Voting Approach for Accurate Eye Center Estimation

    Gagandeep Singh

    2013-05-01

    Full Text Available This paper proposes a novel approach for accurate estimation of eye center in face images. A distributed voting based approach in which every pixel votes is adopted for potential eye center candidates. The votes are distributed over a subset of pixels which lie in a direction which is opposite to gradient direction and the weightage of votes is distributed according to a novel mechanism.  First, image is normalized to eliminate illumination variations and its edge map is generated using Canny edge detector. Distributed voting is applied on the edge image to generate different eye center candidates. Morphological closing and local maxima search are used to reduce the number of candidates. A classifier based on spatial and intensity information is used to choose the correct candidates for the locations of eye center. The proposed approach was tested on BioID face database and resulted in better Iris detection rate than the state-of-the-art. The proposed approach is robust against illumination variation, small pose variations, presence of eye glasses and partial occlusion of eyes.Defence Science Journal, 2013, 63(3, pp.292-297, DOI:http://dx.doi.org/10.14429/dsj.63.2763

  17. Accurate reading with sequential presentation of single letters

    Nicholas Seow Chiang Price

    2012-10-01

    Full Text Available Rapid, accurate reading is possible when isolated, single words from a sentence are sequentially presented at a fixed spatial location. We investigated if reading of words and sentences is possible when single letters are rapidly presented at the fovea under user-controlled or automatically-controlled rates. When tested with complete sentences, trained participants achieved reading rates of over 60 words/minute and accuracies of over 90% with the single letter reading (SLR method and naive participants achieved average reading rates over 30 wpm with >90% accuracy. Accuracy declined as individual letters were presented for shorter periods of time, even when the overall reading rate was maintained by increasing the duration of spaces between words. Words in the lexicon that occur more frequently were identified with higher accuracy and more quickly, demonstrating that trained participants have lexical access. In combination, our data strongly suggest that comprehension is possible and that SLR is a practicable form of reading under conditions in which normal scanning of text is not possible, or for scenarios with limited spatial and temporal resolution such as patients with low vision or prostheses.

  18. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

    Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.; Fournier, Marcia V.

    2008-10-20

    One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasets having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds prognostic

  19. Radio Astronomers Set New Standard for Accurate Cosmic Distance Measurement

    1999-06-01

    A team of radio astronomers has used the National Science Foundation's Very Long Baseline Array (VLBA) to make the most accurate measurement ever made of the distance to a faraway galaxy. Their direct measurement calls into question the precision of distance determinations made by other techniques, including those announced last week by a team using the Hubble Space Telescope. The radio astronomers measured a distance of 23.5 million light-years to a galaxy called NGC 4258 in Ursa Major. "Ours is a direct measurement, using geometry, and is independent of all other methods of determining cosmic distances," said Jim Herrnstein, of the National Radio Astronomy Observatory (NRAO) in Socorro, NM. The team says their measurement is accurate to within less than a million light-years, or four percent. The galaxy is also known as Messier 106 and is visible with amateur telescopes. Herrnstein, along with James Moran and Lincoln Greenhill of the Harvard- Smithsonian Center for Astrophysics; Phillip Diamond, of the Merlin radio telescope facility at Jodrell Bank and the University of Manchester in England; Makato Inoue and Naomasa Nakai of Japan's Nobeyama Radio Observatory; Mikato Miyoshi of Japan's National Astronomical Observatory; Christian Henkel of Germany's Max Planck Institute for Radio Astronomy; and Adam Riess of the University of California at Berkeley, announced their findings at the American Astronomical Society's meeting in Chicago. "This is an incredible achievement to measure the distance to another galaxy with this precision," said Miller Goss, NRAO's Director of VLA/VLBA Operations. "This is the first time such a great distance has been measured this accurately. It took painstaking work on the part of the observing team, and it took a radio telescope the size of the Earth -- the VLBA -- to make it possible," Goss said. "Astronomers have sought to determine the Hubble Constant, the rate of expansion of the universe, for decades. This will in turn lead to an

  20. Accurate MTF measurement in digital radiography using noise response

    Kuhls-Gilcrist, Andrew; Jain, Amit; Bednarek, Daniel R.; Hoffmann, Kenneth R.; Rudin, Stephen [Toshiba Stroke Research Center, University at Buffalo, State University of New York, Biomedical Research Building, Room 445, 3435 Main Street, Buffalo, New York 14214 (United States)

    2010-02-15

    .4%. Above 0.5 f{sub N}, differences increased to an average of 20%. Deviations of the experimental results largely followed the trend seen in the simulation results, suggesting that differences between the two methods could be explained as resulting from the inherent inaccuracies of the edge-response measurement technique used in this study. Aliasing of the correlated noise component was shown to have a minimal effect on the measured MTF for the three detectors studied. Systems with significant aliasing of the correlated noise component (e.g., a-Se based detectors) would likely require a more sophisticated fitting scheme to provide accurate results. Conclusions: Results indicate that the noise-response method, a simple technique, can be used to accurately measure the MTF of digital x-ray detectors, while alleviating the problems and inaccuracies associated with use of precision test objects, such as a slit or an edge.

  1. An accurately delineated Permian-Triassic Boundary in continental successions

    2007-01-01

    The Permian-Triassic Boundary Stratigraphic Set (PTBST), characteristic of the GSSP section of Meishan and widespread in marine Permian-Triassic Boundary (PTB) sequences of South China, is used to trace and recognize the PTB in a continental sequence at Chahe (Beds 66f―68c). Diversified Permian plant fossils extended to the PTBST, and a few relicts survived above that level. Sporomorphs are dominated by fern spores of Permian nature below the PTBST, above which they are replaced by gymnosperm pollen of Triassic aspect. In the nearby Zhejue Section, the continental PTBST is characterized by the fungal 'spike' recorded in many places throughout the world. The boundary claybeds (66f and 68a,c) of the PTBST are composed of mixed illite-montmorillonite layers analogous with those at Meishan. They contain volcanogenic minerals such as β quartz and zircon. U/Pb dating of the upper claybed gives ages of 247.5 and 252.6 Ma for Beds 68a and 68c respectively, averaging 250 Ma. In contrast to the situation in Xinjiang and South Africa, the sediment sequence of the Permian-Triassic transition in the Chahe section (Beds 56―80) become finer upward. Shallowing and coarsening upward is not, therefore, characteristic of the Permian-Triassic transition everywhere. The occurrence of relicts of the Gigantopteris Flora in the Kayitou Fm. indicates that, unlike most marine biota, relicts of this paleophytic flora survived into the earliest Triassic. It is concluded that Bed 67 at Chahe corresponds to Bed 27 at Meishan, and that the PTB should be put within the 60-cm-thick Bed 67b④, now put at its base tentatively. This is the most accurate correlation of the PTB in continental facies with that in the marine GSSP.

  2. Accurate mobile malware detection and classification in the cloud.

    Wang, Xiaolei; Yang, Yuexiang; Zeng, Yingzhi

    2015-01-01

    As the dominator of the Smartphone operating system market, consequently android has attracted the attention of s malware authors and researcher alike. The number of types of android malware is increasing rapidly regardless of the considerable number of proposed malware analysis systems. In this paper, by taking advantages of low false-positive rate of misuse detection and the ability of anomaly detection to detect zero-day malware, we propose a novel hybrid detection system based on a new open-source framework CuckooDroid, which enables the use of Cuckoo Sandbox's features to analyze Android malware through dynamic and static analysis. Our proposed system mainly consists of two parts: anomaly detection engine performing abnormal apps detection through dynamic analysis; signature detection engine performing known malware detection and classification with the combination of static and dynamic analysis. We evaluate our system using 5560 malware samples and 6000 benign samples. Experiments show that our anomaly detection engine with dynamic analysis is capable of detecting zero-day malware with a low false negative rate (1.16 %) and acceptable false positive rate (1.30 %); it is worth noting that our signature detection engine with hybrid analysis can accurately classify malware samples with an average positive rate 98.94 %. Considering the intensive computing resources required by the static and dynamic analysis, our proposed detection system should be deployed off-device, such as in the Cloud. The app store markets and the ordinary users can access our detection system for malware detection through cloud service.

  3. Guidelines for accurate EC50/IC50 estimation.

    Sebaugh, J L

    2011-01-01

    This article provides minimum requirements for having confidence in the accuracy of EC50/IC50 estimates. Two definitions of EC50/IC50s are considered: relative and absolute. The relative EC50/IC50 is the parameter c in the 4-parameter logistic model and is the concentration corresponding to a response midway between the estimates of the lower and upper plateaus. The absolute EC50/IC50 is the response corresponding to the 50% control (the mean of the 0% and 100% assay controls). The guidelines first describe how to decide whether to use the relative EC50/IC50 or the absolute EC50/IC50. Assays for which there is no stable 100% control must use the relative EC50/IC50. Assays having a stable 100% control but for which there may be more than 5% error in the estimate of the 50% control mean should use the relative EC50/IC50. Assays that can be demonstrated to produce an accurate and stable 100% control and less than 5% error in the estimate of the 50% control mean may gain efficiency as well as accuracy by using the absolute EC50/IC50. Next, the guidelines provide rules for deciding when the EC50/IC50 estimates are reportable. The relative EC50/IC50 should only be used if there are at least two assay concentrations beyond the lower and upper bend points. The absolute EC50/IC50 should only be used if there are at least two assay concentrations whose predicted response is less than 50% and two whose predicted response is greater than 50%. A wide range of typical assay conditions are considered in the development of the guidelines.

  4. SNPdetector: a software tool for sensitive and accurate SNP detection.

    Jinghui Zhang

    2005-10-01

    Full Text Available Identification of single nucleotide polymorphisms (SNPs and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool, and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozygosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov.

  5. SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection.

    2005-10-01

    Full Text Available Identification of single nucleotide polymorphisms (SNPs and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool, and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozgyosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov.

  6. Accurate source location from waves scattered by surface topography

    Wang, Nian; Shen, Yang; Flinders, Ashton; Zhang, Wei

    2016-06-01

    Accurate source locations of earthquakes and other seismic events are fundamental in seismology. The location accuracy is limited by several factors, including velocity models, which are often poorly known. In contrast, surface topography, the largest velocity contrast in the Earth, is often precisely mapped at the seismic wavelength (>100 m). In this study, we explore the use of P coda waves generated by scattering at surface topography to obtain high-resolution locations of near-surface seismic events. The Pacific Northwest region is chosen as an example to provide realistic topography. A grid search algorithm is combined with the 3-D strain Green's tensor database to improve search efficiency as well as the quality of hypocenter solutions. The strain Green's tensor is calculated using a 3-D collocated-grid finite difference method on curvilinear grids. Solutions in the search volume are obtained based on the least squares misfit between the "observed" and predicted P and P coda waves. The 95% confidence interval of the solution is provided as an a posteriori error estimation. For shallow events tested in the study, scattering is mainly due to topography in comparison with stochastic lateral velocity heterogeneity. The incorporation of P coda significantly improves solution accuracy and reduces solution uncertainty. The solution remains robust with wide ranges of random noises in data, unmodeled random velocity heterogeneities, and uncertainties in moment tensors. The method can be extended to locate pairs of sources in close proximity by differential waveforms using source-receiver reciprocity, further reducing errors caused by unmodeled velocity structures.

