Revision of Begomovirus taxonomy based on pairwise sequence comparisons

KAUST Repository

Brown, Judith K.; Zerbini, F. Murilo; Navas-Castillo, Jesú s; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C. F.; Fiallo-Olivé , Elvira; Briddon, Rob W.; Herná ndez-Zepeda, Cecilia; Idris, Ali; Malathi, V. G.; Martin, Darren P.; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, Arvind

2015-01-01

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Revision of Begomovirus taxonomy based on pairwise sequence comparisons

KAUST Repository

Brown, Judith K.

2015-04-18

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Pareto optimal pairwise sequence alignment.

Science.gov (United States)

DeRonne, Kevin W; Karypis, George

2013-01-01

Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

Theory of pairwise lesion interaction

International Nuclear Information System (INIS)

Harder, Dietrich; Virsik-Peuckert, Patricia; Bartels, Ernst

1992-01-01

A comparison between repair time constants measured both at the molecular and cellular levels has shown that the DNA double strand break is the molecular change of key importance in the causation of cellular effects such as chromosome aberrations and cell inactivation. Cell fusion experiments provided the evidence that it needs the pairwise interaction between two double strand breaks - or more exactly between the two ''repair sites'' arising from them in the course of enzymatic repair - to provide the faulty chromatin crosslink which leads to cytogenetic and cytolethal effects. These modern experiments have confirmed the classical assumption of pairwise lesion interaction (PLI) on which the models of Lea and Neary were based. It seems worthwhile to continue and complete the mathematical treatment of their proposed mechanism in order to show in quantitative terms that the well-known fractionation, protraction and linear energy transfer (LET) irradiation effects are consequences of or can at least be partly attributed to PLI. Arithmetic treatment of PLI - a second order reaction - has also the advantage of providing a prerequisite for further investigations into the stages of development of misrepair products such as chromatin crosslinks. It has been possible to formulate a completely arithmetic theory of PLI by consequently applying three biophysically permitted approximations - pure first order lesion repair kinetics, dose-independent repair time constants and low yield of the ionization/lesion conversion. The mathematical approach will be summarized here, including several formulae not elaborated at the time of previous publications. We will also study an application which sheds light on the chain of events involved in PLI. (author)

Metabolic network prediction through pairwise rational kernels.

Science.gov (United States)

Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

2014-09-26

Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy

SVM-dependent pairwise HMM: an application to protein pairwise alignments.

Science.gov (United States)

Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim F

2017-12-15

Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study

Science.gov (United States)

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias

2018-01-01

Abstract Objective To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) (“living” network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Design Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Data sources Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Eligibility criteria for study selection Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. Results 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing

Robust Subjective Visual Property Prediction from Crowdsourced Pairwise Labels.

Science.gov (United States)

Fu, Yanwei; Hospedales, Timothy M; Xiang, Tao; Xiong, Jiechao; Gong, Shaogang; Wang, Yizhou; Yao, Yuan

2016-03-01

The problem of estimating subjective visual properties from image and video has attracted increasing interest. A subjective visual property is useful either on its own (e.g. image and video interestingness) or as an intermediate representation for visual recognition (e.g. a relative attribute). Due to its ambiguous nature, annotating the value of a subjective visual property for learning a prediction model is challenging. To make the annotation more reliable, recent studies employ crowdsourcing tools to collect pairwise comparison labels. However, using crowdsourced data also introduces outliers. Existing methods rely on majority voting to prune the annotation outliers/errors. They thus require a large amount of pairwise labels to be collected. More importantly as a local outlier detection method, majority voting is ineffective in identifying outliers that can cause global ranking inconsistencies. In this paper, we propose a more principled way to identify annotation outliers by formulating the subjective visual property prediction task as a unified robust learning to rank problem, tackling both the outlier detection and learning to rank jointly. This differs from existing methods in that (1) the proposed method integrates local pairwise comparison labels together to minimise a cost that corresponds to global inconsistency of ranking order, and (2) the outlier detection and learning to rank problems are solved jointly. This not only leads to better detection of annotation outliers but also enables learning with extremely sparse annotations.

Estimators of the Relations of Equivalence, Tolerance and Preference Based on Pairwise Comparisons with Random Errors

Directory of Open Access Journals (Sweden)

Leszek Klukowski

2012-01-01

Full Text Available This paper presents a review of results of the author in the area of estimation of the relations of equivalence, tolerance and preference within a finite set based on multiple, independent (in a stochastic way pairwise comparisons with random errors, in binary and multivalent forms. These estimators require weaker assumptions than those used in the literature on the subject. Estimates of the relations are obtained based on solutions to problems from discrete optimization. They allow application of both types of comparisons - binary and multivalent (this fact relates to the tolerance and preference relations. The estimates can be verified in a statistical way; in particular, it is possible to verify the type of the relation. The estimates have been applied by the author to problems regarding forecasting, financial engineering and bio-cybernetics. (original abstract

ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.

Science.gov (United States)

Otto, Thomas Dan; Catanho, Marcos; Tristão, Cristian; Bezerra, Márcia; Fernandes, Renan Mathias; Elias, Guilherme Steinberger; Scaglia, Alexandre Capeletto; Bovermann, Bill; Berstis, Viktors; Lifschitz, Sergio; de Miranda, Antonio Basílio; Degrave, Wim

2010-03-01

Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith-Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. The database can be accessed through http://proteinworlddb.org

Analyzing the drivers of green manufacturing with fuzzy approach

DEFF Research Database (Denmark)

Govindan, Kannan; Diabat, Ali; Madan Shankar, K.

2015-01-01

India, and aided by their replies; a pair-wise comparison was made among the drivers. The pair-wise comparison is used as an input data and the drivers were analyzed on its basis. The analysis resorted to the use of a fuzzy Multi Criteria Decision Making (MCDM) approach. The obtained results...

Pairwise conjoint analysis of activity engagement choice

NARCIS (Netherlands)

Wang, Donggen; Oppewal, H.; Timmermans, H.J.P.

2000-01-01

Information overload is a well-known problem of conjoint choice models when respondents have to evaluate a large number of attributes and/or attribute levels. In this paper we develop an alternative conjoint modelling approach, called pairwise conjoint analysis. It differs from conventional conjoint

Evaluation of users' satisfaction on pedestrian facilities using pair-wise comparison approach

Science.gov (United States)

Zainol, R.; Ahmad, F.; Nordin, N. A.; Aripin, A. W. M.

2014-02-01

Global climate change issues demand people of the world to change the way they live today. Thus, current cities need to be redeveloped towards less use of carbon in their day to day operations. Pedestrianized environment is one of the approaches used in reducing carbon foot print in cities. Heritage cities are the first to be looked into since they were built in the era in which motorized vehicles were minimal. Therefore, the research explores users' satisfaction on assessment of physical attributes of pedestrianization in Melaka Historical City, a UNESCO World Heritage Site. It aims to examine users' satisfaction on pedestrian facilities provided within the study area using pair wise questionnaire comparison approach. A survey of 200 respondents using random sampling was conducted in six different sites namely Jonker Street, Church Street, Kota Street, Goldsmith Street, Merdeka Street to Taming Sari Tower and Merdeka Street to River Cruise terminal. The survey consists of an assessment tool based on a nine-point scale of users' satisfaction level of pathway properties, zebra pedestrian crossing, street furniture, personal safety, adjacent to traffic flow, aesthetic and amenities. Analytical hierarchical process (AHP) was used to avoid any biasness in analyzing the data collected. Findings show that Merdeka Street to Taming Sari Tower as the street that scores the highest satisfaction level that fulfils all the required needs of a pedestrianized environment. Similar assessment elements can be used to evaluate existing streets in other cities and these criteria should also be used in planning for future cities.

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study.

Science.gov (United States)

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias; Salanti, Georgia

2018-02-28

To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) ("living" network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided

Statistical physics of pairwise probability models

Directory of Open Access Journals (Sweden)

Yasser Roudi

2009-11-01

Full Text Available Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of data: knowledge of the means and correlations between pairs of elements in the system is sufficient. Not surprisingly, then, using pairwise models for studying neural data has been the focus of many studies in recent years. In this paper, we describe how tools from statistical physics can be employed for studying and using pairwise models. We build on our previous work on the subject and study the relation between different methods for fitting these models and evaluating their quality. In particular, using data from simulated cortical networks we study how the quality of various approximate methods for inferring the parameters in a pairwise model depends on the time bin chosen for binning the data. We also study the effect of the size of the time bin on the model quality itself, again using simulated data. We show that using finer time bins increases the quality of the pairwise model. We offer new ways of deriving the expressions reported in our previous work for assessing the quality of pairwise models.

Evaluation of users' satisfaction on pedestrian facilities using pair-wise comparison approach

International Nuclear Information System (INIS)

Zainol, R; Ahmad, F; Nordin, N A; Aripin, A W M

2014-01-01

Global climate change issues demand people of the world to change the way they live today. Thus, current cities need to be redeveloped towards less use of carbon in their day to day operations. Pedestrianized environment is one of the approaches used in reducing carbon foot print in cities. Heritage cities are the first to be looked into since they were built in the era in which motorized vehicles were minimal. Therefore, the research explores users' satisfaction on assessment of physical attributes of pedestrianization in Melaka Historical City, a UNESCO World Heritage Site. It aims to examine users' satisfaction on pedestrian facilities provided within the study area using pair wise questionnaire comparison approach. A survey of 200 respondents using random sampling was conducted in six different sites namely Jonker Street, Church Street, Kota Street, Goldsmith Street, Merdeka Street to Taming Sari Tower and Merdeka Street to River Cruise terminal. The survey consists of an assessment tool based on a nine-point scale of users' satisfaction level of pathway properties, zebra pedestrian crossing, street furniture, personal safety, adjacent to traffic flow, aesthetic and amenities. Analytical hierarchical process (AHP) was used to avoid any biasness in analyzing the data collected. Findings show that Merdeka Street to Taming Sari Tower as the street that scores the highest satisfaction level that fulfils all the required needs of a pedestrianized environment. Similar assessment elements can be used to evaluate existing streets in other cities and these criteria should also be used in planning for future cities

Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

International Nuclear Information System (INIS)

Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal; Thomsen, Bo; Larsen, Knud; Hedegaard, Jakob; Bendixen, Christian; Madsen, Lone Bruhn

2013-01-01

Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

Directory of Open Access Journals (Sweden)

Brejnev Muhizi Muhire

Full Text Available The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV. There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT, a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms.

Geometric measure of pairwise quantum discord for superpositions of multipartite generalized coherent states

International Nuclear Information System (INIS)

Daoud, M.; Ahl Laamara, R.

2012-01-01

We give the explicit expressions of the pairwise quantum correlations present in superpositions of multipartite coherent states. A special attention is devoted to the evaluation of the geometric quantum discord. The dynamics of quantum correlations under a dephasing channel is analyzed. A comparison of geometric measure of quantum discord with that of concurrence shows that quantum discord in multipartite coherent states is more resilient to dissipative environments than is quantum entanglement. To illustrate our results, we consider some special superpositions of Weyl–Heisenberg, SU(2) and SU(1,1) coherent states which interpolate between Werner and Greenberger–Horne–Zeilinger states. -- Highlights: ► Pairwise quantum correlations multipartite coherent states. ► Explicit expression of geometric quantum discord. ► Entanglement sudden death and quantum discord robustness. ► Generalized coherent states interpolating between Werner and Greenberger–Horne–Zeilinger states

Geometric measure of pairwise quantum discord for superpositions of multipartite generalized coherent states

Energy Technology Data Exchange (ETDEWEB)

Daoud, M., E-mail: m_daoud@hotmail.com [Department of Physics, Faculty of Sciences, University Ibnou Zohr, Agadir (Morocco); Ahl Laamara, R., E-mail: ahllaamara@gmail.com [LPHE-Modeling and Simulation, Faculty of Sciences, University Mohammed V, Rabat (Morocco); Centre of Physics and Mathematics, CPM, CNESTEN, Rabat (Morocco)

2012-07-16

We give the explicit expressions of the pairwise quantum correlations present in superpositions of multipartite coherent states. A special attention is devoted to the evaluation of the geometric quantum discord. The dynamics of quantum correlations under a dephasing channel is analyzed. A comparison of geometric measure of quantum discord with that of concurrence shows that quantum discord in multipartite coherent states is more resilient to dissipative environments than is quantum entanglement. To illustrate our results, we consider some special superpositions of Weyl–Heisenberg, SU(2) and SU(1,1) coherent states which interpolate between Werner and Greenberger–Horne–Zeilinger states. -- Highlights: ► Pairwise quantum correlations multipartite coherent states. ► Explicit expression of geometric quantum discord. ► Entanglement sudden death and quantum discord robustness. ► Generalized coherent states interpolating between Werner and Greenberger–Horne–Zeilinger states.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

OpenAIRE

Maréchal Eric; Ortet Philippe; Roy Sylvaine; Bastien Olivier

2005-01-01

Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic recon...

Statistical physics of pairwise probability models

DEFF Research Database (Denmark)

Roudi, Yasser; Aurell, Erik; Hertz, John

2009-01-01

(dansk abstrakt findes ikke) Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of  data......: knowledge of the means and correlations between pairs of elements in the system is sufficient. Not surprisingly, then, using pairwise models for studying neural data has been the focus of many studies in recent years. In this paper, we describe how tools from statistical physics can be employed for studying...

Randomized Approaches for Nearest Neighbor Search in Metric Space When Computing the Pairwise Distance Is Extremely Expensive

Science.gov (United States)

Wang, Lusheng; Yang, Yong; Lin, Guohui

Finding the closest object for a query in a database is a classical problem in computer science. For some modern biological applications, computing the similarity between two objects might be very time consuming. For example, it takes a long time to compute the edit distance between two whole chromosomes and the alignment cost of two 3D protein structures. In this paper, we study the nearest neighbor search problem in metric space, where the pair-wise distance between two objects in the database is known and we want to minimize the number of distances computed on-line between the query and objects in the database in order to find the closest object. We have designed two randomized approaches for indexing metric space databases, where objects are purely described by their distances with each other. Analysis and experiments show that our approaches only need to compute O(logn) objects in order to find the closest object, where n is the total number of objects in the database.

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

Science.gov (United States)

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures.

Science.gov (United States)

Filippi, Sarah; Holmes, Chris C; Nieto-Barajas, Luis E

2016-11-16

In this article we propose novel Bayesian nonparametric methods using Dirichlet Process Mixture (DPM) models for detecting pairwise dependence between random variables while accounting for uncertainty in the form of the underlying distributions. A key criteria is that the procedures should scale to large data sets. In this regard we find that the formal calculation of the Bayes factor for a dependent-vs.-independent DPM joint probability measure is not feasible computationally. To address this we present Bayesian diagnostic measures for characterising evidence against a "null model" of pairwise independence. In simulation studies, as well as for a real data analysis, we show that our approach provides a useful tool for the exploratory nonparametric Bayesian analysis of large multivariate data sets.

Pairwise harmonics for shape analysis

KAUST Repository

Zheng, Youyi

2013-07-01

This paper introduces a simple yet effective shape analysis mechanism for geometry processing. Unlike traditional shape analysis techniques which compute descriptors per surface point up to certain neighborhoods, we introduce a shape analysis framework in which the descriptors are based on pairs of surface points. Such a pairwise analysis approach leads to a new class of shape descriptors that are more global, discriminative, and can effectively capture the variations in the underlying geometry. Specifically, we introduce new shape descriptors based on the isocurves of harmonic functions whose global maximum and minimum occur at the point pair. We show that these shape descriptors can infer shape structures and consistently lead to simpler and more efficient algorithms than the state-of-the-art methods for three applications: intrinsic reflectional symmetry axis computation, matching shape extremities, and simultaneous surface segmentation and skeletonization. © 2012 IEEE.

Pairwise Constraint-Guided Sparse Learning for Feature Selection.

Science.gov (United States)

Liu, Mingxia; Zhang, Daoqiang

2016-01-01

Feature selection aims to identify the most informative features for a compact and accurate data representation. As typical supervised feature selection methods, Lasso and its variants using L1-norm-based regularization terms have received much attention in recent studies, most of which use class labels as supervised information. Besides class labels, there are other types of supervised information, e.g., pairwise constraints that specify whether a pair of data samples belong to the same class (must-link constraint) or different classes (cannot-link constraint). However, most of existing L1-norm-based sparse learning methods do not take advantage of the pairwise constraints that provide us weak and more general supervised information. For addressing that problem, we propose a pairwise constraint-guided sparse (CGS) learning method for feature selection, where the must-link and the cannot-link constraints are used as discriminative regularization terms that directly concentrate on the local discriminative structure of data. Furthermore, we develop two variants of CGS, including: 1) semi-supervised CGS that utilizes labeled data, pairwise constraints, and unlabeled data and 2) ensemble CGS that uses the ensemble of pairwise constraint sets. We conduct a series of experiments on a number of data sets from University of California-Irvine machine learning repository, a gene expression data set, two real-world neuroimaging-based classification tasks, and two large-scale attribute classification tasks. Experimental results demonstrate the efficacy of our proposed methods, compared with several established feature selection methods.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

Science.gov (United States)

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

A scalable pairwise class interaction framework for multidimensional classification

DEFF Research Database (Denmark)

Arias, Jacinto; Gámez, Jose A.; Nielsen, Thomas Dyhre

2016-01-01

We present a general framework for multidimensional classification that cap- tures the pairwise interactions between class variables. The pairwise class inter- actions are encoded using a collection of base classifiers (Phase 1), for which the class predictions are combined in a Markov random fie...

Dynamics of pairwise motions in the Cosmic Web

Science.gov (United States)

Hellwing, Wojciech A.

2016-10-01

We present results of analysis of the dark matter (DM) pairwise velocity statistics in different Cosmic Web environments. We use the DM velocity and density field from the Millennium 2 simulation together with the NEXUS+ algorithm to segment the simulation volume into voxels uniquely identifying one of the four possible environments: nodes, filaments, walls or cosmic voids. We show that the PDFs of the mean infall velocities v 12 as well as its spatial dependence together with the perpendicular and parallel velocity dispersions bear a significant signal of the large-scale structure environment in which DM particle pairs are embedded. The pairwise flows are notably colder and have smaller mean magnitude in wall and voids, when compared to much denser environments of filaments and nodes. We discuss on our results, indicating that they are consistent with a simple theoretical predictions for pairwise motions as induced by gravitational instability mechanism. Our results indicate that the Cosmic Web elements are coherent dynamical entities rather than just temporal geometrical associations. In addition it should be possible to observationally test various Cosmic Web finding algorithms by segmenting available peculiar velocity data and studying resulting pairwise velocity statistics.

A Relative-Localization Algorithm Using Incomplete Pairwise Distance Measurements for Underwater Applications

Directory of Open Access Journals (Sweden)

Kae Y. Foo

2010-01-01

Full Text Available The task of localizing underwater assets involves the relative localization of each unit using only pairwise distance measurements, usually obtained from time-of-arrival or time-delay-of-arrival measurements. In the fluctuating underwater environment, a complete set of pair-wise distance measurements can often be difficult to acquire, thus hindering a straightforward closed-form solution in deriving the assets' relative coordinates. An iterative multidimensional scaling approach is presented based upon a weighted-majorization algorithm that tolerates missing or inaccurate distance measurements. Substantial modifications are proposed to optimize the algorithm, while the effects of refractive propagation paths are considered. A parametric study of the algorithm based upon simulation results is shown. An acoustic field-trial was then carried out, presenting field measurements to highlight the practical implementation of this algorithm.

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

Science.gov (United States)

Ruan, Peiying; Hayashida, Morihiro; Akutsu, Tatsuya; Vert, Jean-Philippe

2018-02-19

Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several computational methods have been proposed to predict complexes from the topology and structure of experimental protein-protein interaction (PPI) network. These methods work well to predict complexes involving at least three proteins, but generally fail at identifying complexes involving only two different proteins, called heterodimeric complexes or heterodimers. There is however an urgent need for efficient methods to predict heterodimers, since the majority of known protein complexes are precisely heterodimers. In this paper, we use three promising kernel functions, Min kernel and two pairwise kernels, which are Metric Learning Pairwise Kernel (MLPK) and Tensor Product Pairwise Kernel (TPPK). We also consider the normalization forms of Min kernel. Then, we combine Min kernel or its normalization form and one of the pairwise kernels by plugging. We applied kernels based on PPI, domain, phylogenetic profile, and subcellular localization properties to predicting heterodimers. Then, we evaluate our method by employing C-Support Vector Classification (C-SVC), carrying out 10-fold cross-validation, and calculating the average F-measures. The results suggest that the combination of normalized-Min-kernel and MLPK leads to the best F-measure and improved the performance of our previous work, which had been the best existing method so far. We propose new methods to predict heterodimers, using a machine learning-based approach. We train a support vector machine (SVM) to discriminate interacting vs non-interacting protein pairs, based on informations extracted from PPI, domain, phylogenetic profiles and subcellular localization. We evaluate in detail new kernel functions to encode these data, and report prediction performance that outperforms the state-of-the-art.

Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

Directory of Open Access Journals (Sweden)

Inês Soares

2012-01-01

Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

Science.gov (United States)

Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

Directory of Open Access Journals (Sweden)

Maréchal Eric

2005-03-01

Full Text Available Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons and be the basis for a novel method of consistent and stable phylogenetic reconstruction. Results We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. Conclusion The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

A Bayesian approach to PET reconstruction using image-modeling Gibbs priors: Implementation and comparison

International Nuclear Information System (INIS)

Chan, M.T.; Herman, G.T.; Levitan, E.

1996-01-01

We demonstrate that (i) classical methods of image reconstruction from projections can be improved upon by considering the output of such a method as a distorted version of the original image and applying a Bayesian approach to estimate from it the original image (based on a model of distortion and on a Gibbs distribution as the prior) and (ii) by selecting an open-quotes image-modelingclose quotes prior distribution (i.e., one which is such that it is likely that a random sample from it shares important characteristics of the images of the application area) one can improve over another Gibbs prior formulated using only pairwise interactions. We illustrate our approach using simulated Positron Emission Tomography (PET) data from realistic brain phantoms. Since algorithm performance ultimately depends on the diagnostic task being performed. we examine a number of different medically relevant figures of merit to give a fair comparison. Based on a training-and-testing evaluation strategy, we demonstrate that statistically significant improvements can be obtained using the proposed approach

Measuring pair-wise molecular interactions in a complex mixture

Science.gov (United States)

Chakraborty, Krishnendu; Varma, Manoj M.; Venkatapathi, Murugesan

2016-03-01

Complex biological samples such as serum contain thousands of proteins and other molecules spanning up to 13 orders of magnitude in concentration. Present measurement techniques do not permit the analysis of all pair-wise interactions between the components of such a complex mixture to a given target molecule. In this work we explore the use of nanoparticle tags which encode the identity of the molecule to obtain the statistical distribution of pair-wise interactions using their Localized Surface Plasmon Resonance (LSPR) signals. The nanoparticle tags are chosen such that the binding between two molecules conjugated to the respective nanoparticle tags can be recognized by the coupling of their LSPR signals. This numerical simulation is done by DDA to investigate this approach using a reduced system consisting of three nanoparticles (a gold ellipsoid with aspect ratio 2.5 and short axis 16 nm, and two silver ellipsoids with aspect ratios 3 and 2 and short axes 8 nm and 10 nm respectively) and the set of all possible dimers formed between them. Incident light was circularly polarized and all possible particle and dimer orientations were considered. We observed that minimum peak separation between two spectra is 5 nm while maximum is 184nm.

Pairwise Choice Markov Chains

OpenAIRE

Ragain, Stephen; Ugander, Johan

2016-01-01

As datasets capturing human choices grow in richness and scale---particularly in online domains---there is an increasing need for choice models that escape traditional choice-theoretic axioms such as regularity, stochastic transitivity, and Luce's choice axiom. In this work we introduce the Pairwise Choice Markov Chain (PCMC) model of discrete choice, an inferentially tractable model that does not assume any of the above axioms while still satisfying the foundational axiom of uniform expansio...

The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks

Directory of Open Access Journals (Sweden)

Wingender Edgar

2008-05-01

Full Text Available Abstract Background Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emphasize the global characterization of regulatory systems, the practical approaches focus on the role of distinct molecules and genes in regulation. To bridge the gap between these opposite approaches, one needs to combine 'general' with 'particular' properties and translate abstract topological features of large systems into testable functional characteristics of individual components. Here, we propose a new topological parameter – the pairwise disconnectivity index of a network's element – that is capable of such bridging. Results The pairwise disconnectivity index quantifies how crucial an individual element is for sustaining the communication ability between connected pairs of vertices in a network that is displayed as a directed graph. Such an element might be a vertex (i.e., molecules, genes, an edge (i.e., reactions, interactions, as well as a group of vertices and/or edges. The index can be viewed as a measure of topological redundancy of regulatory paths which connect different parts of a given network and as a measure of sensitivity (robustness of this network to the presence (absence of each individual element. Accordingly, we introduce the notion of a path-degree of a vertex in terms of its corresponding incoming, outgoing and mediated paths, respectively. The pairwise disconnectivity index has been applied to the analysis of several regulatory networks from various organisms. The importance of an individual vertex or edge for the coherence of the network is determined by the particular position of the given element in the whole network. Conclusion Our approach enables to evaluate the effect of removing each element (i.e., vertex, edge, or their combinations from a network. The greatest potential value of

The Role of Middlemen inEfficient and Strongly Pairwise Stable Networks

NARCIS (Netherlands)

Gilles, R.P.; Chakrabarti, S.; Sarangi, S.; Badasyan, N.

2004-01-01

We examine the strong pairwise stability concept in network formation theory under collective network benefits.Strong pairwise stability considers a pair of players to add a link through mutual consent while permitting them to unilaterally delete any subset of links under their control.We examine

Reducing Post-Decision Dissonance in International Decisions: The Analytic Hierarchy Process Approach.

Science.gov (United States)

DuBois, Frank L.

1999-01-01

Describes use of the analytic hierarchy process (AHP) as a teaching tool to illustrate the complexities of decision making in an international environment. The AHP approach uses managerial input to develop pairwise comparisons of relevant decision criteria to efficiently generate an appropriate solution. (DB)

Historical demography of common carp estimated from individuals collected from various parts of the world using the pairwise sequentially markovian coalescent approach.

Science.gov (United States)

Yuan, Zihao; Huang, Wei; Liu, Shikai; Xu, Peng; Dunham, Rex; Liu, Zhanjiang

2018-04-01

The inference of historical demography of a species is helpful for understanding species' differentiation and its population dynamics. However, such inference has been previously difficult due to the lack of proper analytical methods and availability of genetic data. A recently developed method called Pairwise Sequentially Markovian Coalescent (PSMC) offers the capability for estimation of the trajectories of historical populations over considerable time periods using genomic sequences. In this study, we applied this approach to infer the historical demography of the common carp using samples collected from Europe, Asia and the Americas. Comparison between Asian and European common carp populations showed that the last glacial period starting 100 ka BP likely caused a significant decline in population size of the wild common carp in Europe, while it did not have much of an impact on its counterparts in Asia. This was probably caused by differences in glacial activities in East Asia and Europe, and suggesting a separation of the European and Asian clades before the last glacial maximum. The North American clade which is an invasive population shared a similar demographic history as those from Europe, consistent with the idea that the North American common carp probably had European ancestral origins. Our analysis represents the first reconstruction of the historical population demography of the common carp, which is important to elucidate the separation of European and Asian common carp clades during the Quaternary glaciation, as well as the dispersal of common carp across the world.

A comparison of verbal and numerical judgments in the analytic hierarchy process

NARCIS (Netherlands)

Huizingh, EKRE; Vrolijk, HCJ

In the Analytic Hierarchy Process (AHP), decision makers make pairwise comparisons of alternatives and criteria. The AHP allows to make these pairwise comparisons verbally or numerically. Although verbal statements are intuitively attractive for preference elicitation, there is overwhelming evidence

Automatic Camera Calibration Using Multiple Sets of Pairwise Correspondences.

Science.gov (United States)

Vasconcelos, Francisco; Barreto, Joao P; Boyer, Edmond

2018-04-01

We propose a new method to add an uncalibrated node into a network of calibrated cameras using only pairwise point correspondences. While previous methods perform this task using triple correspondences, these are often difficult to establish when there is limited overlap between different views. In such challenging cases we must rely on pairwise correspondences and our solution becomes more advantageous. Our method includes an 11-point minimal solution for the intrinsic and extrinsic calibration of a camera from pairwise correspondences with other two calibrated cameras, and a new inlier selection framework that extends the traditional RANSAC family of algorithms to sampling across multiple datasets. Our method is validated on different application scenarios where a lack of triple correspondences might occur: addition of a new node to a camera network; calibration and motion estimation of a moving camera inside a camera network; and addition of views with limited overlap to a Structure-from-Motion model.