  7. Robust, accurate and fast automatic segmentation of the spinal cord.

    De Leener, Benjamin; Kadoury, Samuel; Cohen-Adad, Julien

    2014-09-01

    Spinal cord segmentation provides measures of atrophy and facilitates group analysis via inter-subject correspondence. Automatizing this procedure enables studies with large throughput and minimizes user bias. Although several automatic segmentation methods exist, they are often restricted in terms of image contrast and field-of-view. This paper presents a new automatic segmentation method (PropSeg) optimized for robustness, accuracy and speed. The algorithm is based on the propagation of a deformable model and is divided into three parts: firstly, an initialization step detects the spinal cord position and orientation using a circular Hough transform on multiple axial slices rostral and caudal to the starting plane and builds an initial elliptical tubular mesh. Secondly, a low-resolution deformable model is propagated along the spinal cord. To deal with highly variable contrast levels between the spinal cord and the cerebrospinal fluid, the deformation is coupled with a local contrast-to-noise adaptation at each iteration. Thirdly, a refinement process and a global deformation are applied on the propagated mesh to provide an accurate segmentation of the spinal cord. Validation was performed in 15 healthy subjects and two patients with spinal cord injury, using T1- and T2-weighted images of the entire spinal cord and on multiecho T2*-weighted images. Our method was compared against manual segmentation and against an active surface method. Results show high precision for all the MR sequences. Dice coefficients were 0.9 for the T1- and T2-weighted cohorts and 0.86 for the T2*-weighted images. The proposed method runs in less than 1min on a normal computer and can be used to quantify morphological features such as cross-sectional area along the whole spinal cord.

  8. Accurate deterministic solutions for the classic Boltzmann shock profile

    Yue, Yubei

    The Boltzmann equation or Boltzmann transport equation is a classical kinetic equation devised by Ludwig Boltzmann in 1872. It is regarded as a fundamental law in rarefied gas dynamics. Rather than using macroscopic quantities such as density, temperature, and pressure to describe the underlying physics, the Boltzmann equation uses a distribution function in phase space to describe the physical system, and all the macroscopic quantities are weighted averages of the distribution function. The information contained in the Boltzmann equation is surprisingly rich, and the Euler and Navier-Stokes equations of fluid dynamics can be derived from it using series expansions. Moreover, the Boltzmann equation can reach regimes far from the capabilities of fluid dynamical equations, such as the realm of rarefied gases---the topic of this thesis. Although the Boltzmann equation is very powerful, it is extremely difficult to solve in most situations. Thus the only hope is to solve it numerically. But soon one finds that even a numerical simulation of the equation is extremely difficult, due to both the complex and high-dimensional integral in the collision operator, and the hyperbolic phase-space advection terms. For this reason, until few years ago most numerical simulations had to rely on Monte Carlo techniques. In this thesis I will present a new and robust numerical scheme to compute direct deterministic solutions of the Boltzmann equation, and I will use it to explore some classical gas-dynamical problems. In particular, I will study in detail one of the most famous and intrinsically nonlinear problems in rarefied gas dynamics, namely the accurate determination of the Boltzmann shock profile for a gas of hard spheres.

  9. Imaging tests for accurate diagnosis of acute biliary pancreatitis.

    Şurlin, Valeriu; Săftoiu, Adrian; Dumitrescu, Daniela

    2014-11-28

    Gallstones represent the most frequent aetiology of acute pancreatitis in many statistics all over the world, estimated between 40%-60%. Accurate diagnosis of acute biliary pancreatitis (ABP) is of outmost importance because clearance of lithiasis [gallbladder and common bile duct (CBD)] rules out recurrences. Confirmation of biliary lithiasis is done by imaging. The sensitivity of the ultrasonography (US) in the detection of gallstones is over 95% in uncomplicated cases, but in ABP, sensitivity for gallstone detection is lower, being less than 80% due to the ileus and bowel distension. Sensitivity of transabdominal ultrasonography (TUS) for choledocolithiasis varies between 50%-80%, but the specificity is high, reaching 95%. Diameter of the bile duct may be orientative for diagnosis. Endoscopic ultrasonography (EUS) seems to be a more effective tool to diagnose ABP rather than endoscopic retrograde cholangiopancreatography (ERCP), which should be performed only for therapeutic purposes. As the sensitivity and specificity of computerized tomography are lower as compared to state-of-the-art magnetic resonance cholangiopancreatography (MRCP) or EUS, especially for small stones and small diameter of CBD, the later techniques are nowadays preferred for the evaluation of ABP patients. ERCP has the highest accuracy for the diagnosis of choledocholithiasis and is used as a reference standard in many studies, especially after sphincterotomy and balloon extraction of CBD stones. Laparoscopic ultrasonography is a useful tool for the intraoperative diagnosis of choledocholithiasis. Routine exploration of the CBD in cases of patients scheduled for cholecystectomy after an attack of ABP was not proven useful. A significant rate of the so-called idiopathic pancreatitis is actually caused by microlithiasis and/or biliary sludge. In conclusion, the general algorithm for CBD stone detection starts with anamnesis, serum biochemistry and then TUS, followed by EUS or MRCP. In the end

  10. Accurate Classification of RNA Structures Using Topological Fingerprints

    Li, Kejie; Gribskov, Michael

    2016-01-01

    While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint. PMID:27755571

  11. Accurate source location from P waves scattered by surface topography

    Wang, N.; Shen, Y.

    2015-12-01

    Accurate source locations of earthquakes and other seismic events are fundamental in seismology. The location accuracy is limited by several factors, including velocity models, which are often poorly known. In contrast, surface topography, the largest velocity contrast in the Earth, is often precisely mapped at the seismic wavelength (> 100 m). In this study, we explore the use of P-coda waves generated by scattering at surface topography to obtain high-resolution locations of near-surface seismic events. The Pacific Northwest region is chosen as an example. The grid search method is combined with the 3D strain Green's tensor database type method to improve the search efficiency as well as the quality of hypocenter solution. The strain Green's tensor is calculated by the 3D collocated-grid finite difference method on curvilinear grids. Solutions in the search volume are then obtained based on the least-square misfit between the 'observed' and predicted P and P-coda waves. A 95% confidence interval of the solution is also provided as a posterior error estimation. We find that the scattered waves are mainly due to topography in comparison with random velocity heterogeneity characterized by the von Kάrmάn-type power spectral density function. When only P wave data is used, the 'best' solution is offset from the real source location mostly in the vertical direction. The incorporation of P coda significantly improves solution accuracy and reduces its uncertainty. The solution remains robust with a range of random noises in data, un-modeled random velocity heterogeneities, and uncertainties in moment tensors that we tested.

  12. Accurate estimation of the boundaries of a structured light pattern.

    Lee, Sukhan; Bui, Lam Quang

    2011-06-01

    Depth recovery based on structured light using stripe patterns, especially for a region-based codec, demands accurate estimation of the true boundary of a light pattern captured on a camera image. This is because the accuracy of the estimated boundary has a direct impact on the accuracy of the depth recovery. However, recovering the true boundary of a light pattern is considered difficult due to the deformation incurred primarily by the texture-induced variation of the light reflectance at surface locales. Especially for heavily textured surfaces, the deformation of pattern boundaries becomes rather severe. We present here a novel (to the best of our knowledge) method to estimate the true boundaries of a light pattern that are severely deformed due to the heavy textures involved. First, a general formula that models the deformation of the projected light pattern at the imaging end is presented, taking into account not only the light reflectance variation but also the blurring along the optical passages. The local reflectance indices are then estimated by applying the model to two specially chosen reference projections, all-bright and all-dark. The estimated reflectance indices are to transform the edge-deformed, captured pattern signal into the edge-corrected, canonical pattern signal. A canonical pattern implies the virtual pattern that would have resulted if there were neither the reflectance variation nor the blurring in imaging optics. Finally, we estimate the boundaries of a light pattern by intersecting the canonical form of a light pattern with that of its inverse pattern. The experimental results show that the proposed method results in significant improvements in the accuracy of the estimated boundaries under various adverse conditions.

  13. Bioaccessibility tests accurately estimate bioavailability of lead to quail

    Beyer, W. Nelson; Basta, Nicholas T; Chaney, Rufus L.; Henry, Paula F.; Mosby, David; Rattner, Barnett A.; Scheckel, Kirk G.; Sprague, Dan; Weber, John

    2016-01-01

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contaminated soils. Relative bioavailabilities were expressed by comparison with blood Pb concentrations in quail fed a Pb acetate reference diet. Diets containing soil from five Pb-contaminated Superfund sites had relative bioavailabilities from 33%-63%, with a mean of about 50%. Treatment of two of the soils with phosphorus significantly reduced the bioavailability of Pb. Bioaccessibility of Pb in the test soils was then measured in six in vitro tests and regressed on bioavailability. They were: the “Relative Bioavailability Leaching Procedure” (RBALP) at pH 1.5, the same test conducted at pH 2.5, the “Ohio State University In vitro Gastrointestinal” method (OSU IVG), the “Urban Soil Bioaccessible Lead Test”, the modified “Physiologically Based Extraction Test” and the “Waterfowl Physiologically Based Extraction Test.” All regressions had positive slopes. Based on criteria of slope and coefficient of determination, the RBALP pH 2.5 and OSU IVG tests performed very well. Speciation by X-ray absorption spectroscopy demonstrated that, on average, most of the Pb in the sampled soils was sorbed to minerals (30%), bound to organic matter (24%), or present as Pb sulfate (18%). Additional Pb was associated with P (chloropyromorphite, hydroxypyromorphite and tertiary Pb phosphate), and with Pb carbonates, leadhillite (a lead sulfate carbonate hydroxide), and Pb sulfide. The formation of chloropyromorphite reduced the bioavailability of Pb and the amendment of Pb-contaminated soils with P may be a thermodynamically favored means to sequester Pb.

  14. Accurate Sound Velocity Measurement in Ocean Near-Surface Layer

    Lizarralde, D.; Xu, B. L.

    2015-12-01

    Accurate sound velocity measurement is essential in oceanography because sound is the only wave that can propagate in sea water. Due to its measuring difficulties, sound velocity is often not measured directly but instead calculated from water temperature, salinity, and depth, which are much easier to obtain. This research develops a new method to directly measure the sound velocity in the ocean's near-surface layer using multi-channel seismic (MCS) hydrophones. This system consists of a device to make a sound pulse and a long cable with hundreds of hydrophones to record the sound. The distance between the source and each receiver is the offset. The time it takes the pulse to arrive to each receiver is the travel time.The errors of measuring offset and travel time will affect the accuracy of sound velocity if we calculated with just one offset and one travel time. However, by analyzing the direct arrival signal from hundreds of receivers, the velocity can be determined as the slope of a straight line in the travel time-offset graph. The errors in distance and time measurement result in only an up or down shift of the line and do not affect the slope. This research uses MCS data of survey MGL1408 obtained from the Marine Geoscience Data System and processed with Seismic Unix. The sound velocity can be directly measured to an accuracy of less than 1m/s. The included graph shows the directly measured velocity verses the calculated velocity along 100km across the Mid-Atlantic continental margin. The directly measured velocity shows a good coherence to the velocity computed from temperature and salinity. In addition, the fine variations in the sound velocity can be observed, which is hardly seen from the calculated velocity. Using this methodology, both large area acquisition and fine resolution can be achieved. This directly measured sound velocity will be a new and powerful tool in oceanography.

  15. Cephalometric analysis for accurately determining the vertical dimension (case report

    Wahipa Wiro

    2017-04-01

    Full Text Available Objective : Determination of the vertical dimension of occlusion (DVO tends to changes throughout the human life. The vertical dimension is determined by the interocclusal point of the upper and lower teeth contact so the application is limited when the natural teeth was missing. As the result, many functional and aesthetic changes are occurred in the whole orofacial region and stomatognathic system. DVO is one of the difficult stages in prosthodontic treatment. Most of the techniques to determine DVO in edentulous patients are based on the soft tissue references, which can cause the different measurements. Cephalometric analysis allows the evaluation of bone growth changes and can be used as a diagnostic tool in prosthodontics to evaluate the results of prosthodontic rehabilitation. Methods : The purpose of this case report was to find out the results of the vertical dimension of occlusion measurements in maxillomandibular relation by using cephalometric photo in patients who have been long lost their teeth and have never been using denture. Results : A 50 year old female patient, partially edentulous on the upper and lower jaw with the remaining teeth were 12 (residual root, 11,21,23,33 and 43. The remaining teeth were endodontically treated prior the complete denture procedure. Cephalometric photo was done in patients after making bite rim, upper and lower bite rim were given metal marker, the image was traced, then measured between metal to get the vertical dimension of occlusion. Conclusion : The measurement results of the vertical dimension of occlusion by using cephalometric photo on making full denture were more accurate, so it could improve and restore the masticatory function, aesthetic function and phonetics.

  16. Accurate absolute measurement of trapped Cs atoms in a MOT

    Talavera O, M.; Lopez R, M.; Carlos L, E. de [Division de Tiempo y Frecuencia, Centro Nacional de Metrologia, CENAM, km 4.5 Carretera a los Cues, El Marques, 76241 Queretaro (Mexico); Jimenez S, S. [Centro de Investigacion y Estudios Avanzados del lPN, Unidad Queretaro, Libramiento Norponiente No. 2000, Fracc. Real de Juriquilla, 76230 Queretaro (Mexico)

    2007-07-01

    A Cs-133 Magneto-Optical Trap (MOT) has been developed at the Time and Frequency Division of the Centro Nacional de Metrologia, CENAM, in Mexico. This MOT is part of a primary frequency standard based on ultra-cold Cs atoms, called CsF-1 clock, under development at CENAM. In this Cs MOT, we use the standard configuration ({sigma}{sup +} - {sigma}{sup -}) 4-horizontal 2-vertical laser beams 1.9 cm in diameter, with 5 mW each. We use a 852 nm, 5 mW, DBR laser as a master laser which is stabilized by saturation spectroscopy. Emission linewidth of the master laser is l MHz. In order to amplify the light of the master laser, a 50 mW, 852 nm AlGaAs laser is used as slave laser. This slave laser is stabilized by light injection technique. A 12 MHz red shift of the light is performed by two double passes through two Acusto-Optic Modulators (AOMs). The optical part of the CENAMs MOT is very robust against mechanical vibration, acoustic noise and temperature changes in our laboratory, because none of our diode lasers use an extended cavity to reduce the linewidth. In this paper, we report results of our MOT characterization as a function of several operation parameters such as the intensity of laser beams, the laser beam diameter, the red shift of light, and the gradient of the magnetic field. We also report accurate absolute measurement of the number of Cs atoms trapped in our Cs MOT. We found up to 6 x 10{sup 7} Cs atoms trapped in our MOT measured with an uncertainty no greater than 6.4%. (Author)

  17. Artificial neural network accurately predicts hepatitis B surface antigen seroclearance.

    Ming-Hua Zheng

    Full Text Available BACKGROUND & AIMS: Hepatitis B surface antigen (HBsAg seroclearance and seroconversion are regarded as favorable outcomes of chronic hepatitis B (CHB. This study aimed to develop artificial neural networks (ANNs that could accurately predict HBsAg seroclearance or seroconversion on the basis of available serum variables. METHODS: Data from 203 untreated, HBeAg-negative CHB patients with spontaneous HBsAg seroclearance (63 with HBsAg seroconversion, and 203 age- and sex-matched HBeAg-negative controls were analyzed. ANNs and logistic regression models (LRMs were built and tested according to HBsAg seroclearance and seroconversion. Predictive accuracy was assessed with area under the receiver operating characteristic curve (AUROC. RESULTS: Serum quantitative HBsAg (qHBsAg and HBV DNA levels, qHBsAg and HBV DNA reduction were related to HBsAg seroclearance (P<0.001 and were used for ANN/LRM-HBsAg seroclearance building, whereas, qHBsAg reduction was not associated with ANN-HBsAg seroconversion (P = 0.197 and LRM-HBsAg seroconversion was solely based on qHBsAg (P = 0.01. For HBsAg seroclearance, AUROCs of ANN were 0.96, 0.93 and 0.95 for the training, testing and genotype B subgroups respectively. They were significantly higher than those of LRM, qHBsAg and HBV DNA (all P<0.05. Although the performance of ANN-HBsAg seroconversion (AUROC 0.757 was inferior to that for HBsAg seroclearance, it tended to be better than those of LRM, qHBsAg and HBV DNA. CONCLUSIONS: ANN identifies spontaneous HBsAg seroclearance in HBeAg-negative CHB patients with better accuracy, on the basis of easily available serum data. More useful predictors for HBsAg seroconversion are still needed to be explored in the future.

  18. Towards accurate and precise estimates of lion density.

    Elliot, Nicholas B; Gopalaswamy, Arjun M

    2016-12-13

    Reliable estimates of animal density are fundamental to our understanding of ecological processes and population dynamics. Furthermore, their accuracy is vital to conservation biology since wildlife authorities rely on these figures to make decisions. However, it is notoriously difficult to accurately estimate density for wide-ranging species such as carnivores that occur at low densities. In recent years, significant progress has been made in density estimation of Asian carnivores, but the methods have not been widely adapted to African carnivores. African lions (Panthera leo) provide an excellent example as although abundance indices have been shown to produce poor inferences, they continue to be used to estimate lion density and inform management and policy. In this study we adapt a Bayesian spatially explicit capture-recapture model to estimate lion density in the Maasai Mara National Reserve (MMNR) and surrounding conservancies in Kenya. We utilize sightings data from a three-month survey period to produce statistically rigorous spatial density estimates. Overall posterior mean lion density was estimated to be 16.85 (posterior standard deviation = 1.30) lions over one year of age per 100km(2) with a sex ratio of 2.2♀:1♂. We argue that such methods should be developed, improved and favored over less reliable methods such as track and call-up surveys. We caution against trend analyses based on surveys of differing reliability and call for a unified framework to assess lion numbers across their range in order for better informed management and policy decisions to be made. This article is protected by copyright. All rights reserved.

  19. A fast and accurate algorithm for diploid individual haplotype reconstruction.

    Wu, Jingli; Liang, Binbin

    2013-08-01

    Haplotypes can provide significant information in many research fields, including molecular biology and medical therapy. However, haplotyping is much more difficult than genotyping by using only biological techniques. With the development of sequencing technologies, it becomes possible to obtain haplotypes by combining sequence fragments. The haplotype reconstruction problem of diploid individual has received considerable attention in recent years. It assembles the two haplotypes for a chromosome given the collection of fragments coming from the two haplotypes. Fragment errors significantly increase the difficulty of the problem, and which has been shown to be NP-hard. In this paper, a fast and accurate algorithm, named FAHR, is proposed for haplotyping a single diploid individual. Algorithm FAHR reconstructs the SNP sites of a pair of haplotypes one after another. The SNP fragments that cover some SNP site are partitioned into two groups according to the alleles of the corresponding SNP site, and the SNP values of the pair of haplotypes are ascertained by using the fragments in the group that contains more SNP fragments. The experimental comparisons were conducted among the FAHR, the Fast Hare and the DGS algorithms by using the haplotypes on chromosome 1 of 60 individuals in CEPH samples, which were released by the International HapMap Project. Experimental results under different parameter settings indicate that the reconstruction rate of the FAHR algorithm is higher than those of the Fast Hare and the DGS algorithms, and the running time of the FAHR algorithm is shorter than those of the Fast Hare and the DGS algorithms. Moreover, the FAHR algorithm has high efficiency even for the reconstruction of long haplotypes and is very practical for realistic applications.

  20. How accurate are the weather forecasts for Bierun (southern Poland)?

    Gawor, J.

    2012-04-01

    Weather forecast accuracy has increased in recent times mainly thanks to significant development of numerical weather prediction models. Despite the improvements, the forecasts should be verified to control their quality. The evaluation of forecast accuracy can also be an interesting learning activity for students. It joins natural curiosity about everyday weather and scientific process skills: problem solving, database technologies, graph construction and graphical analysis. The examination of the weather forecasts has been taken by a group of 14-year-old students from Bierun (southern Poland). They participate in the GLOBE program to develop inquiry-based investigations of the local environment. For the atmospheric research the automatic weather station is used. The observed data were compared with corresponding forecasts produced by two numerical weather prediction models, i.e. COAMPS (Coupled Ocean/Atmosphere Mesoscale Prediction System) developed by Naval Research Laboratory Monterey, USA; it runs operationally at the Interdisciplinary Centre for Mathematical and Computational Modelling in Warsaw, Poland and COSMO (The Consortium for Small-scale Modelling) used by the Polish Institute of Meteorology and Water Management. The analysed data included air temperature, precipitation, wind speed, wind chill and sea level pressure. The prediction periods from 0 to 24 hours (Day 1) and from 24 to 48 hours (Day 2) were considered. The verification statistics that are commonly used in meteorology have been applied: mean error, also known as bias, for continuous data and a 2x2 contingency table to get the hit rate and false alarm ratio for a few precipitation thresholds. The results of the aforementioned activity became an interesting basis for discussion. The most important topics are: 1) to what extent can we rely on the weather forecasts? 2) How accurate are the forecasts for two considered time ranges? 3) Which precipitation threshold is the most predictable? 4) Why

  1. Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.

    Jie Zhu

    Full Text Available DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.

  2. Accurate Quantification of microRNA via Single Strand Displacement Reaction on DNA Origami Motif

    Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

    2013-01-01

    DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs. PMID:23990889

  3. Simple, rapid and accurate molecular diagnosis of acute promyelocytic leukemia by loop mediated amplification technology.

    Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia

    2015-01-01

    The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10(-3) for bcr1 and bcr3 and 10(-)2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL.

  4. Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection.

    Giske Biesbroek

    Full Text Available INTRODUCTION: Accurate analyses of microbiota composition of low-density communities (10(3-10(4 bacteria/sample can be challenging. Background DNA from chemicals and consumables, extraction biases as well as differences in PCR efficiency can significantly interfere with microbiota assessment. This study was aiming to establish protocols for accurate microbiota analysis at low microbial density. METHODS: To examine possible effects of bacterial density on microbiota analyses we compared microbiota profiles of serial diluted saliva and low (nares, nasopharynx and high-density (oropharynx upper airway communities in four healthy individuals. DNA was extracted with four different extraction methods (Epicentre Masterpure, Qiagen DNeasy, Mobio Powersoil and a phenol bead-beating protocol combined with Agowa-Mag-mini. Bacterial DNA recovery was analysed by 16S qPCR and microbiota profiles through GS-FLX-Titanium-Sequencing of 16S rRNA gene amplicons spanning the V5-V7 regions. RESULTS: Lower template concentrations significantly impacted microbiota profiling results. With higher dilutions, low abundant species were overrepresented. In samples of <10(5 bacteria per ml, e.g. DNA <1 pg/µl, microbiota profiling deviated from the original sample and other dilutions showing a significant increase in the taxa Proteobacteria and decrease in Bacteroidetes. In similar low density samples, DNA extraction method determined if DNA levels were below or above 1 pg/µl and, together with lysis preferences per method, had profound impact on microbiota analyses in both relative abundance as well as representation of species. CONCLUSION: This study aimed to interpret microbiota analyses of low-density communities. Bacterial density seemed to interfere with microbiota analyses at < than 10(6 bacteria per ml or DNA <1 pg/µl. We therefore recommend this threshold for working with low density materials. This study underlines that bias reduction is crucial for adequate

  5. Accurate and Timely Forecasting of CME-Driven Geomagnetic Storms

    Chen, J.; Kunkel, V.; Skov, T. M.