Revisiting the classification of curtoviruses based on genome-wide pairwise identity

KAUST Repository

Varsani, Arvind; Martin, Darren Patrick; Navas-Castillo, Jesú s; Moriones, Enrique; Herná ndez-Zepeda, Cecilia; Idris, Ali; Murilo Zerbini, F.; Brown, Judith K.

2014-01-01

Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). © 2014 Springer-Verlag Wien.

Revisiting the classification of curtoviruses based on genome-wide pairwise identity

KAUST Repository

Varsani, Arvind

2014-01-25

Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). © 2014 Springer-Verlag Wien.

Probing dark energy models with extreme pairwise velocities of galaxy clusters from the DEUS-FUR simulations

Science.gov (United States)

Bouillot, Vincent R.; Alimi, Jean-Michel; Corasaniti, Pier-Stefano; Rasera, Yann

2015-06-01

Observations of colliding galaxy clusters with high relative velocity probe the tail of the halo pairwise velocity distribution with the potential of providing a powerful test of cosmology. As an example it has been argued that the discovery of the Bullet Cluster challenges standard Λ cold dark matter (ΛCDM) model predictions. Halo catalogues from N-body simulations have been used to estimate the probability of Bullet-like clusters. However, due to simulation volume effects previous studies had to rely on a Gaussian extrapolation of the pairwise velocity distribution to high velocities. Here, we perform a detail analysis using the halo catalogues from the Dark Energy Universe Simulation Full Universe Runs (DEUS-FUR), which enables us to resolve the high-velocity tail of the distribution and study its dependence on the halo mass definition, redshift and cosmology. Building upon these results, we estimate the probability of Bullet-like systems in the framework of Extreme Value Statistics. We show that the tail of extreme pairwise velocities significantly deviates from that of a Gaussian, moreover it carries an imprint of the underlying cosmology. We find the Bullet Cluster probability to be two orders of magnitude larger than previous estimates, thus easing the tension with the ΛCDM model. Finally, the comparison of the inferred probabilities for the different DEUS-FUR cosmologies suggests that observations of extreme interacting clusters can provide constraints on dark energy models complementary to standard cosmological tests.

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting

Science.gov (United States)

Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-01-01

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes. PMID:29453930

Unjamming in models with analytic pairwise potentials

Science.gov (United States)

Kooij, Stefan; Lerner, Edan

2017-06-01

Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the coordination number z , which has an unambiguous definition in these cases. Pairwise potentials without a sharp cutoff in the interaction range have not been studied in this context, but should in fact be considered to understand the relevance of the unjamming phenomenology in systems where such a cutoff is not present. In this work we explore two systems with such interactions: an inverse power law and an exponentially decaying pairwise potential, with the control parameters being the exponent (of the inverse power law) for the former and the number density for the latter. Both systems are shown to exhibit the characteristic features of the unjamming transition, among which are the vanishing of the shear-to-bulk modulus ratio and the emergence of an excess of low-frequency vibrational modes. We establish a relation between the pressure-to-bulk modulus ratio and the distance to unjamming in each of our model systems. This allows us to predict the dependence of other key observables on the distance to unjamming. Our results provide the means for a quantitative estimation of the proximity of generic glass-forming models to the unjamming transition in the absence of a clear-cut definition of the coordination number and highlight the general irrelevance of nonaffine contributions to the bulk modulus.

PAIRWISE BLENDING OF HIGH LEVEL WASTE

International Nuclear Information System (INIS)

CERTA, P.J.

2006-01-01

The primary objective of this study is to demonstrate a mission scenario that uses pairwise and incidental blending of high level waste (HLW) to reduce the total mass of HLW glass. Secondary objectives include understanding how recent refinements to the tank waste inventory and solubility assumptions affect the mass of HLW glass and how logistical constraints may affect the efficacy of HLW blending

Hierarchical ordering with partial pairwise hierarchical relationships on the macaque brain data sets.

Directory of Open Access Journals (Sweden)

Woosang Lim

Full Text Available Hierarchical organizations of information processing in the brain networks have been known to exist and widely studied. To find proper hierarchical structures in the macaque brain, the traditional methods need the entire pairwise hierarchical relationships between cortical areas. In this paper, we present a new method that discovers hierarchical structures of macaque brain networks by using partial information of pairwise hierarchical relationships. Our method uses a graph-based manifold learning to exploit inherent relationship, and computes pseudo distances of hierarchical levels for every pair of cortical areas. Then, we compute hierarchy levels of all cortical areas by minimizing the sum of squared hierarchical distance errors with the hierarchical information of few cortical areas. We evaluate our method on the macaque brain data sets whose true hierarchical levels are known as the FV91 model. The experimental results show that hierarchy levels computed by our method are similar to the FV91 model, and its errors are much smaller than the errors of hierarchical clustering approaches.

Unjamming in models with analytic pairwise potentials

NARCIS (Netherlands)

Kooij, S.; Lerner, E.

Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the

A Comparative Study of Pairwise Learning Methods Based on Kernel Ridge Regression.

Science.gov (United States)

Stock, Michiel; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

2018-06-12

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction, or network inference problems. During the past decade, kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression, and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency, and spectral filtering properties. Our theoretical results provide valuable insights into assessing the advantages and limitations of existing pairwise learning methods.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

Science.gov (United States)

Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe

2015-08-01

The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The effect of fiscal incentives on market penetration of electric vehicles: A pairwise comparison of total cost of ownership

International Nuclear Information System (INIS)

Lévay, Petra Zsuzsa; Drossinos, Yannis; Thiel, Christian

2017-01-01

An important barrier to electric vehicle (EV) sales is their high purchase price compared to internal combustion engine (ICE) vehicles. We conducted total cost of ownership (TCO) calculations to study how costs and sales of EVs relate to each other and to examine the role of fiscal incentives in reducing TCO and increasing EV sales. We composed EV-ICE vehicle pairs that allowed cross-segment and cross-country comparison in eight European countries. Actual car prices were used to calculate the incentives for each model in each country. We found a negative TCO-sales relationship that differs across car segments. Compared to their ICE vehicle pair, big EVs have lower TCO, higher sales, and seem to be less price responsive than small EVs. Three country groups can be distinguished according to the level of fiscal incentives and their impact on TCO and EV sales. In Norway, incentives led to the lowest TCO for the EVs. In the Netherlands, France, and UK the TCO of EVs is close to the TCO of the ICE pairs. In the other countries the TCO of EVs exceeds that of the ICE vehicles. We found that exemptions from flat taxes favour big EVs, while lump-sum subsidies favour small EVs. - Highlights: • Pairwise comparison of EV and ICE vehicle TCO and sales in eight European countries. • In NO, EV TCO is lower than ICE TCO; in NL, FR, and UK, EV TCO is slightly higher. • Compared to ICE vehicles, big EVs have lower TCO and higher sales than small EVs. • Exemptions from flat taxes favour big EVs, lump-sum subsidies favour small EVs. • Most popular EV models: Tesla Model S, Nissan Leaf, Mitsubishi Outlander PHEV.

Predicting community composition from pairwise interactions

Science.gov (United States)

Friedman, Jonathan; Higgins, Logan; Gore, Jeff

The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

A water market simulator considering pair-wise trades between agents

Science.gov (United States)

Huskova, I.; Erfani, T.; Harou, J. J.

2012-04-01

In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

Criteria for the singularity of a pairwise l1-distance matrix and their generalizations

International Nuclear Information System (INIS)

D'yakonov, Alexander G

2012-01-01

We study the singularity problem for the pairwise distance matrix of a system of points, as well as generalizations of this problem that are connected with applications to interpolation theory and with an algebraic approach to recognition problems. We obtain necessary and sufficient conditions on a system under which the dimension of the range space of polynomials of bounded degree over the columns of the distance matrix is less than the number of points in the system.

A pairwise unit-root-test based approach to investigating convergence of household debts in South Africa and the United States

Directory of Open Access Journals (Sweden)

Ntebogang Dinah Moroke

2015-05-01

Full Text Available The purpose of this paper was to test convergence of household debts in the United States and South Africa taking a pairwise unit root tests based approaches into account. Substantial number of studies dealt with convergence of several macroeconomic variables but to my knowledge no study considered this subject with respect to household debts of the identified countries. Quarterly data on household debts consisting of 88 observations in the South Africa and United States spanning the period 1990 to 2013 was collected from the South African and St. Louis Federal Reserve Banks. Focused on the absolute value of household debts, this study proved that South Africa is far from catching-up with the United States in terms of overcoming household debts for the selected period. The findings of this study can be used by relevant authorities to help improve ways and means of dealing with household debts South Africa

Pairwise Trajectory Management (PTM): Concept Overview

Science.gov (United States)

Jones, Kenneth M.; Graff, Thomas J.; Chartrand, Ryan C.; Carreno, Victor; Kibler, Jennifer L.

2017-01-01

Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the precision of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the PTM minimum spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This paper provides an overview of the proposed application, description of a few key scenarios, high level discussion of expected air and ground equipment and procedure changes, overview of a potential flight crew human-machine interface that would support PTM operations and some initial PTM benefits results.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

Directory of Open Access Journals (Sweden)

Manuel Gil

2014-09-01

Full Text Available Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989 which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

Science.gov (United States)

Gil, Manuel

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Pair-Wise and Many-Body Dispersive Interactions Coupled to an Optimally Tuned Range-Separated Hybrid Functional.

Science.gov (United States)

Agrawal, Piyush; Tkatchenko, Alexandre; Kronik, Leeor

2013-08-13

We propose a nonempirical, pair-wise or many-body dispersion-corrected, optimally tuned range-separated hybrid functional. This functional retains the advantages of the optimal-tuning approach in the prediction of the electronic structure. At the same time, it gains accuracy in the prediction of binding energies for dispersively bound systems, as demonstrated on the S22 and S66 benchmark sets of weakly bound dimers.

Comparison of Fuzzy AHP and Fuzzy TOPSIS for Road Pavement Maintenance Prioritization: Methodological Exposition and Case Study

OpenAIRE

Yashon O. Ouma; J. Opudo; S. Nyambenya

2015-01-01

For road pavement maintenance and repairs prioritization, a multiattribute approach that compares fuzzy Analytical Hierarchy Process (AHP) and fuzzy Technique for Order Preference by Ideal Situation (TOPSIS) is evaluated. The pavement distress data was collected through empirical condition surveys and rating by pavement experts. In comparison to the crisp AHP, the fuzzy AHP and fuzzy TOPSIS pairwise comparison techniques are considered to be more suitable for the subjective analysis of the pa...

Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.

Science.gov (United States)

Newberg, Lee A

2008-08-15

A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward-backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

Pair-Wise Trajectory Management-Oceanic (PTM-O) . [Concept of Operations—Version 3.9

Science.gov (United States)

Jones, Kenneth M.

2014-01-01

This document describes the Pair-wise Trajectory Management-Oceanic (PTM-O) Concept of Operations (ConOps). Pair-wise Trajectory Management (PTM) is a concept that includes airborne and ground-based capabilities designed to enable and to benefit from, airborne pair-wise distance-monitoring capability. PTM includes the capabilities needed for the controller to issue a PTM clearance that resolves a conflict for a specific pair of aircraft. PTM avionics include the capabilities needed for the flight crew to manage their trajectory relative to specific designated aircraft. Pair-wise Trajectory Management PTM-Oceanic (PTM-O) is a regional specific application of the PTM concept. PTM is sponsored by the National Aeronautics and Space Administration (NASA) Concept and Technology Development Project (part of NASA's Airspace Systems Program). The goal of PTM is to use enhanced and distributed communications and surveillance along with airborne tools to permit reduced separation standards for given aircraft pairs, thereby increasing the capacity and efficiency of aircraft operations at a given altitude or volume of airspace.

Atomic pairwise distribution function analysis of the amorphous phase prepared by different manufacturing routes

DEFF Research Database (Denmark)

Boetker, Johan P.; Koradia, Vishal; Rades, Thomas

2012-01-01

was subjected to quench cooling thereby creating an amorphous form of the drug from both starting materials. The milled and quench cooled samples were, together with the crystalline starting materials, analyzed with X-ray powder diffraction (XRPD), Raman spectroscopy and atomic pair-wise distribution function...... (PDF) analysis of the XRPD pattern. When compared to XRPD and Raman spectroscopy, the PDF analysis was superior in displaying the difference between the amorphous samples prepared by milling and quench cooling approaches of the two starting materials....

Predictive Modeling of Expressed Emotions in Music Using Pairwise Comparisons

DEFF Research Database (Denmark)

Madsen, Jens; Jensen, Bjørn Sand; Larsen, Jan

2013-01-01

We introduce a two-alternative forced-choice (2AFC) experimental paradigm to quantify expressed emotions in music using the arousal and valence (AV) dimensions. A wide range of well-known audio features are investigated for predicting the expressed emotions in music using learning curves...... and essential baselines. We furthermore investigate the scalability issues of using 2AFC in quantifying emotions expressed in music on large-scale music databases. The possibility of dividing the annotation task between multiple individuals, while pooling individuals’ comparisons is investigated by looking...... comparisons at random by using learning curves. We show that a suitable predictive model of expressed valence in music can be achieved from only 15% of the total number of comparisons when using the Expected Value of Information (EVOI) active learning scheme. For the arousal dimension we require 9...

A decomposition of pairwise continuity via ideals

Directory of Open Access Journals (Sweden)

Mahes Wari

2016-02-01

Full Text Available In this paper, we introduce and study the notions of (i, j - regular - ℐ -closed sets, (i, j - Aℐ -sets, (i, j - ℐ -locally closed sets, p- Aℐ -continuous functions and p- ℐ -LC-continuous functions in ideal bitopological spaces and investigate some of their properties. Also, a new decomposition of pairwise continuity is obtained using these sets.