    2015-12-01

    Wide-spread and severe geomagnetic storms are primarily caused by theejecta of coronal mass ejections (CMEs) that impose long durations ofstrong southward interplanetary magnetic field (IMF) on themagnetosphere, the duration and magnitude of the southward IMF (Bs)being the main determinants of geoeffectiveness. Another importantquantity to forecast is the arrival time of the expected geoeffectiveCME ejecta. In order to accurately forecast these quantities in atimely manner (say, 24--48 hours of advance warning time), it isnecessary to calculate the evolving CME ejecta---its structure andmagnetic field vector in three dimensions---using remote sensing solardata alone. We discuss a method based on the validated erupting fluxrope (EFR) model of CME dynamics. It has been shown using STEREO datathat the model can calculate the correct size, magnetic field, and theplasma parameters of a CME ejecta detected at 1 AU, using the observedCME position-time data alone as input (Kunkel and Chen 2010). Onedisparity is in the arrival time, which is attributed to thesimplified geometry of circular toroidal axis of the CME flux rope.Accordingly, the model has been extended to self-consistently includethe transverse expansion of the flux rope (Kunkel 2012; Kunkel andChen 2015). We show that the extended formulation provides a betterprediction of arrival time even if the CME apex does not propagatedirectly toward the earth. We apply the new method to a number of CMEevents and compare predicted flux ropes at 1 AU to the observed ejectastructures inferred from in situ magnetic and plasma data. The EFRmodel also predicts the asymptotic ambient solar wind speed (Vsw) foreach event, which has not been validated yet. The predicted Vswvalues are tested using the ENLIL model. We discuss the minimum andsufficient required input data for an operational forecasting systemfor predicting the drivers of large geomagnetic storms.Kunkel, V., and Chen, J., ApJ Lett, 715, L80, 2010. Kunkel, V., Ph

  6. Fast and accurate line scanner based on white light interferometry

    Lambelet, Patrick; Moosburger, Rudolf

    2013-04-01

    White-light interferometry is a highly accurate technology for 3D measurements. The principle is widely utilized in surface metrology instruments but rarely adopted for in-line inspection systems. The main challenges for rolling out inspection systems based on white-light interferometry to the production floor are its sensitivity to environmental vibrations and relatively long measurement times: a large quantity of data needs to be acquired and processed in order to obtain a single topographic measurement. Heliotis developed a smart-pixel CMOS camera (lock-in camera) which is specially suited for white-light interferometry. The demodulation of the interference signal is treated at the level of the pixel which typically reduces the acquisition data by one orders of magnitude. Along with the high bandwidth of the dedicated lock-in camera, vertical scan-speeds of more than 40mm/s are reachable. The high scan speed allows for the realization of inspection systems that are rugged against external vibrations as present on the production floor. For many industrial applications such as the inspection of wafer-bumps, surface of mechanical parts and solar-panel, large areas need to be measured. In this case either the instrument or the sample are displaced laterally and several measurements are stitched together. The cycle time of such a system is mostly limited by the stepping time for multiple lateral displacements. A line-scanner based on white light interferometry would eliminate most of the stepping time while maintaining robustness and accuracy. A. Olszak proposed a simple geometry to realize such a lateral scanning interferometer. We demonstrate that such inclined interferometers can benefit significantly from the fast in-pixel demodulation capabilities of the lock-in camera. One drawback of an inclined observation perspective is that its application is limited to objects with scattering surfaces. We therefore propose an alternate geometry where the incident light is

  7. Technological Basis and Scientific Returns for Absolutely Accurate Measurements

    Dykema, J. A.; Anderson, J.

    2011-12-01

    The 2006 NRC Decadal Survey fostered a new appreciation for societal objectives as a driving motivation for Earth science. Many high-priority societal objectives are dependent on predictions of weather and climate. These predictions are based on numerical models, which derive from approximate representations of well-founded physics and chemistry on space and timescales appropriate to global and regional prediction. These laws of chemistry and physics in turn have a well-defined quantitative relationship with physical measurement units, provided these measurement units are linked to international measurement standards that are the foundation of contemporary measurement science and standards for engineering and commerce. Without this linkage, measurements have an ambiguous relationship to scientific principles that introduces avoidable uncertainty in analyses, predictions, and improved understanding of the Earth system. Since the improvement of climate and weather prediction is fundamentally dependent on the improvement of the representation of physical processes, measurement systems that reduce the ambiguity between physical truth and observations represent an essential component of a national strategy for understanding and living with the Earth system. This paper examines the technological basis and potential science returns of sensors that make measurements that are quantitatively tied on-orbit to international measurement standards, and thus testable to systematic errors. This measurement strategy provides several distinct benefits. First, because of the quantitative relationship between these international measurement standards and fundamental physical constants, measurements of this type accurately capture the true physical and chemical behavior of the climate system and are not subject to adjustment due to excluded measurement physics or instrumental artifacts. In addition, such measurements can be reproduced by scientists anywhere in the world, at any time

  8. Measurement of Fracture Geometry for Accurate Computation of Hydraulic Conductivity

    Chae, B.; Ichikawa, Y.; Kim, Y.

    2003-12-01

    Fluid flow in rock mass is controlled by geometry of fractures which is mainly characterized by roughness, aperture and orientation. Fracture roughness and aperture was observed by a new confocal laser scanning microscope (CLSM; Olympus OLS1100). The wavelength of laser is 488nm, and the laser scanning is managed by a light polarization method using two galvano-meter scanner mirrors. The system improves resolution in the light axis (namely z) direction because of the confocal optics. The sampling is managed in a spacing 2.5 μ m along x and y directions. The highest measurement resolution of z direction is 0.05 μ m, which is the more accurate than other methods. For the roughness measurements, core specimens of coarse and fine grained granites were provided. Measurements were performed along three scan lines on each fracture surface. The measured data were represented as 2-D and 3-D digital images showing detailed features of roughness. Spectral analyses by the fast Fourier transform (FFT) were performed to characterize on the roughness data quantitatively and to identify influential frequency of roughness. The FFT results showed that components of low frequencies were dominant in the fracture roughness. This study also verifies that spectral analysis is a good approach to understand complicate characteristics of fracture roughness. For the aperture measurements, digital images of the aperture were acquired under applying five stages of uniaxial normal stresses. This method can characterize the response of aperture directly using the same specimen. Results of measurements show that reduction values of aperture are different at each part due to rough geometry of fracture walls. Laboratory permeability tests were also conducted to evaluate changes of hydraulic conductivities related to aperture variation due to different stress levels. The results showed non-uniform reduction of hydraulic conductivity under increase of the normal stress and different values of

  9. Fast and accurate predictions of covalent bonds in chemical space

    Chang, K. Y. Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O. Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (˜1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H 2+ . Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  10. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.

    Oscar Westesson

    Full Text Available The Multiple Sequence Alignment (MSA is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history, it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.

  11. On the relation between gene flow theory and genetic gain

    Woolliams John A

    2000-01-01

    Full Text Available Abstract In conventional gene flow theory the rate of genetic gain is calculated as the summed products of genetic selection differential and asymptotic proportion of genes deriving from sex-age groups. Recent studies have shown that asymptotic proportions of genes predicted from conventional gene flow theory may deviate considerably from true proportions. However, the rate of genetic gain predicted from conventional gene flow theory was accurate. The current note shows that the connection between asymptotic proportions of genes and rate of genetic gain that is embodied in conventional gene flow theory is invalid, even though genetic gain may be predicted correctly from it.

  12. Interaction potentials for water from accurate cluster calculations

    Xantheas, Sotiris S.

    2006-03-15

    simulations such as the first computer simulation of liquid water by Barker and Watts and Rahman and Stillinger, the first parametrization of a pair potential for water from ab-initio calculations by Clementi and co-workers and the first simulation of liquid water from first principles by Parrinello and Carr. Many of the empirical pair potentials for water that are used widely even nowadays were developed in the early 1980's. These early models were mainly parameterized in order to reproduce measured thermodynamic bulk properties due to the fact that molecular level information for small water clusters was limited or even nonexisting at that time. Subsequent attempts have focused in introducing self-consistent polarization as a means of explicitly accounting for the magnitude of the non-additive many-body effects via an induction scheme. Again the lack of accurate experimental or theoretical water cluster energetic information has prevented the assessment of the accuracy of those models.

  13. Quantifying Methane Fluxes Simply and Accurately: The Tracer Dilution Method

    Rella, Christopher; Crosson, Eric; Green, Roger; Hater, Gary; Dayton, Dave; Lafleur, Rick; Merrill, Ray; Tan, Sze; Thoma, Eben

    2010-05-01

    Methane is an important atmospheric constituent with a wide variety of sources, both natural and anthropogenic, including wetlands and other water bodies, permafrost, farms, landfills, and areas with significant petrochemical exploration, drilling, transport, or processing, or refining occurs. Despite its importance to the carbon cycle, its significant impact as a greenhouse gas, and its ubiquity in modern life as a source of energy, its sources and sinks in marine and terrestrial ecosystems are only poorly understood. This is largely because high quality, quantitative measurements of methane fluxes in these different environments have not been available, due both to the lack of robust field-deployable instrumentation as well as to the fact that most significant sources of methane extend over large areas (from 10's to 1,000,000's of square meters) and are heterogeneous emitters - i.e., the methane is not emitted evenly over the area in question. Quantifying the total methane emissions from such sources becomes a tremendous challenge, compounded by the fact that atmospheric transport from emission point to detection point can be highly variable. In this presentation we describe a robust, accurate, and easy-to-deploy technique called the tracer dilution method, in which a known gas (such as acetylene, nitrous oxide, or sulfur hexafluoride) is released in the same vicinity of the methane emissions. Measurements of methane and the tracer gas are then made downwind of the release point, in the so-called far-field, where the area of methane emissions cannot be distinguished from a point source (i.e., the two gas plumes are well-mixed). In this regime, the methane emissions are given by the ratio of the two measured concentrations, multiplied by the known tracer emission rate. The challenges associated with atmospheric variability and heterogeneous methane emissions are handled automatically by the transport and dispersion of the tracer. We present detailed methane flux

  14. Evidence based selection of housekeeping genes.

    Hendrik J M de Jonge

    Full Text Available For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes (reference or internal control genes is required. It is known that commonly used housekeeping genes (e.g. ACTB, GAPDH, HPRT1, and B2M vary considerably under different experimental conditions and therefore their use for normalization is limited. We performed a meta-analysis of 13,629 human gene array samples in order to identify the most stable expressed genes. Here we show novel candidate housekeeping genes (e.g. RPS13, RPL27, RPS20 and OAZ1 with enhanced stability among a multitude of different cell types and varying experimental conditions. None of the commonly used housekeeping genes were present in the top 50 of the most stable expressed genes. In addition, using 2,543 diverse mouse gene array samples we were able to confirm the enhanced stability of the candidate novel housekeeping genes in another mammalian species. Therefore, the identified novel candidate housekeeping genes seem to be the most appropriate choice for normalizing gene expression data.

  15. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph.

    Yonghui Wu

    2008-10-01

    Full Text Available Genetic linkage maps are cornerstones of a wide spectrum of biotechnology applications, including map-assisted breeding, association genetics, and map-assisted gene cloning. During the past several years, the adoption of high-throughput genotyping technologies has been paralleled by a substantial increase in the density and diversity of genetic markers. New genetic mapping algorithms are needed in order to efficiently process these large datasets and accurately construct high-density genetic maps. In this paper, we introduce a novel algorithm to order markers on a genetic linkage map. Our method is based on a simple yet fundamental mathematical property that we prove under rather general assumptions. The validity of this property allows one to determine efficiently the correct order of markers by computing the minimum spanning tree of an associated graph. Our empirical studies obtained on genotyping data for three mapping populations of barley (Hordeum vulgare, as well as extensive simulations on synthetic data, show that our algorithm consistently outperforms the best available methods in the literature, particularly when the input data are noisy or incomplete. The software implementing our algorithm is available in the public domain as a web tool under the name MSTmap.

  16. Accurate determination of plasmid copy number of flow-sorted cells using droplet digital PCR.

    Jahn, Michael; Vorpahl, Carsten; Türkowsky, Dominique; Lindmeyer, Martin; Bühler, Bruno; Harms, Hauke; Müller, Susann

    2014-06-17

    Many biotechnological processes rely on the expression of a plasmid-based target gene. A constant and sufficient number of plasmids per cell is desired for efficient protein production. To date, only a few methods for the determination of plasmid copy number (PCN) are available, and most of them average the PCN of total populations disregarding heterogeneous distributions. Here, we utilize the highly precise quantification of DNA molecules by droplet digital PCR (ddPCR) and combine it with cell sorting using flow cytometry. A duplex PCR assay was set up requiring only 1000 sorted cells for precise determination of PCN. The robustness of this method was proven by thorough optimization of cell sorting, cell disruption, and PCR conditions. When non plasmid-harboring cells of Pseudomonas putida KT2440 were spiked with different dilutions of the expression plasmid pA-EGFP_B, a PCN from 1 to 64 could be accurately detected. As a proof of principle, induced cultures of P. putida KT2440 producing an EGFP-fused model protein by means of the plasmid pA-EGFP_B were investigated by flow cytometry and showed two distinct subpopulations, fluorescent and nonfluorescent cells. These two subpopulations were sorted for PCN determination with ddPCR. A remarkably diverging plasmid distribution was found within the population, with nonfluorescent cells showing a much lower PCN (≤1) than fluorescent cells (PCN of up to 5) under standard conditions.

  17. ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers

    Visel, Axel; Blow, Matthew J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Ren, Bing; Rubin, Edward M.; Pennacchio, Len A.

    2009-02-01

    A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover since they are scattered amongst the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here, we performed chromatin immunoprecipitation with the enhancer-associated protein p300, followed by massively-parallel sequencing, to map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain, and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases revealed reproducible enhancer activity in those tissues predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities and suggest that such datasets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.

  18. Reranking candidate gene models with cross-species comparison for improved gene prediction

    Pereira Fernando CN

    2008-10-01

    Full Text Available Abstract Background Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc. Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models.

  19. An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test

    Rodriguez, Jesse M.

    2013-01-01

    Studies that map disease genes rely on accurate annotations that indicate whether individuals in the studied cohorts are related to each other or not. For example, in genome-wide association studies, the cohort members are assumed to be unrelated to one another. Investigators can correct for individuals in a cohort with previously-unknown shared familial descent by detecting genomic segments that are shared between them, which are considered to be identical by descent (IBD). Alternatively, elevated frequencies of IBD segments near a particular locus among affected individuals can be indicative of a disease-associated gene. As genotyping studies grow to use increasingly large sample sizes and meta-analyses begin to include many data sets, accurate and efficient detection of hidden relatedness becomes a challenge. To enable disease-mapping studies of increasingly large cohorts, a fast and accurate method to detect IBD segments is required. We present PARENTE, a novel method for detecting related pairs of individuals and shared haplotypic segments within these pairs. PARENTE is a computationally-efficient method based on an embedded likelihood ratio test. As demonstrated by the results of our simulations, our method exhibits better accuracy than the current state of the art, and can be used for the analysis of large genotyped cohorts. PARENTE\\'s higher accuracy becomes even more significant in more challenging scenarios, such as detecting shorter IBD segments or when an extremely low false-positive rate is required. PARENTE is publicly and freely available at http://parente.stanford.edu/. © 2013 Springer-Verlag.

  20. FunGeneClusterS

    Vesth, Tammi Camilla; Brandl, Julian; Andersen, Mikael Rørdam

    2016-01-01

    and industrial biotechnology applications. We have previously published a method for accurate prediction of clusters from genome and transcriptome data, which could also suggest cross-chemistry, however, this method was limited both in the number of parameters which could be adjusted as well as in user......Secondary metabolites of fungi are receiving an increasing amount of interest due to their prolific bioactivities and the fact that fungal biosynthesis of secondary metabolites often occurs from co-regulated and co-located gene clusters. This makes the gene clusters attractive for synthetic biology...

  1. MRI Reporter Genes for Noninvasive Molecular Imaging

    Caixia Yang

    2016-05-01

    Full Text Available Magnetic resonance imaging (MRI is one of the most important imaging technologies used in clinical diagnosis. Reporter genes for MRI can be applied to accurately track the delivery of cell in cell therapy, evaluate the therapy effect of gene delivery, and monitor tissue/cell-specific microenvironments. Commonly used reporter genes for MRI usually include genes encoding the enzyme (e.g., tyrosinase and β-galactosidase, the receptor on the cells (e.g., transferrin receptor, and endogenous reporter genes (e.g., ferritin reporter gene. However, low sensitivity limits the application of MRI and reporter gene-based multimodal imaging strategies are common including optical imaging and radionuclide imaging. These can significantly improve diagnostic efficiency and accelerate the development of new therapies.

  2. Gene therapy

    2005-01-01

    2005147 CNHK200-hA-a gene-viral therapeutic system and its antitumor effect on lung cancer. WANG Wei-guo(王伟国),et al. Viral & Gene Ther Center, Eastern Hepatobilli Surg Instit 2nd Milit Univ, Shanghai 200438. Chin J Oncol,2005:27(2):69-72. Objective: To develop a novel vector system, which combines the advantages of the gene therapy,

  3. Efficient exploration of the space of reconciled gene trees.

    Szöllõsi, Gergely J; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

    2013-11-01

    Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree-species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source

  4. Trichoderma genes

    Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  5. Rapid and accurate evaluation of the quality of commercial organic fertilizers using near infrared spectroscopy.

    Wang, Chang; Huang, Chichao; Qian, Jian; Xiao, Jian; Li, Huan; Wen, Yongli; He, Xinhua; Ran, Wei; Shen, Qirong; Yu, Guanghui

    2014-01-01

    The composting industry has been growing rapidly in China because of a boom in the animal industry. Therefore, a rapid and accurate assessment of the quality of commercial organic fertilizers is of the utmost importance. In this study, a novel technique that combines near infrared (NIR) spectroscopy with partial least squares (PLS) analysis is developed for rapidly and accurately assessing commercial organic fertilizers quality. A total of 104 commercial organic fertilizers were collected from full-scale compost factories in Jiangsu Province, east China. In general, the NIR-PLS technique showed accurate predictions of the total organic matter, water soluble organic nitrogen, pH, and germination index; less accurate results of the moisture, total nitrogen, and electrical conductivity; and the least accurate results for water soluble organic carbon. Our results suggested the combined NIR-PLS technique could be applied as a valuable tool to rapidly and accurately assess the quality of commercial organic fertilizers.

  6. The gene tree delusion.

    Springer, Mark S; Gatesy, John

    2016-01-01

    Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel deep-level phylogenetic problems that have stymied concatenation. Here, we reanalyze Song et al.'s (2012) data and leverage these re-analyses to explore key issues in systematics including the recombination ratchet, gene tree stoichiometry, the proportion of gene tree incongruence that results from deep coalescence versus other factors, and simulations that compare the performance of coalescence and concatenation methods in species tree estimation. Song et al. (2012) reported an average locus length of 3.1 kb for the 447 protein-coding genes in their phylogenomic dataset, but the true mean length of these loci (start codon to stop codon) is 139.6 kb. Empirical estimates of recombination breakpoints in primates, coupled with consideration of the recombination ratchet, suggest that individual coalescence genes (c-genes) approach ∼12 bp or less for Song et al.'s (2012) dataset, three to four orders of magnitude shorter than the c-genes reported by these authors. This result has general implications for the application of coalescence methods in species tree estimation. We contend that it is illogical to apply coalescence methods to complete protein-coding sequences. Such analyses amalgamate c-genes with different evolutionary histories (i.e., exons separated by >100,000 bp), distort true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescence methods to difficult phylogenetic problems. In addition, Song et al.'s (2012) dataset of 447 genes includes 21 loci with switched taxonomic names, eight duplicated loci, 26 loci with non-homologous sequences that are

  7. Genometa--a fast and accurate classifier for short metagenomic shotgun reads.

    Colin F Davenport

    Full Text Available Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.The Genometa program, a step by step tutorial and Java source code are freely available from http://genomics1.mh-hannover.de/genometa/ and on http://code.google.com/p/genometa/. This program has been tested on Ubuntu Linux and Windows XP/7.

  8. A general pairwise interaction model provides an accurate description of in vivo transcription factor binding sites.

    Marc Santolini

    Full Text Available The identification of transcription factor binding sites (TFBSs on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs, in which each DNA base pair contributes independently to the transcription factor (TF binding. However, this description ignores correlations between nucleotides at different positions, and is generally inaccurate: analysing fly and mouse in vivo ChIPseq data, we show that in most cases the PWM model fails to reproduce the observed statistics of TFBSs. To overcome this issue, we introduce the pairwise interaction model (PIM, a generalization of the PWM model. The model is based on the principle of maximum entropy and explicitly describes pairwise correlations between nucleotides at different positions, while being otherwise as unconstrained as possible. It is mathematically equivalent to considering a TF-DNA binding energy that depends additively on each nucleotide identity at all positions in the TFBS, like the PWM model, but also additively on pairs of nucleotides. We find that the PIM significantly improves over the PWM model, and even provides an optimal description of TFBS statistics within statistical noise. The PIM generalizes previous approaches to interdependent positions: it accounts for co-variation of two or more base pairs, and predicts secondary motifs, while outperforming multiple-motif models consisting of mixtures of PWMs. We analyse the structure of pairwise interactions between nucleotides, and find that they are sparse and dominantly located between consecutive base pairs in the flanking region of TFBS. Nonetheless, interactions between pairs of non-consecutive nucleotides are found to play a significant role in the obtained accurate description of TFBS statistics. The PIM is computationally tractable, and provides a general framework that should be useful for describing and predicting

  9. Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.

    Duncan K Ralph

    2016-01-01

    Full Text Available VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion. Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/, is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.