Criteria for the singularity of a pairwise l{sub 1}-distance matrix and their generalizations

Energy Technology Data Exchange (ETDEWEB)

D' yakonov, Alexander G [M. V. Lomonosov Moscow State University, Faculty of Computational Mathematics and Cybernetics, Moscow (Russian Federation)

2012-06-30

We study the singularity problem for the pairwise distance matrix of a system of points, as well as generalizations of this problem that are connected with applications to interpolation theory and with an algebraic approach to recognition problems. We obtain necessary and sufficient conditions on a system under which the dimension of the range space of polynomials of bounded degree over the columns of the distance matrix is less than the number of points in the system.

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

KAUST Repository

Cui, Xuefeng

2015-09-09

To detect and evaluate the similarities between the three-dimensional (3D) structures of two molecules, various kinds of methods have been proposed for the pairwise structure alignment problem [6, 9, 7, 11]. The problem plays important roles when studying the function and the evolution of biological molecules. Recently, pairwise structure alignment methods have been extended and applied on surface pocket structures [10, 3, 5] and interaction interface structures [8, 4]. The results show that, even when there are no global similarities discovered between the global sequences and the global structures, biological molecules or complexes could share similar functions because of well conserved pockets and interfaces. Thus, pairwise pocket and interface structure alignments are promising to unveil such shared functions that cannot be discovered by the well-studied global sequence and global structure alignments. State-of-the-art methods for pairwise pocket and interface structure alignments [4, 5] are direct extensions of the classic pairwise protein structure alignment methods, and thus such methods share a few limitations. First, the goal of the classic protein structure alignment methods is to align single-chain protein structures (i.e., a single fragment of residues connected by peptide bonds). However, we observed that pockets and interfaces tend to consist of tens of extremely short backbone fragments (i.e., three or fewer residues connected by peptide bonds). Thus, existing pocket and interface alignment methods based on the protein structure alignment methods still rely on the existence of long-enough backbone fragments, and the fragmentation issue of pockets and interfaces rises the risk of missing the optimal alignments. Moreover, existing interface structure alignment methods focus on protein-protein interfaces, and require a "blackbox preprocessing" before aligning protein-DNA and protein-RNA interfaces. Therefore, we introduce the PROtein STucture Alignment

Linear VSS and Distributed Commitments Based on Secret Sharing and Pairwise Checks

DEFF Research Database (Denmark)

Fehr, Serge; Maurer, Ueli M.

2002-01-01

. VSS and DC are main building blocks for unconditional secure multi-party computation protocols. This general approach covers all known linear VSS and DC schemes. The main theorem states that the security of a scheme is equivalent to a pure linear-algebra condition on the linear mappings (e.......g. described as matrices and vectors) describing the scheme. The security of all known schemes follows as corollaries whose proofs are pure linear-algebra arguments, in contrast to some hybrid arguments used in the literature. Our approach is demonstrated for the CDM DC scheme, which we generalize to be secure......We present a general treatment of all non-cryptographic (i.e., information-theoretically secure) linear veriable-secret-sharing (VSS) and distributed-commitment (DC) schemes, based on an underlying secret sharing scheme, pairwise checks between players, complaints, and accusations of the dealer...

Perceptron learning of pairwise contact energies for proteins incorporating the amino acid environment

Science.gov (United States)

Heo, Muyoung; Kim, Suhkmann; Moon, Eun-Joung; Cheon, Mookyung; Chung, Kwanghoon; Chang, Iksoo

2005-07-01

Although a coarse-grained description of proteins is a simple and convenient way to attack the protein folding problem, the construction of a global pairwise energy function which can simultaneously recognize the native folds of many proteins has resulted in partial success. We have sought the possibility of a systematic improvement of this pairwise-contact energy function as we extended the parameter space of amino acids, incorporating local environments of amino acids, beyond a 20×20 matrix. We have studied the pairwise contact energy functions of 20×20 , 60×60 , and 180×180 matrices depending on the extent of parameter space, and compared their effect on the learnability of energy parameters in the context of a gapless threading, bearing in mind that a 20×20 pairwise contact matrix has been shown to be too simple to recognize the native folds of many proteins. In this paper, we show that the construction of a global pairwise energy function was achieved using 1006 training proteins of a homology of less than 30%, which include all representatives of different protein classes. After parametrizing the local environments of the amino acids into nine categories depending on three secondary structures and three kinds of hydrophobicity (desolvation), the 16290 pairwise contact energies (scores) of the amino acids could be determined by perceptron learning and protein threading. These could simultaneously recognize all the native folds of the 1006 training proteins. When these energy parameters were tested on the 382 test proteins of a homology of less than 90%, 370 (96.9%) proteins could recognize their native folds. We set up a simple thermodynamic framework in the conformational space of decoys to calculate the unfolded fraction and the specific heat of real proteins. The different thermodynamic stabilities of E.coli ribonuclease H (RNase H) and its mutants were well described in our calculation, agreeing with the experiment.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

OpenAIRE

Kelly, Brendan J.; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D.; Collman, Ronald G.; Bushman, Frederic D.; Li, Hongzhe

2015-01-01

Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-...

Pairwise Trajectory Management (PTM): Concept Description and Documentation

Science.gov (United States)

Jones, Kenneth M.; Graff, Thomas J.; Carreno, Victor; Chartrand, Ryan C.; Kibler, Jennifer L.

2018-01-01

Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the accuracy of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the minimum PTM spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This document provides an overview of the proposed application, a description of several key scenarios, a high level discussion of expected air and ground equipment and procedure changes, a description of a NASA human-machine interface (HMI) prototype for the flight crew that would support PTM operations, and initial benefits analysis results. Additionally, included as appendices, are the following documents: the PTM Operational Services and Environment Definition (OSED) document and a companion "Future Considerations for the Pairwise Trajectory Management (PTM) Concept: Potential Future Updates for the PTM OSED" paper, a detailed description of the PTM algorithm and PTM Limit Mach rules, initial PTM safety requirements and safety assessment documents, a detailed description of the design, development, and initial evaluations of the proposed flight crew HMI, an overview of the methodology and results of PTM pilot training

Incorporating risk attitude into comparison of reforestation alternatives

International Nuclear Information System (INIS)

Kangas, J.

1994-01-01

By using the approach presented in this paper, the decision-maker's risk can be ascertained and taken into account in the comparison of reforestation alternatives of a forest stand. Risks which reforestation alternatives include are described using distributions of outcomes. Cardinal utility values of five accumulation points of cumulative distributions of outcomes, calculated without considering risk preferences, are the variables included in a preference function. The parameters of that additive preference function represent the importance of the accumulation points in the choice of the reforestation alternatives. They indicate the decision-maker's attitude towards risk. The parameters are estimated on the basis of pairwise comparisons between the importance of variables, using Saaty's eigenvalue method. Estimation, application, and interpretation of preference function are simple to carry out, which is important for an approach applied to practical decision-making. The approach could be applied also, for example, to other forestry decision-making problems. 42 refs, 2 figs, 1 tab

Grip-Pattern Verification for Smart Gun Based on Maximum-Pairwise Comparison and Mean-Template Comparison

NARCIS (Netherlands)

Shang, X.; Veldhuis, Raymond N.J.

2008-01-01

In our biometric verification system of a smart gun, the rightful user of a gun is authenticated by grip-pattern recognition. In this work verification will be done using two types of comparison methods, respectively. One is mean-template comparison, where the matching score between a test image and

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

Science.gov (United States)

Daily, Jeff

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

Left auditory cortex is involved in pairwise comparisons of the direction of frequency modulated tones

Directory of Open Access Journals (Sweden)

Nicole eAngenstein

2013-07-01

Full Text Available Evaluating series of complex sounds like those in speech and music requires sequential comparisons to extract task-relevant relations between subsequent sounds. With the present functional magnetic resonance imaging (fMRI study, we investigated whether sequential comparison of a specific acoustic feature within pairs of tones leads to a change in lateralized processing in the auditory cortex of humans. For this we used the active categorization of the direction (up versus down of slow frequency modulated (FM tones. Several studies suggest that this task is mainly processed in the right auditory cortex. These studies, however, tested only the categorization of the FM direction of each individual tone. In the present study we ask the question whether the right lateralized processing changes when, in addition, the FM direction is compared within pairs of successive tones. For this we use an experimental approach involving contralateral noise presentation in order to explore the contributions made by the left and right auditory cortex in the completion of the auditory task. This method has already been applied to confirm the right-lateralized processing of the FM direction of individual tones. In the present study, the subjects were required to perform, in addition, a sequential comparison of the FM-direction in pairs of tones. The results suggest a division of labor between the two hemispheres such that the FM direction of each individual tone is mainly processed in the right auditory cortex whereas the sequential comparison of this feature between tones in a pair is probably performed in the left auditory cortex.

Advances in the GRADE approach to rate the certainty in estimates from a network meta-analysis.

Science.gov (United States)

Brignardello-Petersen, Romina; Bonner, Ashley; Alexander, Paul E; Siemieniuk, Reed A; Furukawa, Toshi A; Rochwerg, Bram; Hazlewood, Glen S; Alhazzani, Waleed; Mustafa, Reem A; Murad, M Hassan; Puhan, Milo A; Schünemann, Holger J; Guyatt, Gordon H

2018-01-01

This article describes conceptual advances of the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) working group guidance to evaluate the certainty of evidence (confidence in evidence, quality of evidence) from network meta-analysis (NMA). Application of the original GRADE guidance, published in 2014, in a number of NMAs has resulted in advances that strengthen its conceptual basis and make the process more efficient. This guidance will be useful for systematic review authors who aim to assess the certainty of all pairwise comparisons from an NMA and who are familiar with the basic concepts of NMA and the traditional GRADE approach for pairwise meta-analysis. Two principles of the original GRADE NMA guidance are that we need to rate the certainty of the evidence for each pairwise comparison within a network separately and that in doing so we need to consider both the direct and indirect evidence. We present, discuss, and illustrate four conceptual advances: (1) consideration of imprecision is not necessary when rating the direct and indirect estimates to inform the rating of NMA estimates, (2) there is no need to rate the indirect evidence when the certainty of the direct evidence is high and the contribution of the direct evidence to the network estimate is at least as great as that of the indirect evidence, (3) we should not trust a statistical test of global incoherence of the network to assess incoherence at the pairwise comparison level, and (4) in the presence of incoherence between direct and indirect evidence, the certainty of the evidence of each estimate can help decide which estimate to believe. Copyright © 2017 Elsevier Inc. All rights reserved.

Statistical pairwise interaction model of stock market

Science.gov (United States)

Bury, Thomas

2013-03-01

Financial markets are a classical example of complex systems as they are compound by many interacting stocks. As such, we can obtain a surprisingly good description of their structure by making the rough simplification of binary daily returns. Spin glass models have been applied and gave some valuable results but at the price of restrictive assumptions on the market dynamics or they are agent-based models with rules designed in order to recover some empirical behaviors. Here we show that the pairwise model is actually a statistically consistent model with the observed first and second moments of the stocks orientation without making such restrictive assumptions. This is done with an approach only based on empirical data of price returns. Our data analysis of six major indices suggests that the actual interaction structure may be thought as an Ising model on a complex network with interaction strengths scaling as the inverse of the system size. This has potentially important implications since many properties of such a model are already known and some techniques of the spin glass theory can be straightforwardly applied. Typical behaviors, as multiple equilibria or metastable states, different characteristic time scales, spatial patterns, order-disorder, could find an explanation in this picture.

A spreadsheet template compatible with Microsoft Excel and iWork Numbers that returns the simultaneous confidence intervals for all pairwise differences between multiple sample means.

Science.gov (United States)

Brown, Angus M

2010-04-01

The objective of the method described in this paper is to develop a spreadsheet template for the purpose of comparing multiple sample means. An initial analysis of variance (ANOVA) test on the data returns F--the test statistic. If F is larger than the critical F value drawn from the F distribution at the appropriate degrees of freedom, convention dictates rejection of the null hypothesis and allows subsequent multiple comparison testing to determine where the inequalities between the sample means lie. A variety of multiple comparison methods are described that return the 95% confidence intervals for differences between means using an inclusive pairwise comparison of the sample means. 2009 Elsevier Ireland Ltd. All rights reserved.

Classification between normal and tumor tissues based on the pair-wise gene expression ratio

International Nuclear Information System (INIS)

Yap, YeeLeng; Zhang, XueWu; Ling, MT; Wang, XiangHong; Wong, YC; Danchin, Antoine

2004-01-01

Precise classification of cancer types is critically important for early cancer diagnosis and treatment. Numerous efforts have been made to use gene expression profiles to improve precision of tumor classification. However, reliable cancer-related signals are generally lacking. Using recent datasets on colon and prostate cancer, a data transformation procedure from single gene expression to pair-wise gene expression ratio is proposed. Making use of the internal consistency of each expression profiling dataset this transformation improves the signal to noise ratio of the dataset and uncovers new relevant cancer-related signals (features). The efficiency in using the transformed dataset to perform normal/tumor classification was investigated using feature partitioning with informative features (gene annotation) as discriminating axes (single gene expression or pair-wise gene expression ratio). Classification results were compared to the original datasets for up to 10-feature model classifiers. 82 and 262 genes that have high correlation to tissue phenotype were selected from the colon and prostate datasets respectively. Remarkably, data transformation of the highly noisy expression data successfully led to lower the coefficient of variation (CV) for the within-class samples as well as improved the correlation with tissue phenotypes. The transformed dataset exhibited lower CV when compared to that of single gene expression. In the colon cancer set, the minimum CV decreased from 45.3% to 16.5%. In prostate cancer, comparable CV was achieved with and without transformation. This improvement in CV, coupled with the improved correlation between the pair-wise gene expression ratio and tissue phenotypes, yielded higher classification efficiency, especially with the colon dataset – from 87.1% to 93.5%. Over 90% of the top ten discriminating axes in both datasets showed significant improvement after data transformation. The high classification efficiency achieved suggested

A comparison of approaches for simultaneous inference of fixed effects for multiple outcomes using linear mixed models

DEFF Research Database (Denmark)

Jensen, Signe Marie; Ritz, Christian

2018-01-01

Longitudinal studies with multiple outcomes often pose challenges for the statistical analysis. A joint model including all outcomes has the advantage of incorporating the simultaneous behavior but is often difficult to fit due to computational challenges. We consider 2 alternative approaches to ......, pairwise fitting shows a larger loss in efficiency than the marginal models approach. Using an alternative to the joint modelling strategy will lead to some but not necessarily a large loss of efficiency for small sample sizes....

Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r-1 summation

International Nuclear Information System (INIS)

Wolf, D.; Keblinski, P.; Phillpot, S.R.; Eggebrecht, J.