  10. On accurate computations of bound state properties in three- and four-electron atomic systems

    Frolov, Alexei M

    2016-01-01

    Results of accurate computations of bound states in three- and four-electron atomic systems are discussed. Bound state properties of the four-electron lithium ion Li$^{-}$ in its ground $2^{2}S-$state are determined from the results of accurate, variational computations. We also consider a closely related problem of accurate numerical evaluation of the half-life of the beryllium-7 isotope. This problem is of paramount importance for modern radiochemistry.

  11. Smart and Accurate State-of-Charge Indication in Portable Applications

    Pop, V.; Bergveld, H.J.; Notten, P.H.L.; Regtien, P.P.L.

    2005-01-01

    Accurate State-of-Charge (SoC) and remaining run-time indication for portable devices is important for the user-convenience and to prolong the lifetime of batteries. However, the known methods of SoC indication in portable applications are not accurate enough under all practical conditions. The meth

  12. Validation of a method for accurate and highly reproducible quantification of brain dopamine transporter SPECT studies

    Jensen, Peter S; Ziebell, Morten; Skouboe, Glenna

    2011-01-01

    In nuclear medicine brain imaging, it is important to delineate regions of interest (ROIs) so that the outcome is both accurate and reproducible. The purpose of this study was to validate a new time-saving algorithm (DATquan) for accurate and reproducible quantification of the striatal dopamine...... transporter (DAT) with appropriate radioligands and SPECT and without the need for structural brain scanning....

  13. A water-renewal system that accurately delivers small volumes of water to exposure chambers

    Zumwalt, D. C.; Dwyer, F.J.; Greer, I.E.; Ingersoll, C.G.

    1994-01-01

    This paper describes a system that can accurately deliver small volumes of water (50 ml per cycle) to eight 300-ml beakers. The system is inexpensive <$100), easy to build (<8 h), and easy to calibrate (<15 min), and accurately delivers small volumes of water (<5% variability).

  14. Using In-Service and Coaching to Increase Teachers' Accurate Use of Research-Based Strategies

    Kretlow, Allison G.; Cooke, Nancy L.; Wood, Charles L.

    2012-01-01

    Increasing the accurate use of research-based practices in classrooms is a critical issue. Professional development is one of the most practical ways to provide practicing teachers with training related to research-based practices. This study examined the effects of in-service plus follow-up coaching on first grade teachers' accurate delivery of…

  15. A thermal displacement sensor in MEMS [Towards accurate small-scale manipulation

    Krijnen, Bram; Hogervorst, Richard; Dijkstra, Jan Willem; Engelen, Johan; Woldering, Léon; Brouwer, Dannis; Abelmann, Leon; Soemers, Herman

    2011-01-01

    Accurate manipulation of small objects is becoming more and more important. Besides accurate manipulation, the demand for small manipulators is also increasing. Some examples are high-density data storage, (digital) light processing, accelerometers, rate sensors, and the use of cantilevers in atomic

  16. A new method and instrument for accurately measuring interval between ultrashort pulses

    Zhonggang Ji; Yuxin Leng; Yunpei Deng; Bin Tang; Haihe Lu; Ruxin Li; Zhizhan Xu

    2005-01-01

    @@ Using second-order autocorrelation conception, a novel method and instrument for accurately measuring interval between two linearly polarized ultrashort pulses with real time were presented. The experiment demonstrated that the measuring method and instrument were simple and accurate (the measurement error < 5 fs). During measuring, there was no moving element resulting in dynamic measurement error.

  17. Identification of reference genes for gene expression studies during seed germination and seedling establishment Ricinus communis L.

    Ribeiro de Jesus, P.R.; Dekkers, S.J.W.; Fernandez, L.G.; Castro, De R.D.; Ligterink, W.; Hilhorst, H.W.M.

    2014-01-01

    Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an important technology to analyse gene expression levels during plant development or in response to different treatments. An important requirement to measure gene expression levels accurately is a properly validated set of re

  18. Accurate location estimation of moving object with energy constraint & adaptive update algorithms to save data

    Semwal, Vijay Bhaskar; Bhaskar, Vinay S; Sati, Meenakshi

    2011-01-01

    In research paper "Accurate estimation of the target location of object with energy constraint & Adaptive Update Algorithms to Save Data" one of the central issues in sensor networks is track the location, of moving object which have overhead of saving data, an accurate estimation of the target location of object with energy constraint .We do not have any mechanism which control and maintain data .The wireless communication bandwidth is also very limited. Some field which is using this technique are flood and typhoon detection, forest fire detection, temperature and humidity and ones we have these information use these information back to a central air conditioning and ventilation system. In this research paper, we propose protocol based on the prediction and adaptive based algorithm which is using less sensor node reduced by an accurate estimation of the target location. we are using minimum three sensor node to get the accurate position .We can extend it upto four or five to find more accurate location ...

  19. Evolution vs the number of gene copies per primitive cell.

    Koch, A L

    1984-01-01

    Computer simulations are presented of the rate at which an advantageous mutant would displace the prototype in a replicating system without an accurate segregation mechanism. If the number of gene copies in the system is indefinitely large, Darwinian evolution is essentially stopped because there is no coupling of phenotype with genotype, i.e., there is no growth advantage to the advantageous gene relative to the prototype and therefore no "survival of the fittest." The inhibition of evolution due to a number of gene copies less than 100 would have been not insurmountable. Although the presence of multiple copies would have allowed replacement by an advantageous mutant, it provided a way for the primitive cell to conserve less immediately useful genes that could evolve into different or more effective genes. This possibility was lost as accurate segregation mechanisms evolved and cells with few copies of each gene, such as modern procaryotes, arose.

  20. Accurate, Fast and Cost-Effective Diagnostic Test for Monosomy 1p36 Using Real-Time Quantitative PCR

    Pricila da Silva Cunha

    2014-01-01

    Full Text Available Monosomy 1p36 is considered the most common subtelomeric deletion syndrome in humans and it accounts for 0.5–0.7% of all the cases of idiopathic intellectual disability. The molecular diagnosis is often made by microarray-based comparative genomic hybridization (aCGH, which has the drawback of being a high-cost technique. However, patients with classic monosomy 1p36 share some typical clinical characteristics that, together with its common prevalence, justify the development of a less expensive, targeted diagnostic method. In this study, we developed a simple, rapid, and inexpensive real-time quantitative PCR (qPCR assay for targeted diagnosis of monosomy 1p36, easily accessible for low-budget laboratories in developing countries. For this, we have chosen two target genes which are deleted in the majority of patients with monosomy 1p36: PRKCZ and SKI. In total, 39 patients previously diagnosed with monosomy 1p36 by aCGH, fluorescent in situ hybridization (FISH, and/or multiplex ligation-dependent probe amplification (MLPA all tested positive on our qPCR assay. By simultaneously using these two genes we have been able to detect 1p36 deletions with 100% sensitivity and 100% specificity. We conclude that qPCR of PRKCZ and SKI is a fast and accurate diagnostic test for monosomy 1p36, costing less than 10 US dollars in reagent costs.

  1. State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation.

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-04-01

    The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space

  2. Three-stage Stiffly Accurate Runge-Kutta Methods for Stiff Stochastic Differential Equations

    WANG PENG

    2011-01-01

    In this paper we discuss diagonally implicit and semi-implicit methods based on the three-stage stiffly accurate Runge-Kutta methods for solving Stratonovich stochastic differential equations (SDEs). Two methods, a three-stage stiffly accurate semi-implicit (SASI3) method and a three-stage stiffly accurate diagonally implicit (SADI3) method, are constructed in this paper. In particular, the truncated random variable is used in the implicit method. The stability properties and numerical results show the effectiveness of these methods in the pathwise approximation of stiff SDEs.

  3. An accurate potential energy curve for helium based on ab initio calculations

    Janzen, A. R.; Aziz, R. A.

    1997-07-01

    Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.

  4. Highly accurate local pseudopotentials of Li, Na, and Mg for orbital free density functional theory

    Legrain, Fleur; Manzhos, Sergei

    2015-02-01

    We present a method to make highly accurate pseudopotentials for use with orbital-free density functional theory (OF-DFT) with given exchange-correlation and kinetic energy functionals, which avoids the compounding of errors of Kohn-Sham DFT and OF-DFT. The pseudopotentials are fitted to reference (experimental or highly accurate quantum chemistry) values of interaction energies, geometries, and mechanical properties, using a genetic algorithm. This can enable routine large-scale ab initio simulations of many practically relevant materials. Pseudopotentials for Li, Na, and Mg resulting in accurate geometries and energies of different phases as well as of vacancy formation and bulk moduli are presented as examples.

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

    Chen, Chun; Xie, Tingna; Ye, Sudan;

    2016-01-01

    The selection of suitable reference genes is crucial for accurate quantification of gene expres-sion and can add to our understanding of host–pathogen interactions. To identify suitablereference genes in Pandora neoaphidis, an obligate aphid pathogenic fungus, the expressionof three traditional...

  6. Accurate and Precise Determination of Uranium by Means of Extraction Spectrophotometric

    2008-01-01

    <正>Uranium is an important nuclear material. Accurate determination of uranium is significant in the nuclear fuel production, accountancy, nuclear safeguards and other procedures of nuclear fuel cycle.

  7. Efficient and Accurate Computational Framework for Injector Design and Analysis Project

    National Aeronautics and Space Administration — CFD codes used to simulate upper stage expander cycle engines are not adequately mature to support design efforts. Rapid and accurate simulations require more...

  8. Effective Temperatures of Selected Main-sequence Stars with Most Accurate Parameters

    Soydugan, F; Soydugan, E; Bilir, S; Gökçe, E Yaz; Steer, I; Tüysüz, M; Şenyüz, T; Demircan, O

    2014-01-01

    In this study, the distributions of the double-lined detached binaries (DBs) on the planes of mass-luminosity, mass radius and mass-effective temperature have been studied. We improved the classical mass-luminosity relation based on the database of DBs by Eker et al. (2004a). With accurate observational data available to us, a method for improving effective temperatures for eclipsing binaries with accurate masses and radii were suggested.

  9. Effective Temperatures of Selected Main-Sequence Stars with the Most Accurate Parameters

    Soydugan, F.; Eker, Z.; Soydugan, E.; Bilir, S.; Gökçe, E. Y.; Steer, I.; Tüysüz, M.; Šenyüz, T.; Demircan, O.

    2015-07-01

    In this study we investigate the distributions of the properties of detached double-lined binaries (DBs) in the mass-luminosity, mass-radius, and mass-effective temperature diagrams. We have improved the classical mass-luminosity relation based on the database of DBs by Eker et al. (2014a). Based on the accurate observational data available to us we propose a method for improving the effective temperatures of eclipsing binaries with accurate mass and radius determinations.

  10. Accurate Mass Determination of Amino Alcohols by Turboionspray/Time-of-Flight Mass Spectrometry

    GENG,Yu(耿昱); GUO,Yin-Long(郭寅龙); ZHAO,Shi-Min(赵士民); MA,Sheng-Ming(麻生明)

    2002-01-01

    Amino alcohols were studied by turboionspray/time-of-flight mass spectrometry (TIS/TOF-MS) with the aim of determining the accurate mass of their protonated molecule ions.Polyethylene glycol (PEG) was used as the internal reference.Compared with the theoretical values, all relative errors were less than 5×10-6. The effects of nozzle potential, nozzle temperature, acquisition rate etc. on accurate mass determination were also studied.

  11. Equation of state for hard sphere fluids offering accurate virial coefficients

    Tian, Jianxiang; Gui, Yuanxing; Mulero, A

    2016-01-01

    The asymptotic expansion method is extended by using currently available accurate values for the first ten virial coefficients for hard sphere fluids. It is then used to yield an equation of state for hard sphere fluids, which accurately represents the currently accepted values for the first sixteen virial coefficients and compressibility factor data in both the stable and the metastable regions of the phase diagram.