1999-01-01

Based on a recent result showing that the net Coulomb potential in condensed ionic systems is rather short ranged, an exact and physically transparent method permitting the evaluation of the Coulomb potential by direct summation over the r -1 Coulomb pair potential is presented. The key observation is that the problems encountered in determining the Coulomb energy by pairwise, spherically truncated r -1 summation are a direct consequence of the fact that the system summed over is practically never neutral. A simple method is developed that achieves charge neutralization wherever the r -1 pair potential is truncated. This enables the extraction of the Coulomb energy, forces, and stresses from a spherically truncated, usually charged environment in a manner that is independent of the grouping of the pair terms. The close connection of our approach with the Ewald method is demonstrated and exploited, providing an efficient method for the simulation of even highly disordered ionic systems by direct, pairwise r -1 summation with spherical truncation at rather short range, i.e., a method which fully exploits the short-ranged nature of the interactions in ionic systems. The method is validated by simulations of crystals, liquids, and interfacial systems, such as free surfaces and grain boundaries. copyright 1999 American Institute of Physics

A gradient approximation for calculating Debye temperatures from pairwise interatomic potentials

International Nuclear Information System (INIS)

Jackson, D.P.

1975-09-01

A simple gradient approximation is given for calculating the effective Debye temperature of a cubic crystal from central pairwise interatomic potentials. For examples of the Morse potential applied to cubic metals the results are in generally good agreement with experiment. (author)

A general transformation to canonical form for potentials in pairwise interatomic interactions.

Science.gov (United States)

Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

2015-06-14

A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models.

Science.gov (United States)

Rostami, Vahid; Porta Mana, PierGianLuca; Grün, Sonja; Helias, Moritz

2017-10-01

Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations, given only the time-averaged correlations of the neuron activities. This paper provides evidence that the pairwise model, applied to experimental recordings, would produce a bimodal distribution for the population-averaged activity, and for some population sizes the second mode would peak at high activities, that experimentally would be equivalent to 90% of the neuron population active within time-windows of few milliseconds. Several problems are connected with this bimodality: 1. The presence of the high-activity mode is unrealistic in view of observed neuronal activity and on neurobiological grounds. 2. Boltzmann learning becomes non-ergodic, hence the pairwise maximum-entropy distribution cannot be found: in fact, Boltzmann learning would produce an incorrect distribution; similarly, common variants of mean-field approximations also produce an incorrect distribution. 3. The Glauber dynamics associated with the model is unrealistically bistable and cannot be used to generate realistic surrogate data. This bimodality problem is first demonstrated for an experimental dataset from 159 neurons in the motor cortex of macaque monkey. Evidence is then provided that this problem affects typical neural recordings of population sizes of a couple of hundreds or more neurons. The cause of the bimodality problem is identified as the inability of standard maximum-entropy distributions with a uniform reference measure to model neuronal inhibition. To eliminate this problem a modified maximum-entropy model is presented, which reflects a basic effect of inhibition in the form of a simple but non-uniform reference measure. This model does not lead to unrealistic bimodalities, can be found with Boltzmann learning, and has an associated Glauber dynamics which incorporates a minimal asymmetric inhibition.

Extension of Pairwise Broadcast Clock Synchronization for Multicluster Sensor Networks

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Bruce W. Suter

2008-01-01

Full Text Available Time synchronization is crucial for wireless sensor networks (WSNs in performing a number of fundamental operations such as data coordination, power management, security, and localization. The Pairwise Broadcast Synchronization (PBS protocol was recently proposed to minimize the number of timing messages required for global network synchronization, which enables the design of highly energy-efficient WSNs. However, PBS requires all nodes in the network to lie within the communication ranges of two leader nodes, a condition which might not be available in some applications. This paper proposes an extension of PBS to the more general class of sensor networks. Based on the hierarchical structure of the network, an energy-efficient pair selection algorithm is proposed to select the best pairwise synchronization sequence to reduce the overall energy consumption. It is shown that in a multicluster networking environment, PBS requires a far less number of timing messages than other well-known synchronization protocols and incurs no loss in synchronization accuracy. Moreover, the proposed scheme presents significant energy savings for densely deployed WSNs.

A time warping approach to multiple sequence alignment.

Science.gov (United States)

Arribas-Gil, Ana; Matias, Catherine

2017-04-25

We propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise alignments of all the sequences (viewed as paths in a certain space), we construct a median path that represents the MSA we are looking for. We establish a proof of concept that our method could be an interesting ingredient to include into refined MSA techniques. We present a simple synthetic experiment as well as the study of a benchmark dataset, together with comparisons with 2 widely used MSA softwares.

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Lyngsø, Rune B.; Stormo, Gary D.

2005-01-01

detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include...... the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy....... The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability...

Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

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Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

2016-05-01

Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

Dynamics of pairwise entanglement between two Tavis-Cummings atoms

International Nuclear Information System (INIS)

Guo Jinliang; Song Heshan

2008-01-01

We investigate the time evolution of pairwise entanglement between two Tavis-Cummings atoms for various entangled initial states, including pure and mixed states. We find that the phenomenon of entanglement sudden death behaviors is distinct in the evolution of entanglement for different initial states. What deserves mentioning here is that the initial portion of the excited state in the initial state is responsible for the sudden death of entanglement, and the degree of this effect also depends on the initial states

Simultaneous-Fault Diagnosis of Gas Turbine Generator Systems Using a Pairwise-Coupled Probabilistic Classifier

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Zhixin Yang

2013-01-01

Full Text Available A reliable fault diagnostic system for gas turbine generator system (GTGS, which is complicated and inherent with many types of component faults, is essential to avoid the interruption of electricity supply. However, the GTGS diagnosis faces challenges in terms of the existence of simultaneous-fault diagnosis and high cost in acquiring the exponentially increased simultaneous-fault vibration signals for constructing the diagnostic system. This research proposes a new diagnostic framework combining feature extraction, pairwise-coupled probabilistic classifier, and decision threshold optimization. The feature extraction module adopts wavelet packet transform and time-domain statistical features to extract vibration signal features. Kernel principal component analysis is then applied to further reduce the redundant features. The features of single faults in a simultaneous-fault pattern are extracted and then detected using a probabilistic classifier, namely, pairwise-coupled relevance vector machine, which is trained with single-fault patterns only. Therefore, the training dataset of simultaneous-fault patterns is unnecessary. To optimize the decision threshold, this research proposes to use grid search method which can ensure a global solution as compared with traditional computational intelligence techniques. Experimental results show that the proposed framework performs well for both single-fault and simultaneous-fault diagnosis and is superior to the frameworks without feature extraction and pairwise coupling.

GapMis: a tool for pairwise sequence alignment with a single gap.

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Flouri, Tomás; Frousios, Kimon; Iliopoulos, Costas S; Park, Kunsoo; Pissis, Solon P; Tischler, German

2013-08-01

Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.

Locating one pairwise interaction: Three recursive constructions

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Charles J. Colbourn

2016-09-01

Full Text Available In a complex component-based system, choices (levels for components (factors may interact tocause faults in the system behaviour. When faults may be caused by interactions among few factorsat specific levels, covering arrays provide a combinatorial test suite for discovering the presence offaults. While well studied, covering arrays do not enable one to determine the specific levels of factorscausing the faults; locating arrays ensure that the results from test suite execution suffice to determinethe precise levels and factors causing faults, when the number of such causes is small. Constructionsfor locating arrays are at present limited to heuristic computational methods and quite specific directconstructions. In this paper three recursive constructions are developed for locating arrays to locateone pairwise interaction causing a fault.

On the calculation of x-ray scattering signals from pairwise radial distribution functions

DEFF Research Database (Denmark)

Dohn, Asmus Ougaard; Biasin, Elisa; Haldrup, Kristoffer

2015-01-01

We derive a formulation for evaluating (time-resolved) x-ray scattering signals of solvated chemical systems, based on pairwise radial distribution functions, with the aim of this formulation to accompany molecular dynamics simulations. The derivation is described in detail to eliminate any possi...

On the comparison of group performance with categorical data.

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Carmen Herrero

Full Text Available There are many different evaluation problems that involve several groups (societies, firms or institutions whose members can be classified into ordered categories, pursuant to their characteristics or their achievements. This paper addresses these types of problems and provides an evaluation criterion based on the distribution of the agents across categories. The starting point is that of dominance relations in pair-wise comparisons. We say that group i dominates group j when the expected category of a member of i is higher than the expected category of a member of j. We introduce the notion of relative advantage of a group to extend this principle to multi-group comparisons and show that there is a unique evaluation function that ranks all groups consistently in terms of this criterion. This function associates to each evaluation problem the (unique dominant eigenvector of a matrix whose entries describe the dominance relations between groups in pair-wise comparisons. The working of the model is illustrated by means of three different applications.

Document Level Assessment of Document Retrieval Systems in a Pairwise System Evaluation

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Rajagopal, Prabha; Ravana, Sri Devi

2017-01-01

Introduction: The use of averaged topic-level scores can result in the loss of valuable data and can cause misinterpretation of the effectiveness of system performance. This study aims to use the scores of each document to evaluate document retrieval systems in a pairwise system evaluation. Method: The chosen evaluation metrics are document-level…

Evaluation of criteria for sustainability of community-based rural homestay programs via a modified pairwise comparison method

Science.gov (United States)

Ramli, Rohaini; Kasim, Maznah Mat; Ramli, Razamin; Kayat, Kalsom; Razak, Rafidah Abd

2014-12-01

Ministry of Tourism and Culture Malaysia has long introduced homestay programs across the country to enhance the quality of life of people, especially those living in rural areas. This type of program is classified as a community-based tourism (CBT) as it is expected to economically improve livelihood through cultural and community associated activities. It is the aspiration of the ministry to see that the income imbalance between people in the rural and urban areas is reduced, thus would contribute towards creating more developed states of Malaysia. Since 1970s, there are 154 homestay programs registered with the ministry. However, the performance and sustainability of the programs are still not satisfying. There are only a number of homestay programs that perform well and able to sustain. Thus, the aim of this paper is to identify relevant criteria contributing to the sustainability of a homestay program. The criteria are evaluated for their levels of importance via the use of a modified pairwise method and analyzed for other potentials. The findings will help the homestay operators to focus on the necessary criteria and thus, effectively perform as the CBT business initiative.

Analysis of pairwise correlations in multi-parametric PET/MR data for biological tumor characterization and treatment individualization strategies

Energy Technology Data Exchange (ETDEWEB)

Leibfarth, Sara; Moennich, David; Thorwarth, Daniela [University Hospital Tuebingen, Section for Biomedical Physics, Department of Radiation Oncology, Tuebingen (Germany); Simoncic, Urban [University Hospital Tuebingen, Section for Biomedical Physics, Department of Radiation Oncology, Tuebingen (Germany); University of Ljubljana, Faculty of Mathematics and Physics, Ljubljana (Slovenia); Jozef Stefan Institute, Ljubljana (Slovenia); Welz, Stefan; Zips, Daniel [University Hospital Tuebingen, Department of Radiation Oncology, Tuebingen (Germany); Schmidt, Holger; Schwenzer, Nina [University Hospital Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany)

2016-07-15

The aim of this pilot study was to explore simultaneous functional PET/MR for biological characterization of tumors and potential future treatment adaptations. To investigate the extent of complementarity between different PET/MR-based functional datasets, a pairwise correlation analysis was performed. Functional datasets of N=15 head and neck (HN) cancer patients were evaluated. For patients of group A (N=7), combined PET/MR datasets including FDG-PET and ADC maps were available. Patients of group B (N=8) had FMISO-PET, DCE-MRI and ADC maps from combined PET/MRI, an additional dynamic FMISO-PET/CT acquired directly after FMISO tracer injection as well as an FDG-PET/CT acquired a few days earlier. From DCE-MR, parameter maps K{sup trans}, v{sub e} and v{sub p} were obtained with the extended Tofts model. Moreover, parameter maps of mean DCE enhancement, ΔS{sub DCE}, and mean FMISO signal 0-4 min p.i., anti A{sub FMISO}, were derived. Pairwise correlations were quantified using the Spearman correlation coefficient (r) on both a voxel and a regional level within the gross tumor volume. Between some pairs of functional imaging modalities moderate correlations were observed with respect to the median over all patient datasets, whereas distinct correlations were only present on an individual basis. Highest inter-modality median correlations on the voxel level were obtained for FDG/FMISO (r = 0.56), FDG/ anti A{sub FMISO} (r = 0.55), anti A{sub FMISO}/ΔS{sub DCE} (r = 0.46), and FDG/ADC (r = -0.39). Correlations on the regional level showed comparable results. The results of this study suggest that the examined functional datasets provide complementary information. However, only pairwise correlations were examined, and correlations could still exist between combinations of three or more datasets. These results might contribute to the future design of individually adapted treatment approaches based on multiparametric functional imaging.

Pairwise contact energy statistical potentials can help to find probability of point mutations.

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Saravanan, K M; Suvaithenamudhan, S; Parthasarathy, S; Selvaraj, S

2017-01-01

To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/β) 8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than i Mutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Time Series Data-fMRI Study.

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Eslami, Taban; Saeed, Fahad

2018-04-20

Functional magnetic resonance imaging (fMRI) is a non-invasive brain imaging technique, which has been regularly used for studying brain’s functional activities in the past few years. A very well-used measure for capturing functional associations in brain is Pearson’s correlation coefficient. Pearson’s correlation is widely used for constructing functional network and studying dynamic functional connectivity of the brain. These are useful measures for understanding the effects of brain disorders on connectivities among brain regions. The fMRI scanners produce huge number of voxels and using traditional central processing unit (CPU)-based techniques for computing pairwise correlations is very time consuming especially when large number of subjects are being studied. In this paper, we propose a graphics processing unit (GPU)-based algorithm called Fast-GPU-PCC for computing pairwise Pearson’s correlation coefficient. Based on the symmetric property of Pearson’s correlation, this approach returns N ( N − 1 ) / 2 correlation coefficients located at strictly upper triangle part of the correlation matrix. Storing correlations in a one-dimensional array with the order as proposed in this paper is useful for further usage. Our experiments on real and synthetic fMRI data for different number of voxels and varying length of time series show that the proposed approach outperformed state of the art GPU-based techniques as well as the sequential CPU-based versions. We show that Fast-GPU-PCC runs 62 times faster than CPU-based version and about 2 to 3 times faster than two other state of the art GPU-based methods.