  12. A self-interaction-free local hybrid functional: Accurate binding energies vis-\\`a-vis accurate ionization potentials from Kohn-Sham eigenvalues

    Schmidt, Tobias; Makmal, Adi; Kronik, Leeor; Kümmel, Stephan

    2014-01-01

    We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potent...

  13. Reference genes for gene expression studies in wheat flag leaves grown under different farming conditions

    Cordeiro Raposo Fernando

    2011-09-01

    Full Text Available Abstract Background Internal control genes with highly uniform expression throughout the experimental conditions are required for accurate gene expression analysis as no universal reference genes exists. In this study, the expression stability of 24 candidate genes from Triticum aestivum cv. Cubus flag leaves grown under organic and conventional farming systems was evaluated in two locations in order to select suitable genes that can be used for normalization of real-time quantitative reverse-transcription PCR (RT-qPCR reactions. The genes were selected among the most common used reference genes as well as genes encoding proteins involved in several metabolic pathways. Findings Individual genes displayed different expression rates across all samples assayed. Applying geNorm, a set of three potential reference genes were suitable for normalization of RT-qPCR reactions in winter wheat flag leaves cv. Cubus: TaFNRII (ferredoxin-NADP(H oxidoreductase; AJ457980.1, ACT2 (actin 2; TC234027, and rrn26 (a putative homologue to RNA 26S gene; AL827977.1. In addition of these three genes that were also top-ranked by NormFinder, two extra genes: CYP18-2 (Cyclophilin A, AY456122.1 and TaWIN1 (14-3-3 like protein, AB042193 were most consistently stably expressed. Furthermore, we showed that TaFNRII, ACT2, and CYP18-2 are suitable for gene expression normalization in other two winter wheat varieties (Tommi and Centenaire grown under three treatments (organic, conventional and no nitrogen and a different environment than the one tested with cv. Cubus. Conclusions This study provides a new set of reference genes which should improve the accuracy of gene expression analyses when using wheat flag leaves as those related to the improvement of nitrogen use efficiency for cereal production.

  14. Endothelial Genes

    2005-06-01

    8217Department of Surgery, Division of Oncology , and 2Department of BRCA-l and BRCA-2 (breast cancer susceptibility genes), Pathology, University of...Suppression subtractive hybridization re- Cancer: principles and practice of oncology . Philadelphia: Lippincott- vealed an RNA sequence (GenBank accession...Lippman ME. Cancer of the breast: molecular biology angiogenesis in sarcomas and carcinomas. Clin Cancer Res 1999;5: of breast cancer. In: DeVita VT

  15. Gene Ontology

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  16. Gene doping: gene delivery for olympic victory

    2012-01-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

  17. Liquid propellant rocket engine combustion simulation with a time-accurate CFD method

    Chen, Y. S.; Shang, H. M.; Liaw, Paul; Hutt, J.

    1993-01-01

    Time-accurate computational fluid dynamics (CFD) algorithms are among the basic requirements as an engineering or research tool for realistic simulations of transient combustion phenomena, such as combustion instability, transient start-up, etc., inside the rocket engine combustion chamber. A time-accurate pressure based method is employed in the FDNS code for combustion model development. This is in connection with other program development activities such as spray combustion model development and efficient finite-rate chemistry solution method implementation. In the present study, a second-order time-accurate time-marching scheme is employed. For better spatial resolutions near discontinuities (e.g., shocks, contact discontinuities), a 3rd-order accurate TVD scheme for modeling the convection terms is implemented in the FDNS code. Necessary modification to the predictor/multi-corrector solution algorithm in order to maintain time-accurate wave propagation is also investigated. Benchmark 1-D and multidimensional test cases, which include the classical shock tube wave propagation problems, resonant pipe test case, unsteady flow development of a blast tube test case, and H2/O2 rocket engine chamber combustion start-up transient simulation, etc., are investigated to validate and demonstrate the accuracy and robustness of the present numerical scheme and solution algorithm.

  18. On the accurate estimation of gap fraction during daytime with digital cover photography

    Hwang, Y. R.; Ryu, Y.; Kimm, H.; Macfarlane, C.; Lang, M.; Sonnentag, O.

    2015-12-01

    Digital cover photography (DCP) has emerged as an indirect method to obtain gap fraction accurately. Thus far, however, the intervention of subjectivity, such as determining the camera relative exposure value (REV) and threshold in the histogram, hindered computing accurate gap fraction. Here we propose a novel method that enables us to measure gap fraction accurately during daytime under various sky conditions by DCP. The novel method computes gap fraction using a single DCP unsaturated raw image which is corrected for scattering effects by canopies and a reconstructed sky image from the raw format image. To test the sensitivity of the novel method derived gap fraction to diverse REVs, solar zenith angles and canopy structures, we took photos in one hour interval between sunrise to midday under dense and sparse canopies with REV 0 to -5. The novel method showed little variation of gap fraction across different REVs in both dense and spares canopies across diverse range of solar zenith angles. The perforated panel experiment, which was used to test the accuracy of the estimated gap fraction, confirmed that the novel method resulted in the accurate and consistent gap fractions across different hole sizes, gap fractions and solar zenith angles. These findings highlight that the novel method opens new opportunities to estimate gap fraction accurately during daytime from sparse to dense canopies, which will be useful in monitoring LAI precisely and validating satellite remote sensing LAI products efficiently.

  19. Second-order accurate finite volume method for well-driven flows

    Dotlić, Milan; Pokorni, Boris; Pušić, Milenko; Dimkić, Milan

    2013-01-01

    We consider a finite volume method for a well-driven fluid flow in a porous medium. Due to the singularity of the well, modeling in the near-well region with standard numerical schemes results in a completely wrong total well flux and an inaccurate hydraulic head. Local grid refinement can help, but it comes at computational cost. In this article we propose two methods to address well singularity. In the first method the flux through well faces is corrected using a logarithmic function, in a way related to the Peaceman correction. Coupling this correction with a second-order accurate two-point scheme gives a greatly improved total well flux, but the resulting scheme is still not even first order accurate on coarse grids. In the second method fluxes in the near-well region are corrected by representing the hydraulic head as a sum of a logarithmic and a linear function. This scheme is second-order accurate.

  20. Accurate, robust and reliable calculations of Poisson-Boltzmann solvation energies

    Wang, Bao

    2016-01-01

    Developing accurate solvers for the Poisson Boltzmann (PB) model is the first step to make the PB model suitable for implicit solvent simulation. Reducing the grid size influence on the performance of the solver benefits to increasing the speed of solver and providing accurate electrostatics analysis for solvated molecules. In this work, we explore the accurate coarse grid PB solver based on the Green's function treatment of the singular charges, matched interface and boundary (MIB) method for treating the geometric singularities, and posterior electrostatic potential field extension for calculating the reaction field energy. We made our previous PB software, MIBPB, robust and provides almost grid size independent reaction field energy calculation. Large amount of the numerical tests verify the grid size independence merit of the MIBPB software. The advantage of MIBPB software directly make the acceleration of the PB solver from the numerical algorithm instead of utilization of advanced computer architectures...

  1. Simple and Accurate Analytical Solutions of the Electrostatically Actuated Curled Beam Problem

    Younis, Mohammad I.

    2014-08-17

    We present analytical solutions of the electrostatically actuated initially deformed cantilever beam problem. We use a continuous Euler-Bernoulli beam model combined with a single-mode Galerkin approximation. We derive simple analytical expressions for two commonly observed deformed beams configurations: the curled and tilted configurations. The derived analytical formulas are validated by comparing their results to experimental data in the literature and numerical results of a multi-mode reduced order model. The derived expressions do not involve any complicated integrals or complex terms and can be conveniently used by designers for quick, yet accurate, estimations. The formulas are found to yield accurate results for most commonly encountered microbeams of initial tip deflections of few microns. For largely deformed beams, we found that these formulas yield less accurate results due to the limitations of the single-mode approximations they are based on. In such cases, multi-mode reduced order models need to be utilized.

  2. Fast and accurate calculation of dilute quantum gas using Uehling-Uhlenbeck model equation

    Yano, Ryosuke

    2017-02-01

    The Uehling-Uhlenbeck (U-U) model equation is studied for the fast and accurate calculation of a dilute quantum gas. In particular, the direct simulation Monte Carlo (DSMC) method is used to solve the U-U model equation. DSMC analysis based on the U-U model equation is expected to enable the thermalization to be accurately obtained using a small number of sample particles and the dilute quantum gas dynamics to be calculated in a practical time. Finally, the applicability of DSMC analysis based on the U-U model equation to the fast and accurate calculation of a dilute quantum gas is confirmed by calculating the viscosity coefficient of a Bose gas on the basis of the Green-Kubo expression and the shock layer of a dilute Bose gas around a cylinder.

  3. Defining Allowable Physical Property Variations for High Accurate Measurements on Polymer Parts

    Mohammadi, Ali; Sonne, Mads Rostgaard; Madruga, Daniel González;

    2015-01-01

    cooling down after injection molding. In order to obtain accurate simulations, accurate inputs to the model are crucial. In reality however, the material and physical properties will have some variations. Although these variations may be small, they can act as a source of uncertainty for the measurement...... high accurate measurements in non-controlled ambient. Most of polymer parts are manufactured by injection moulding and their inspection is carried out after stabilization, around 200 hours. The overall goal of this work is to reach ±5μm in uncertainty measurements a polymer products which...... is a challenge in today‘s production and metrology environments. The residual deformations in polymer products at room temperature after injection molding are important when micrometer accuracy needs to be achieved. Numerical modelling can give a valuable insight to what is happening in the polymer during...

  4. Asymptotic expansion based equation of state for hard-disk fluids offering accurate virial coefficients

    Tian, Jianxiang; Mulero, A

    2016-01-01

    Despite the fact that more that more than 30 analytical expressions for the equation of state of hard-disk fluids have been proposed in the literature, none of them is capable of reproducing the currently accepted numeric or estimated values for the first eighteen virial coefficients. Using the asymptotic expansion method, extended to the first ten virial coefficients for hard-disk fluids, fifty-seven new expressions for the equation of state have been studied. Of these, a new equation of state is selected which reproduces accurately all the first eighteen virial coefficients. Comparisons for the compressibility factor with computer simulations show that this new equation is as accurate as other similar expressions with the same number of parameters. Finally, the location of the poles of the 57 new equations shows that there are some particular configurations which could give both the accurate virial coefficients and the correct closest packing fraction in the future when higher virial coefficients than the t...

  5. An Accurate Arabic Root-Based Lemmatizer for Information Retrieval Purposes

    El-Shishtawy, Tarek

    2012-01-01

    In spite of its robust syntax, semantic cohesion, and less ambiguity, lemma level analysis and generation does not yet focused in Arabic NLP literatures. In the current research, we propose the first non-statistical accurate Arabic lemmatizer algorithm that is suitable for information retrieval (IR) systems. The proposed lemmatizer makes use of different Arabic language knowledge resources to generate accurate lemma form and its relevant features that support IR purposes. As a POS tagger, the experimental results show that, the proposed algorithm achieves a maximum accuracy of 94.8%. For first seen documents, an accuracy of 89.15% is achieved, compared to 76.7% of up to date Stanford accurate Arabic model, for the same, dataset.