Structural profiles of human miRNA families from pairwise clustering

DEFF Research Database (Denmark)

Kaczkowski, Bogumil; Þórarinsson, Elfar; Reiche, Kristin

2009-01-01

secondary structure already predicted, little is known about the patterns of structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment...... of obtained clusters by WAR. As a result, the common secondary structure was successfully determined for four FOLDALIGN clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus structures. Availability: http://genome.ku.dk/resources/mirclust...

High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

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Khaled Benkrid

2012-01-01

Full Text Available This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs, Graphics Processor Units (GPUs, and IBM’s Cell Broadband Engine (Cell BE, in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools, FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs.

Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

OpenAIRE

Liu, Jian-Bin; Wang, Fan; Lang, Xia; Zha, Xi; Sun, Xiao-Ping; Yue, Yao-Jing; Feng, Rui-Lin; Yang, Bo-Hui; Guo, Jian

2013-01-01

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism i...

A Voting TOPSIS Approach for Determining the Priorities of Areas Damaged in Disasters

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Yanjin He

2018-05-01

Full Text Available In this paper, we investigate the priority determination problem for areas that have been damaged during disasters. Relief distribution should be planned while considering the priorities of the damaged areas. To determine the priorities of the damaged areas, we first define four criteria and then propose a voting TOPSIS (technique for order of preference by similarity to ideal solution that utilizes the fuzzy pair-wise comparison, data envelopment analysis, and TOPSIS. Since the voting TOPSIS is based on the voting results of multiple experts, it can be applied to urgent situations quickly, regardless of the consistency of comparison, the number of alternatives, and the number of participating experts. The proposed approach is validated using a real-world case, and this case analysis shows that the voting TOPSIS is viable.

Pairwise correlations via quantum discord and its geometric measure in a four-qubit spin chain

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Abdel-Baset A. Mohamed

2013-04-01

Full Text Available The dynamic of pairwise correlations, including quantum entanglement (QE and discord (QD with geometric measure of quantum discord (GMQD, are shown in the four-qubit Heisenberg XX spin chain. The results show that the effect of the entanglement degree of the initial state on the pairwise correlations is stronger for alternate qubits than it is for nearest-neighbor qubits. This parameter results in sudden death for QE, but it cannot do so for QD and GMQD. With different values for this entanglement parameter of the initial state, QD and GMQD differ and are sensitive for any change in this parameter. It is found that GMQD is more robust than both QD and QE to describe correlations with nonzero values, which offers a valuable resource for quantum computation.

Extraction of tacit knowledge from large ADME data sets via pairwise analysis.

Science.gov (United States)

Keefer, Christopher E; Chang, George; Kauffman, Gregory W

2011-06-15

Pharmaceutical companies routinely collect data across multiple projects for common ADME endpoints. Although at the time of collection the data is intended for use in decision making within a specific project, knowledge can be gained by data mining the entire cross-project data set for patterns of structure-activity relationships (SAR) that may be applied to any project. One such data mining method is pairwise analysis. This method has the advantage of being able to identify small structural changes that lead to significant changes in activity. In this paper, we describe the process for full pairwise analysis of our high-throughput ADME assays routinely used for compound discovery efforts at Pfizer (microsomal clearance, passive membrane permeability, P-gp efflux, and lipophilicity). We also describe multiple strategies for the application of these transforms in a prospective manner during compound design. Finally, a detailed analysis of the activity patterns in pairs of compounds that share the same molecular transformation reveals multiple types of transforms from an SAR perspective. These include bioisosteres, additives, multiplicatives, and a type we call switches as they act to either turn on or turn off an activity. Copyright © 2011 Elsevier Ltd. All rights reserved.

Leaf habit does not determine the investment in both physical and chemical defences and pair-wise correlations between these defensive traits.

Science.gov (United States)

Moreira, X; Pearse, I S

2017-05-01

Plant life-history strategies associated with resource acquisition and economics (e.g. leaf habit) are thought to be fundamental determinants of the traits and mechanisms that drive herbivore pressure, resource allocation to plant defensive traits, and the simultaneous expression (positive correlations) or trade-offs (negative correlations) between these defensive traits. In particular, it is expected that evergreen species - which usually grow slower and support constant herbivore pressure in comparison with deciduous species - will exhibit higher levels of both physical and chemical defences and a higher predisposition to the simultaneous expression of physical and chemical defensive traits. Here, by using a dataset which included 56 oak species (Quercus genus), we investigated whether leaf habit of plant species governs the investment in both physical and chemical defences and pair-wise correlations between these defensive traits. Our results showed that leaf habit does not determine the production of most leaf physical and chemical defences. Although evergreen oak species had higher levels of leaf toughness and specific leaf mass (physical defences) than deciduous oak species, both traits are essentially prerequisites for evergreenness. Similarly, our results also showed that leaf habit does not determine pair-wise correlations between defensive traits because most physical and chemical defensive traits were simultaneously expressed in both evergreen and deciduous oak species. Our findings indicate that leaf habit does not substantially contribute to oak species differences in plant defence investment. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

A pairwise residue contact area-based mean force potential for discrimination of native protein structure

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Pezeshk Hamid

2010-01-01

Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

Nonparametric Analysis of Right Censored Data with Multiple Comparisons

OpenAIRE

Shih, Hwei-Weng

1982-01-01

This report demonstrates the use of a computer program written in FORTRAN for the Burroughs B6800 computer at Utah State University to perform Breslow's (1970) generalization of the Kruskal-Wallis test for right censored data. A pairwise multiple comparison procedure using Bonferroni's inequality is also introduced and demonstrated. Comparisons are also made with a parametric F test and the original Kruskal-Wallis test. Application of these techniques to two data sets indicate that there is l...

DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors

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Kaufmann Michael

2004-09-01

Full Text Available Abstract Background Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Results Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. Conclusions By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.

PairWise Neighbours database: overlaps and spacers among prokaryote genomes

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Garcia-Vallvé Santiago

2009-06-01

Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species

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Deborah Galpert

2015-01-01

Full Text Available Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.

The use of a modified pairwise comparison method in evaluating critical success factors for community-based rural homestay programmes

Science.gov (United States)

Daud, Shahidah Md; Ramli, Razamin; Kasim, Maznah Mat; Kayat, Kalsom; Razak, Rafidah Abd

2014-12-01

Tourism industry has become the highlighted sector which has amazingly increased the national income level. Despite the tourism industry being one of the highest income generating sectors, Homestay Programme as a Community-Based Tourism (CBT) product in Malaysia does not absorbed much of the incoming wealth. Homestay Programme refers to a programme in a community where a tourist stays together with a host family and experiences the everyday way of life of the family in both direct and indirect manner. There are over 100 Homestay Programme currently being registered with the Ministry of Culture and Tourism Malaysia which mostly are located in rural areas, but only a few excel and enjoying the fruit of the booming industry. Hence, this article seeks to identify the critical success factors for a Community-Based Rural Homestay Programme in Malaysia. A modified pairwise method is utilized to further evaluate the identified success factors in a more meaningful way. The findings will help Homestay Programme function as a community development tool that manages tourism resources. Thus, help the community in improving local economy and creating job opportunities.

Assessment of crystalline disorder in cryo-milled samples of indomethacin using atomic pair-wise distribution functions

DEFF Research Database (Denmark)

Bøtker, Johan P; Karmwar, Pranav; Strachan, Clare J

2011-01-01

to analyse the cryo-milled samples. The high similarity between the ¿-indomethacin cryogenic ball milled samples and the crude ¿-indomethacin indicated that milled samples retained residual order of the ¿-form. The PDF analysis encompassed the capability of achieving a correlation with the physical......The aim of this study was to investigate the usefulness of the atomic pair-wise distribution function (PDF) to detect the extension of disorder/amorphousness induced into a crystalline drug using a cryo-milling technique, and to determine the optimal milling times to achieve amorphisation. The PDF...... properties determined from DSC, ss-NMR and stability experiments. Multivariate data analysis (MVDA) was used to visualize the differences in the PDF and XRPD data. The MVDA approach revealed that PDF is more efficient in assessing the introduced degree of disorder in ¿-indomethacin after cryo-milling than...

The structure of pairwise correlation in mouse primary visual cortex reveals functional organization in the absence of an orientation map.

Science.gov (United States)

Denman, Daniel J; Contreras, Diego

2014-10-01

Neural responses to sensory stimuli are not independent. Pairwise correlation can reduce coding efficiency, occur independent of stimulus representation, or serve as an additional channel of information, depending on the timescale of correlation and the method of decoding. Any role for correlation depends on its magnitude and structure. In sensory areas with maps, like the orientation map in primary visual cortex (V1), correlation is strongly related to the underlying functional architecture, but it is unclear whether this correlation structure is an essential feature of the system or arises from the arrangement of cells in the map. We assessed the relationship between functional architecture and pairwise correlation by measuring both synchrony and correlated spike count variability in mouse V1, which lacks an orientation map. We observed significant pairwise synchrony, which was organized by distance and relative orientation preference between cells. We also observed nonzero correlated variability in both the anesthetized (0.16) and awake states (0.18). Our results indicate that the structure of pairwise correlation is maintained in the absence of an underlying anatomical organization and may be an organizing principle of the mammalian visual system preserved by nonrandom connectivity within local networks. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Fuzzy Group Prioritization Method for Deriving Weights and its Software Implementation

Directory of Open Access Journals (Sweden)

Tarifa Almulhim

2013-09-01

Full Text Available Several Multi-Criteria Decision Making (MCDM methods involve pairwise comparisons to obtain the preferences of decision makers (DMs. This paper proposes a fuzzy group prioritization method for deriving group priorities/weights from fuzzy pairwise comparison matrices. The proposed method extends the Fuzzy Preferences Programming Method (FPP by considering the different importance weights of multiple DMs . The elements of the group pairwise comparison matrices are presented as fuzzy numbers rather than exact numerical values, in order to model the uncertainty and imprecision in the DMs’ judgments. Unlike the known fuzzy prioritization techniques, the proposed method is able to derive crisp weights from incomplete and fuzzy set of comparison judgments and does not require additional aggregation procedures. A prototype of a decision tool is developed to assist DMs to implement the proposed method for solving fuzzy group prioritization problems in MATLAB. Detailed numerical examples are used to illustrate the proposed approach.

Assessing compositional variability through graphical analysis and Bayesian statistical approaches: case studies on transgenic crops.

Science.gov (United States)

Harrigan, George G; Harrison, Jay M

2012-01-01

New transgenic (GM) crops are subjected to extensive safety assessments that include compositional comparisons with conventional counterparts as a cornerstone of the process. The influence of germplasm, location, environment, and agronomic treatments on compositional variability is, however, often obscured in these pair-wise comparisons. Furthermore, classical statistical significance testing can often provide an incomplete and over-simplified summary of highly responsive variables such as crop composition. In order to more clearly describe the influence of the numerous sources of compositional variation we present an introduction to two alternative but complementary approaches to data analysis and interpretation. These include i) exploratory data analysis (EDA) with its emphasis on visualization and graphics-based approaches and ii) Bayesian statistical methodology that provides easily interpretable and meaningful evaluations of data in terms of probability distributions. The EDA case-studies include analyses of herbicide-tolerant GM soybean and insect-protected GM maize and soybean. Bayesian approaches are presented in an analysis of herbicide-tolerant GM soybean. Advantages of these approaches over classical frequentist significance testing include the more direct interpretation of results in terms of probabilities pertaining to quantities of interest and no confusion over the application of corrections for multiple comparisons. It is concluded that a standardized framework for these methodologies could provide specific advantages through enhanced clarity of presentation and interpretation in comparative assessments of crop composition.

Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs

OpenAIRE

Lin, Chun-Yuan; Wang, Chung-Hung; Hung, Che-Lun; Lin, Yu-Shiang

2015-01-01

Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is O(n 2), where n is the maximal length of compounds. In general, the length of compounds is tens to hundreds, and the computation time is small. However, more and more compounds have been synthesized and extracted now, even more than tens of millions. Therefore,...

RNA structure alignment by a unit-vector approach.

Science.gov (United States)

Capriotti, Emidio; Marti-Renom, Marc A

2008-08-15

The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

Estimating Function Approaches for Spatial Point Processes

Science.gov (United States)

Deng, Chong

Spatial point pattern data consist of locations of events that are often of interest in biological and ecological studies. Such data are commonly viewed as a realization from a stochastic process called spatial point process. To fit a parametric spatial point process model to such data, likelihood-based methods have been widely studied. However, while maximum likelihood estimation is often too computationally intensive for Cox and cluster processes, pairwise likelihood methods such as composite likelihood, Palm likelihood usually suffer from the loss of information due to the ignorance of correlation among pairs. For many types of correlated data other than spatial point processes, when likelihood-based approaches are not desirable, estimating functions have been widely used for model fitting. In this dissertation, we explore the estimating function approaches for fitting spatial point process models. These approaches, which are based on the asymptotic optimal estimating function theories, can be used to incorporate the correlation among data and yield more efficient estimators. We conducted a series of studies to demonstrate that these estmating function approaches are good alternatives to balance the trade-off between computation complexity and estimating efficiency. First, we propose a new estimating procedure that improves the efficiency of pairwise composite likelihood method in estimating clustering parameters. Our approach combines estimating functions derived from pairwise composite likeli-hood estimation and estimating functions that account for correlations among the pairwise contributions. Our method can be used to fit a variety of parametric spatial point process models and can yield more efficient estimators for the clustering parameters than pairwise composite likelihood estimation. We demonstrate its efficacy through a simulation study and an application to the longleaf pine data. Second, we further explore the quasi-likelihood approach on fitting

Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

Directory of Open Access Journals (Sweden)

Jian-Bin Liu

2013-03-01

Full Text Available This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO and the International Society for Animal Genetics (ISAG. In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST was 0.1184; the genetic differentiation coefficient (GST was 0.0940; and the average gene flow (Nm was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001, suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

Improved scFv Anti-HIV-1 p17 Binding Affinity Guided from the Theoretical Calculation of Pairwise Decomposition Energies and Computational Alanine Scanning

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Panthip Tue-ngeun

2013-01-01

Full Text Available Computational approaches have been used to evaluate and define important residues for protein-protein interactions, especially antigen-antibody complexes. In our previous study, pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants has indicated the key specific residues in the complementary determining regions (CDRs of scFv anti-p17. In this present investigation in order to determine whether a specific side chain group of residue in CDRs plays an important role in bioactivity, computational alanine scanning has been applied. Molecular dynamics simulations were done with several complexes of original scFv anti-p17 and scFv anti-p17mutants with HIV-1 p17 epitope variants with a production run up to 10 ns. With the combination of pairwise decomposition residue interaction and alanine scanning calculations, the point mutation has been initially selected at the position MET100 to improve the residue binding affinity. The calculated docking interaction energy between a single mutation from methionine to either arginine or glycine has shown the improved binding affinity, contributed from the electrostatic interaction with the negative favorably interaction energy, compared to the wild type. Theoretical calculations agreed well with the results from the peptide ELISA results.

Pairwise registration of TLS point clouds using covariance descriptors and a non-cooperative game

Science.gov (United States)

Zai, Dawei; Li, Jonathan; Guo, Yulan; Cheng, Ming; Huang, Pengdi; Cao, Xiaofei; Wang, Cheng

2017-12-01

It is challenging to automatically register TLS point clouds with noise, outliers and varying overlap. In this paper, we propose a new method for pairwise registration of TLS point clouds. We first generate covariance matrix descriptors with an adaptive neighborhood size from point clouds to find candidate correspondences, we then construct a non-cooperative game to isolate mutual compatible correspondences, which are considered as true positives. The method was tested on three models acquired by two different TLS systems. Experimental results demonstrate that our proposed adaptive covariance (ACOV) descriptor is invariant to rigid transformation and robust to noise and varying resolutions. The average registration errors achieved on three models are 0.46 cm, 0.32 cm and 1.73 cm, respectively. The computational times cost on these models are about 288 s, 184 s and 903 s, respectively. Besides, our registration framework using ACOV descriptors and a game theoretic method is superior to the state-of-the-art methods in terms of both registration error and computational time. The experiment on a large outdoor scene further demonstrates the feasibility and effectiveness of our proposed pairwise registration framework.

Approach to Multi-Criteria Group Decision-Making Problems Based on the Best-Worst-Method and ELECTRE Method

Directory of Open Access Journals (Sweden)

Xinshang You

2016-09-01

Full Text Available This paper proposes a novel approach to cope with the multi-criteria group decision-making problems. We give the pairwise comparisons based on the best-worst-method (BWM, which can decrease comparison times. Additionally, our comparison results are determined with the positive and negative aspects. In order to deal with the decision matrices effectively, we consider the elimination and choice translation reality (ELECTRE III method under the intuitionistic multiplicative preference relations environment. The ELECTRE III method is designed for a double-automatic system. Under a certain limitation, without bothering the decision-makers to reevaluate the alternatives, this system can adjust some special elements that have the most influence on the group’s satisfaction degree. Moreover, the proposed method is suitable for both the intuitionistic multiplicative preference relation and the interval valued fuzzy preference relations through the transformation formula. An illustrative example is followed to demonstrate the rationality and availability of the novel method.

Convergent cross-mapping and pairwise asymmetric inference.

Science.gov (United States)

McCracken, James M; Weigel, Robert S

2014-12-01

Convergent cross-mapping (CCM) is a technique for computing specific kinds of correlations between sets of times series. It was introduced by Sugihara et al. [Science 338, 496 (2012).] and is reported to be "a necessary condition for causation" capable of distinguishing causality from standard correlation. We show that the relationships between CCM correlations proposed by Sugihara et al. do not, in general, agree with intuitive concepts of "driving" and as such should not be considered indicative of causality. It is shown that the fact that the CCM algorithm implies causality is a function of system parameters for simple linear and nonlinear systems. For example, in a circuit containing a single resistor and inductor, both voltage and current can be identified as the driver depending on the frequency of the source voltage. It is shown that the CCM algorithm, however, can be modified to identify relationships between pairs of time series that are consistent with intuition for the considered example systems for which CCM causality analysis provided nonintuitive driver identifications. This modification of the CCM algorithm is introduced as "pairwise asymmetric inference" (PAI) and examples of its use are presented.

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

Energy Technology Data Exchange (ETDEWEB)

Bernardis, F. De; Vavagiakis, E.M.; Niemack, M.D.; Gallardo, P.A. [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Aiola, S. [Department of Physics and Astronomy, University of Pittsburgh, and Pittsburgh Particle Physics, Astrophysics, and Cosmology Center, 3941 O' Hara Street, Pittsburgh, PA 15260 (United States); Battaglia, N. [Department of Astrophysical Sciences, Peyton Hall, Princeton University, Princeton, NJ 08544 (United States); Beall, J.; Becker, D.T.; Cho, H.; Fox, A. [National Institute of Standards and Technology, Boulder, CO 80305 (United States); Bond, J.R. [CITA, University of Toronto, 60 St. George St., Toronto, ON M5S 3H8 (Canada); Calabrese, E.; Dunkley, J. [Sub-Department of Astrophysics, University of Oxford, Keble Road, Oxford, OX1 3RH (United Kingdom); Coughlin, K.; Datta, R. [Department of Physics, University of Michigan Ann Arbor, MI 48109 (United States); Devlin, M. [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Dunner, R. [Instituto de Astrofísica and Centro de Astro-Ingeniería, Facultad de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, 7820436 Macul, Santiago (Chile); Ferraro, S. [Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720 (United States); Halpern, M. [University of British Columbia, Department of Physics and Astronomy, 6224 Agricultural Road, Vancouver BC V6T 1Z1 (Canada); Hand, N., E-mail: fdeberna@gmail.com [Astronomy Department, University of California, Berkeley, CA 94720 (United States); and others

2017-03-01

We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.

A convolutional approach to reflection symmetry

DEFF Research Database (Denmark)

Cicconet, Marcelo; Birodkar, Vighnesh; Lund, Mads

2017-01-01

We present a convolutional approach to reflection symmetry detection in 2D. Our model, built on the products of complex-valued wavelet convolutions, simplifies previous edge-based pairwise methods. Being parameter-centered, as opposed to feature-centered, it has certain computational advantages w...

Robot Trajectories Comparison: A Statistical Approach

Directory of Open Access Journals (Sweden)

A. Ansuategui

2014-01-01

Full Text Available The task of planning a collision-free trajectory from a start to a goal position is fundamental for an autonomous mobile robot. Although path planning has been extensively investigated since the beginning of robotics, there is no agreement on how to measure the performance of a motion algorithm. This paper presents a new approach to perform robot trajectories comparison that could be applied to any kind of trajectories and in both simulated and real environments. Given an initial set of features, it automatically selects the most significant ones and performs a statistical comparison using them. Additionally, a graphical data visualization named polygraph which helps to better understand the obtained results is provided. The proposed method has been applied, as an example, to compare two different motion planners, FM2 and WaveFront, using different environments, robots, and local planners.

Robot Trajectories Comparison: A Statistical Approach

Science.gov (United States)

Ansuategui, A.; Arruti, A.; Susperregi, L.; Yurramendi, Y.; Jauregi, E.; Lazkano, E.; Sierra, B.

2014-01-01

The task of planning a collision-free trajectory from a start to a goal position is fundamental for an autonomous mobile robot. Although path planning has been extensively investigated since the beginning of robotics, there is no agreement on how to measure the performance of a motion algorithm. This paper presents a new approach to perform robot trajectories comparison that could be applied to any kind of trajectories and in both simulated and real environments. Given an initial set of features, it automatically selects the most significant ones and performs a statistical comparison using them. Additionally, a graphical data visualization named polygraph which helps to better understand the obtained results is provided. The proposed method has been applied, as an example, to compare two different motion planners, FM2 and WaveFront, using different environments, robots, and local planners. PMID:25525618

Benefits of Using Pairwise Trajectory Management in the Central East Pacific

Science.gov (United States)

Chartrand, Ryan; Ballard, Kathryn

2017-01-01

Pairwise Trajectory Management (PTM) is a concept that utilizes airborne and ground-based capabilities to enable airborne spacing operations in procedural airspace. This concept makes use of updated ground automation, Automatic Dependent Surveillance-Broadcast (ADS-B) and on board avionics generating real time guidance. An experiment was conducted to examine the potential benefits of implementing PTM in the Central East Pacific oceanic region. An explanation of the experiment and some of the results are included in this paper. The PTM concept allowed for an increase in the average time an aircraft is able to spend at its desired flight level and a reduction in fuel burn.

BUSINESS MODEL IN ELECTRICITY INDUSTRY USING BUSINESS MODEL CANVAS APPROACH; THE CASE OF PT. XYZ

Directory of Open Access Journals (Sweden)

Achmad Arief Wicaksono

2017-01-01

Full Text Available The magnitude of opportunities and project values of electricity system in Indonesia encourages PT. XYZ to develop its business in electrical sector which requires business development strategies. This study aims to identify company's business model using Business Model Canvas approach, formulate business development strategy alternatives, and determine the prioritized business development strategy which is appropriate to the manufacturing business model for PT. XYZ. This study utilized a descriptive approach and the nine elements of the Business Model Canvas. Alternative formulation and priority determination of the strategies were obtained by using Strengths, Weaknesses, Opportunities, Threats (SWOT analysis and pairwise comparison. The results of this study are the improvement of Business Model Canvas on the elements of key resources, key activities, key partners and customer segment. In terms of SWOT analysis on the nine elements of the Business Model Canvas for the first business development, the results show an expansion on the power plant construction project as the main contractor, an increase in sales in its core business in supporting equipment industry of oil and gas,  a development in the second business i.e. an investment in the electricity sector as an independent renewable emery-based power producer. On its first business development, PT. XYZ selected three Business Model Canvas elements which become the priorities of the company i.e. key resources weighing 0.252, key activities weighing 0.240, and key partners weighing 0.231. On its second business development, the company selected three elements to become their the priorities i.e. key partners weighing 0.225, customer segments weighing 0.217, and key resources weighing 0.215.Keywords: business model canvas, SWOT, pairwise comparison, business model

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

International Nuclear Information System (INIS)

Hardy, David J.; Schulten, Klaus; Wolff, Matthew A.; Skeel, Robert D.; Xia, Jianlin

2016-01-01

The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short.

Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip.

Science.gov (United States)

Zamora, Jane Louie Fresco; Kashihara, Shigeru; Yamaguchi, Suguru

2015-01-01

Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values.

A composite likelihood approach for spatially correlated survival data

Science.gov (United States)

Paik, Jane; Ying, Zhiliang

2013-01-01

The aim of this paper is to provide a composite likelihood approach to handle spatially correlated survival data using pairwise joint distributions. With e-commerce data, a recent question of interest in marketing research has been to describe spatially clustered purchasing behavior and to assess whether geographic distance is the appropriate metric to describe purchasing dependence. We present a model for the dependence structure of time-to-event data subject to spatial dependence to characterize purchasing behavior from the motivating example from e-commerce data. We assume the Farlie-Gumbel-Morgenstern (FGM) distribution and then model the dependence parameter as a function of geographic and demographic pairwise distances. For estimation of the dependence parameters, we present pairwise composite likelihood equations. We prove that the resulting estimators exhibit key properties of consistency and asymptotic normality under certain regularity conditions in the increasing-domain framework of spatial asymptotic theory. PMID:24223450

A composite likelihood approach for spatially correlated survival data.

Science.gov (United States)

Paik, Jane; Ying, Zhiliang

2013-01-01

The aim of this paper is to provide a composite likelihood approach to handle spatially correlated survival data using pairwise joint distributions. With e-commerce data, a recent question of interest in marketing research has been to describe spatially clustered purchasing behavior and to assess whether geographic distance is the appropriate metric to describe purchasing dependence. We present a model for the dependence structure of time-to-event data subject to spatial dependence to characterize purchasing behavior from the motivating example from e-commerce data. We assume the Farlie-Gumbel-Morgenstern (FGM) distribution and then model the dependence parameter as a function of geographic and demographic pairwise distances. For estimation of the dependence parameters, we present pairwise composite likelihood equations. We prove that the resulting estimators exhibit key properties of consistency and asymptotic normality under certain regularity conditions in the increasing-domain framework of spatial asymptotic theory.

Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip

Directory of Open Access Journals (Sweden)

Jane Louie Fresco Zamora

2015-01-01

Full Text Available Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values.

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Lyngsø, Rune B.; Gorodkin, Jan

2005-01-01

FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural RNA...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

A Comparison of MOOC Development and Delivery Approaches

Science.gov (United States)

Smith, Neil; Caldwell, Helen; Richards, Mike; Bandara, Arosha

2017-01-01

Purpose: The purpose of this paper is to present a comparison of two ways of developing and delivering massive open online courses (MOOCs). One was developed by The Open University in collaboration with FutureLearn; the other was developed independently by a small team at the Northampton University. Design/methodology/approach: The different…

Comparison of Fuzzy AHP and Fuzzy TOPSIS for Road Pavement Maintenance Prioritization: Methodological Exposition and Case Study

Directory of Open Access Journals (Sweden)

Yashon O. Ouma

2015-01-01

Full Text Available For road pavement maintenance and repairs prioritization, a multiattribute approach that compares fuzzy Analytical Hierarchy Process (AHP and fuzzy Technique for Order Preference by Ideal Situation (TOPSIS is evaluated. The pavement distress data was collected through empirical condition surveys and rating by pavement experts. In comparison to the crisp AHP, the fuzzy AHP and fuzzy TOPSIS pairwise comparison techniques are considered to be more suitable for the subjective analysis of the pavement conditions for automated maintenance prioritization. From the case study results, four pavement maintenance objectives were determined as road safety, pavement surface preservation, road operational status and standards, and road aesthetics, with corresponding depreciating significance weights of W=0.37,0.31,0.22,0.10T. The top three maintenance functions were identified as Thin Hot Mix Asphalt (HMA overlays, resurfacing and slurry seals, which were a result of pavement cracking, potholes, raveling, and patching, while the bottom three were cape seal, micro surfacing, and fog seal. The two methods gave nearly the same prioritization ranking. In general, the fuzzy AHP approach tended to overestimate the maintenance prioritization ranking as compared to the fuzzy TOPSIS.

Comparison of attitude determination approaches using multiple Global Positioning System (GPS antennas

Directory of Open Access Journals (Sweden)

Wang Bing

2013-02-01

Full Text Available GPS-based attitude system is an important research field, since it is a valuable technique for the attitude determination of platforms. There exist two classes approaches for attitude determination using the GPS. The one determines attitude via baseline estimates in two frames, the other one solves for attitude by incorporating the attitude parameters directly into the GPS measurements. However, comparisons between these two classes approaches have been unexplored. First of all, two algorithms are introduced in detail which on behalf of these two kinds of approaches. Then we present numerical simulations demonstrating the performance of our algorithms and provide a comparison evaluating.