  6. Measuring Accurate Body Parameters of Dressed Humans with Large-Scale Motion Using a Kinect Sensor

    Sidan Du

    2013-08-01

    Full Text Available Non-contact human body measurement plays an important role in surveillance, physical healthcare, on-line business and virtual fitting. Current methods for measuring the human body without physical contact usually cannot handle humans wearing clothes, which limits their applicability in public environments. In this paper, we propose an effective solution that can measure accurate parameters of the human body with large-scale motion from a Kinect sensor, assuming that the people are wearing clothes. Because motion can drive clothes attached to the human body loosely or tightly, we adopt a space-time analysis to mine the information across the posture variations. Using this information, we recover the human body, regardless of the effect of clothes, and measure the human body parameters accurately. Experimental results show that our system can perform more accurate parameter estimation on the human body than state-of-the-art methods.

  7. An Efficient Multiplex PCR-Based Assay as a Novel Tool for Accurate Inter-Serovar Discrimination of Salmonella Enteritidis, S. Pullorum/Gallinarum and S. Dublin

    Xiong, Dan; Song, Li; Tao, Jing; Zheng, Huijuan; Zhou, Zihao; Geng, Shizhong; Pan, Zhiming; Jiao, Xinan

    2017-01-01

    Salmonella enterica serovars Enteritidis, Pullorum/Gallinarum, and Dublin are infectious pathogens causing serious problems for pig, chicken, and cattle production, respectively. Traditional serotyping for Salmonella is costly and labor-intensive. Here, we established a rapid multiplex PCR method to simultaneously identify three prevalent Salmonella serovars Enteritidis, Pullorum/Gallinarum, and Dublin individually for the first time. The multiplex PCR-based assay focuses on three genes tcpS, lygD, and flhB. Gene tcpS exists only in the three Salmonella serovars, and lygD exists only in S. Enteritidis, while a truncated region of flhB gene is only found in S. Pullorum/Gallinarum. The sensitivity and specificity of the multiplex PCR assay using three pairs of specific primers for these genes were evaluated. The results showed that this multiplex PCR method could accurately identify Salmonella Enteritidis, Pullorum/Gallinarum, and Dublin from eight non-Salmonella species and 27 Salmonella serovars. The least concentration of genomic DNA that could be detected was 58.5 pg/μL and the least number of cells was 100 CFU. Subsequently, this developed method was used to analyze clinical Salmonella isolates from one pig farm, one chicken farm, and one cattle farm. The results showed that blinded PCR testing of Salmonella isolates from the three farms were in concordance with the traditional serotyping tests, indicating the newly developed multiplex PCR system could be used as a novel tool to accurately distinguish the three specific Salmonella serovars individually, which is useful, especially in high-throughput screening.

  8. Prediction of Tumor Outcome Based on Gene Expression Data

    Liu Juan; Hitoshi Iba

    2004-01-01

    Gene expression microarray data can be used to classify tumor types. We proposed a new procedure to classify human tumor samples based on microarray gene expressions by using a hybrid supervised learning method called MOEA+WV (Multi-Objective Evolutionary Algorithm+Weighted Voting). MOEA is used to search for a relatively few subsets of informative genes from the high-dimensional gene space, and WV is used as a classification tool. This new method has been applied to predicate the subtypes of lymphoma and outcomes of medulloblastoma. The results are relatively accurate and meaningful compared to those from other methods.

  9. Accurate quantification of magnetic particle properties by intra-pair magnetophoresis for nanobiotechnology

    van Reenen, Alexander; Gao, Yang; Bos, Arjen H.; de Jong, Arthur M.; Hulsen, Martien A.; den Toonder, Jaap M. J.; Prins, Menno W. J.

    2013-07-01

    The application of magnetic particles in biomedical research and in-vitro diagnostics requires accurate characterization of their magnetic properties, with single-particle resolution and good statistics. Here, we report intra-pair magnetophoresis as a method to accurately quantify the field-dependent magnetic moments of magnetic particles and to rapidly generate histograms of the magnetic moments with good statistics. We demonstrate our method with particles of different sizes and from different sources, with a measurement precision of a few percent. We expect that intra-pair magnetophoresis will be a powerful tool for the characterization and improvement of particles for the upcoming field of particle-based nanobiotechnology.

  10. An Accurate Approach to Large-Scale IP Traffic Matrix Estimation

    Jiang, Dingde; Hu, Guangmin

    This letter proposes a novel method of large-scale IP traffic matrix (TM) estimation, called algebraic reconstruction technique inference (ARTI), which is based on the partial flow measurement and Fratar model. In contrast to previous methods, ARTI can accurately capture the spatio-temporal correlations of TM. Moreover, ARTI is computationally simple since it uses the algebraic reconstruction technique. We use the real data from the Abilene network to validate ARTI. Simulation results show that ARTI can accurately estimate large-scale IP TM and track its dynamics.

  11. Do Voters Learn? Evidence that Voters Respond Accurately to Changes in Political Parties’ Policy Positions

    Seeberg, Henrik Bech; Slothuus, Rune; Stubager, Rune

    2017-01-01

    A premise of the mass–elite linkage at the heart of representative democracy is that voters notice changes in political parties’ policy positions and update their party perceptions accordingly. However, recent studies question the ability of voters accurately to perceive changes in parties...... attention to parties when they visibly change policy position. Second, voters update their perceptions of the party positions much more accurately than would have been expected if they merely relied on a ‘coalition heuristic’ as a rule-of-thumb. These findings imply that under some conditions voters...... are better able to make meaningful political choices than previous work suggests....

  12. Effects of antecedent variables on disruptive behavior and accurate responding in young children in outpatient settings.

    Boelter, Eric W; Wacker, David P; Call, Nathan A; Ringdahl, Joel E; Kopelman, Todd; Gardner, Andrew W

    2007-01-01

    The effects of manipulations of task variables on inaccurate responding and disruption were investigated with 3 children who engaged in noncompliance. With 2 children in an outpatient clinic, task directives were first manipulated to identify directives that guided accurate responding; then, additional dimensions of the task were manipulated to evaluate their influence on disruptive behavior. With a 3rd child, similar procedures were employed at school. Results showed one-step directives set the occasion for accurate responding and that other dimensions of the task (e.g., preference) functioned as motivating operations for negative reinforcement.

  13. Definition of accurate reference pattern for the DTU-ESA VAST12 antenna

    Pivnenko, Sergey; Breinbjerg, Olav; Burgos, Sara;

    2009-01-01

    In this paper, the DTU-ESA 12 GHz validation standard (VAST12) antenna and a dedicated measurement campaign carried out in 2007-2008 for the definition of its accurate reference pattern are first described. Next, a comparison between the results from the three involved measurement facilities...... is presented. Then, an accurate reference pattern of the VAST12 antenna is formed by averaging the three results taking into account the estimated uncertainties of each result. Finally, the potential use of the reference pattern for benchmarking of antenna measurement facilities is outlined....

  14. Building Accurate 3D Spatial Networks to Enable Next Generation Intelligent Transportation Systems

    Kaul, Manohar; Yang, Bin; Jensen, Christian S.

    2013-01-01

    model with elevation information extracted from massive aerial laser scan data and thus yields an accurate 3D model. We present a filtering technique that is capable of pruning irrelevant laser scan points in a single pass, but assumes that the 2D network fits in internal memory and that the points......The use of accurate 3D spatial network models can enable substantial improvements in vehicle routing. Notably, such models enable eco-routing, which reduces the environmental impact of transportation. We propose a novel filtering and lifting framework that augments a standard 2D spatial network...

  15. An accurate predictor-corrector HOC solver for the two dimensional Riemann problem of gas dynamics

    Gogoi, Bidyut B.

    2016-10-01

    The work in the present manuscript is concerned with the simulation of twodimensional (2D) Riemann problem of gas dynamics. We extend our recently developed higher order compact (HOC) method from one-dimensional (1D) to 2D solver and simulate the problem on a square geometry with different initial conditions. The method is fourth order accurate in space and second order accurate in time. We then compare our results with the available benchmark results. The comparison shows an excellent agreement of our results with the existing ones in the literature. Being a finite difference solver, it is quite straight-forward and simple.

  16. Deformable meshes for medical image segmentation accurate automatic segmentation of anatomical structures

    Kainmueller, Dagmar

    2014-01-01

    ? Segmentation of anatomical structures in medical image data is an essential task in clinical practice. Dagmar Kainmueller introduces methods for accurate fully automatic segmentation of anatomical structures in 3D medical image data. The author's core methodological contribution is a novel deformation model that overcomes limitations of state-of-the-art Deformable Surface approaches, hence allowing for accurate segmentation of tip- and ridge-shaped features of anatomical structures. As for practical contributions, she proposes application-specific segmentation pipelines for a range of anatom

  17. Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR

    Reith Michael

    2008-03-01

    Full Text Available Abstract Background Flatfish metamorphosis involves major physiological and morphological changes. Due to its importance in aquaculture and as a model for developmental studies, some gene expression studies have focused on the understanding of this process using quantitative real-time PCR (qRT-PCR technique. Therefore, adequate reference genes for accurate normalization are required. Results The stability of 12 potential reference genes was examined during larval development in Senegalese sole (Solea senegalensis and Atlantic halibut (Hippoglossus hippoglossus to determine the most suitable genes for qRT-PCR analysis. Transcription levels of genes encoding β-Actin (ACTB, glyceraldehyde-3P-dehydrogenase (GAPDH, annexin A2 (ANXA2, glutathione S-transferase (GST, ornithine decarboxylase (ODC, hypoxanthine phosphoribosyltransferase (HPRT1, ubiquitin (UBQ, elongation factor 1 alpha (eEF1A1, 18S ribosomal RNA, and the ribosomal proteins S4 (RPS4 and L13a (RPL13a were quantitated. Two paralogous genes for ACTB were analyzed in each of both flatfish species. In addition, two paralogous genes for GAPDH were studied in Senegalese sole. RPL13a represented non-orthologous genes between both flatfish species. GeNorm and NormFinder analyses for expression stability revealed RPS4, UBQ and eEF1A1 as the most stable genes in Senegalese sole, Atlantic halibut and in a combined analysis. In all cases, paralogous genes exhibited differences in expression stability. Conclusion This work suggests RPS4, UBQ, and eEF1A1 genes as useful reference genes for accurate normalization in qRT-PCR studies in Senegalese sole and Atlantic halibut larvae. The congruent results between both species in spite of the drastic differences in larval development suggest that selected housekeeping genes (HKGs could be useful in other flatfish species. However, the finding of paralogous gene copies differentially expressed during development in some HKGs underscores the necessity to

  18. GeneEd -- A Genetics Educational Resource

    ... Javascript on. Feature: Genetics 101 GeneEd — A Genetics Educational Resource Past Issues / Summer 2013 Table of Contents Science ... The Hereditary Material of Life / GeneEd — A Genetics Educational Resource / Using The Genetics Home Reference Website / Understanding the ...

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

    Teng Shaolei; Yang Jack Y; Wang Liangjiang

    2013-01-01

    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,...

  20. Multiple-resonance local wave functions for accurate excited states in quantum Monte Carlo

    Zulfikri, Habiburrahman; Amovilli, Claudio; Filippi, Claudia

    2016-01-01

    We introduce a novel class of local multideterminant Jastrow–Slater wave functions for the efficient and accurate treatment of excited states in quantum Monte Carlo. The wave function is expanded as a linear combination of excitations built from multiple sets of localized orbitals that correspond to