Effect of pairwise additivity on finite-temperature behavior of classical ideal gas

Science.gov (United States)

Shekaari, Ashkan; Jafari, Mahmoud

2018-05-01

Finite-temperature molecular dynamics simulations have been applied to inquire into the effect of pairwise additivity on the behavior of classical ideal gas within the temperature range of T = 250-4000 K via applying a variety of pair potentials and then examining the temperature dependence of a number of thermodynamical properties. Examining the compressibility factor reveals the most deviation from ideal-gas behavior for the Lennard-Jones system mainly due to the presence of both the attractive and repulsive terms. The systems with either attractive or repulsive intermolecular potentials are found to present no resemblance to real gases, but the most similarity to the ideal one as temperature rises.

Selection of a suitable method for the preparation of polymeric nanoparticles: multi-criteria decision making approach.

Science.gov (United States)

Krishnamoorthy, Kannan; Mahalingam, Manikandan

2015-03-01

The present study is aimed to select the suitable method for preparation of camptothecin loaded polymeric nanoparticles by utilizing the multi-criteria decision making method. Novel approaches of drug delivery by formulation using nanotechnology are revolutionizing the future of medicine. Recent years have witnessed unprecedented growth of research and application in the area of nanotechnology. Nanoparticles have become an important area of research in the field of drug delivery because they have the ability to deliver a wide range of drug to varying areas of body. Despite of extensive research and development, polymeric nanoparticles are frequently used to improve the therapeutic effect of drugs. A number of techniques are available for the preparation of polymeric nanoparticles. The Analytical Hierarchy Process (AHP) is a method for decision making, which are derived from individual judgements for qualitative factors, using the pair-wise comparison matrix. In AHP, a decision hierarchy is constructed with a goal, criteria and alternatives. The model uses three main criteria 1) Instrument, 2) Process and Output and 3) Cost. In addition, there are eight sub-criteria's as well as eight alternatives. Pair-wise comparison matrixes are used to obtain the overall priority weight and ranking for the selection of suitable method. Nanoprecipitation technique is the most suitable method for the preparation of camptothecin loaded polymeric nanoparticles with the highest overall priority weight of 0.297 CONCLUSION: In particular, the result indicates that the priority weights obtained from AHP could be defined as a multiple output for finding out the most suitable method for preparation of camptothecin loaded polymeric nanoparticles.

Multilevel summation methods for efficient evaluation of long-range pairwise interactions in atomistic and coarse-grained molecular simulation.

Energy Technology Data Exchange (ETDEWEB)

Bond, Stephen D.

2014-01-01

The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods whos cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.

The Dynamics of Multiple Pair-Wise Collisions in a Chain for Designing Optimal Shock Amplifiers

Directory of Open Access Journals (Sweden)

Bryan Rodgers

2009-01-01

Full Text Available The major focus of this work is to examine the dynamics of velocity amplification through pair-wise collisions between multiple masses in a chain, in order to develop useful machines. For instance low-cost machines based on this principle could be used for detailed, very-high acceleration shock-testing of MEMS devices. A theoretical basis for determining the number and mass of intermediate stages in such a velocity amplifier, based on simple rigid body mechanics, is proposed. The influence of mass ratios and the coefficient of restitution on the optimisation of the system is identified and investigated. In particular, two cases are examined: in the first, the velocity of the final mass in the chain (that would have the object under test mounted on it is maximised by defining the ratio of adjacent masses according to a power law relationship; in the second, the energy transfer efficiency of the system is maximised by choosing the mass ratios such that all masses except the final mass come to rest following impact. Comparisons are drawn between both cases and the results are used in proposing design guidelines for optimal shock amplifiers. It is shown that for most practical systems, a shock amplifier with mass ratios based on a power law relationship is optimal and can easily yield velocity amplifications of a factor 5–8 times. A prototype shock testing machine that was made using above principles is briefly introduced.

Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon.

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Hanni, Matti; Lantto, Perttu; Vaara, Juha

2009-04-14

Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.

Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time

DEFF Research Database (Denmark)

Tsirogiannis, Constantinos; Sandel, Brody Steven

2014-01-01

The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular measures for computing the phylogenetic distance between a given group of species. More specifically, for a phylogenetic tree and for a set of species R represented by a subset of the leaf nodes of , the MPD of R is equal...... to the average cost of all possible simple paths in that connect pairs of nodes in R. Among other phylogenetic measures, the MPD is used as a tool for deciding if the species of a given group R are closely related. To do this, it is important to compute not only the value of the MPD for this group but also...

PTM Along Track Algorithm to Maintain Spacing During Same Direction Pair-Wise Trajectory Management Operations

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Carreno, Victor A.

2015-01-01

Pair-wise Trajectory Management (PTM) is a cockpit based delegated responsibility separation standard. When an air traffic service provider gives a PTM clearance to an aircraft and the flight crew accepts the clearance, the flight crew will maintain spacing and separation from a designated aircraft. A PTM along track algorithm will receive state information from the designated aircraft and from the own ship to produce speed guidance for the flight crew to maintain spacing and separation

Comparison of sputum collection methods for tuberculosis diagnosis: a systematic review and pairwise and network meta-analysis.

Science.gov (United States)

Datta, Sumona; Shah, Lena; Gilman, Robert H; Evans, Carlton A

2017-08-01

The performance of laboratory tests to diagnose pulmonary tuberculosis is dependent on the quality of the sputum sample tested. The relative merits of sputum collection methods to improve tuberculosis diagnosis are poorly characterised. We therefore aimed to investigate the effects of sputum collection methods on tuberculosis diagnosis. We did a systematic review and meta-analysis to investigate whether non-invasive sputum collection methods in people aged at least 12 years improve the diagnostic performance of laboratory testing for pulmonary tuberculosis. We searched PubMed, Google Scholar, ProQuest, Web of Science, CINAHL, and Embase up to April 14, 2017, to identify relevant experimental, case-control, or cohort studies. We analysed data by pairwise meta-analyses with a random-effects model and by network meta-analysis. All diagnostic performance data were calculated at the sputum-sample level, except where authors only reported data at the individual patient-level. Heterogeneity was assessed, with potential causes identified by logistic meta-regression. We identified 23 eligible studies published between 1959 and 2017, involving 8967 participants who provided 19 252 sputum samples. Brief, on-demand spot sputum collection was the main reference standard. Pooled sputum collection increased tuberculosis diagnosis by microscopy (odds ratio [OR] 1·6, 95% CI 1·3-1·9, pmeta-analysis confirmed these findings, and revealed that both pooled and instructed spot sputum collections were similarly effective techniques for increasing the diagnostic performance of microscopy. Tuberculosis diagnoses were substantially increased by either pooled collection or by providing instruction on how to produce a sputum sample taken at any time of the day. Both interventions had a similar effect to that reported for the introduction of new, expensive laboratory tests, and therefore warrant further exploration in the drive to end the global tuberculosis epidemic. Wellcome Trust

Comparison of Different Approaches for Measuring Tibial Cartilage Thickness

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Maier Jennifer

2017-07-01

Full Text Available Osteoarthritis is a degenerative disease affecting bones and cartilage especially in the human knee. In this context, cartilage thickness is an indicator for knee cartilage health. Thickness measurements are performed on medical images acquired in-vivo. Currently, there is no standard method agreed upon that defines a distance measure in articular cartilage. In this work, we present a comparison of different methods commonly used in literature. These methods are based on nearest neighbors, surface normal vectors, local thickness and potential field lines. All approaches were applied to manual segmentations of tibia and lateral and medial tibial cartilage performed by experienced raters. The underlying data were contrast agent-enhanced cone-beam C-arm CT reconstructions of one healthy subject’s knee. The subject was scanned three times, once in supine position and two times in a standing weight-bearing position. A comparison of the resulting thickness maps shows similar distributions and high correlation coefficients between the approaches above 0.90. The nearest neighbor method results on average in the lowest cartilage thickness values, while the local thickness approach assigns the highest values. We showed that the different methods agree in their thickness distribution. The results will be used for a future evaluation of cartilage change under weight-bearing conditions.

Identifying the Academic Rising Stars via Pairwise Citation Increment Ranking

KAUST Repository

Zhang, Chuxu

2017-08-02

Predicting the fast-rising young researchers (the Academic Rising Stars) in the future provides useful guidance to the research community, e.g., offering competitive candidates to university for young faculty hiring as they are expected to have success academic careers. In this work, given a set of young researchers who have published the first first-author paper recently, we solve the problem of how to effectively predict the top k% researchers who achieve the highest citation increment in Δt years. We explore a series of factors that can drive an author to be fast-rising and design a novel pairwise citation increment ranking (PCIR) method that leverages those factors to predict the academic rising stars. Experimental results on the large ArnetMiner dataset with over 1.7 million authors demonstrate the effectiveness of PCIR. Specifically, it outperforms all given benchmark methods, with over 8% average improvement. Further analysis demonstrates that temporal features are the best indicators for rising stars prediction, while venue features are less relevant.

Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS

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Kim Nora

2012-07-01

analysis of pairwise genetic associations in two GWAS of sporadic ALS revealed a set of genes involved in cellular component organization and actin cytoskeleton, more specifically, that were not reported by prior GWAS. However, prior biological studies have implicated actin cytoskeleton in ALS and other motor neuron diseases. This study supports the idea that pathway-level analysis of GWAS data may discover important associations not revealed using conventional one-SNP-at-a-time approaches.

Reduction in the Number of Comparisons Required to Create Matrix of Expert Judgment in the Comet Method

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Sałabun Wojciech

2014-09-01

Full Text Available Multi-criteria decision-making (MCDM methods are associated with the ranking of alternatives based on expert judgments made using a number of criteria. In the MCDM field, the distance-based approach is one popular method for receiving a final ranking. One of the newest MCDM method, which uses the distance-based approach, is the Characteristic Objects Method (COMET. In this method, the preferences of each alternative are obtained on the basis of the distance from the nearest characteristic ob jects and their values. For this purpose, the domain and fuzzy numbers set for all the considered criteria are determined. The characteristic objects are obtained as the combination of the crisp values of all the fuzzy numbers. The preference values of all the characteristic ob ject are determined based on the tournament method and the principle of indifference. Finally, the fuzzy model is constructed and is used to calculate preference values of the alternatives. In this way, a multi-criteria model is created and it is free of rank reversal phenomenon. In this approach, the matrix of expert judgment is necessary to create. For this purpose, an expert has to compare all the characteristic ob jects with each other. The number of necessary comparisons depends squarely to the number of ob jects. This study proposes the improvement of the COMET method by using the transitivity of pairwise comparisons. Three numerical examples are used to illustrate the efficiency of the proposed improvement with respect to results from the original approach. The proposed improvement reduces significantly the number of necessary comparisons to create the matrix of expert judgment.

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.

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Richard R Stein

2015-07-01

Full Text Available Maximum entropy-based inference methods have been successfully used to infer direct interactions from biological datasets such as gene expression data or sequence ensembles. Here, we review undirected pairwise maximum-entropy probability models in two categories of data types, those with continuous and categorical random variables. As a concrete example, we present recently developed inference methods from the field of protein contact prediction and show that a basic set of assumptions leads to similar solution strategies for inferring the model parameters in both variable types. These parameters reflect interactive couplings between observables, which can be used to predict global properties of the biological system. Such methods are applicable to the important problems of protein 3-D structure prediction and association of gene-gene networks, and they enable potential applications to the analysis of gene alteration patterns and to protein design.

Pythagorean fuzzy analytic hierarchy process to multi-criteria decision making

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Mohd, Wan Rosanisah Wan; Abdullah, Lazim

2017-11-01

A numerous approaches have been proposed in the literature to determine the criteria of weight. The weight of criteria is very significant in the process of decision making. One of the outstanding approaches that used to determine weight of criteria is analytic hierarchy process (AHP). This method involves decision makers (DMs) to evaluate the decision to form the pair-wise comparison between criteria and alternatives. In classical AHP, the linguistic variable of pairwise comparison is presented in terms of crisp value. However, this method is not appropriate to present the real situation of the problems because it involved the uncertainty in linguistic judgment. For this reason, AHP has been extended by incorporating the Pythagorean fuzzy sets. In addition, no one has found in the literature proposed how to determine the weight of criteria using AHP under Pythagorean fuzzy sets. In order to solve the MCDM problem, the Pythagorean fuzzy analytic hierarchy process is proposed to determine the criteria weight of the evaluation criteria. Using the linguistic variables, pairwise comparison for evaluation criteria are made to the weights of criteria using Pythagorean fuzzy numbers (PFNs). The proposed method is implemented in the evaluation problem in order to demonstrate its applicability. This study shows that the proposed method provides us with a useful way and a new direction in solving MCDM problems with Pythagorean fuzzy context.

Towards binary robust fast features using the comparison of pixel blocks

International Nuclear Information System (INIS)

Oszust, Mariusz

2016-01-01

Binary descriptors have become popular in many vision-based applications, as a fast and efficient replacement of floating point, heavy counterparts. They achieve a short computation time and low memory footprint due to many simplifications. Consequently, their robustness against a variety of image transformations is lowered, since they rely on pairwise pixel intensity comparisons. This observation has led to the emergence of techniques performing tests on intensities of predefined pixel regions. These approaches, despite a visible improvement in the quality of the obtained results, suffer from a long computation time, and their patch partitioning strategies produce long binary strings requiring the use of salient bit detection techniques. In this paper, a novel binary descriptor is proposed to address these shortcomings. The approach selects image patches around a keypoint, divides them into a small number of pixel blocks and performs binary tests on gradients which are determined for the blocks. The size of each patch depends on the keypoint’s scale. The robustness and distinctiveness of the descriptor are evaluated according to five demanding image benchmarks. The experimental results show that the proposed approach is faster to compute, produces a short binary string and offers a better performance than state-of-the-art binary and floating point descriptors. (paper)

An approach to solve group-decision-making problems with ordinal interval numbers.

Science.gov (United States)

Fan, Zhi-Ping; Liu, Yang

2010-10-01

The ordinal interval number is a form of uncertain preference information in group decision making (GDM), while it is seldom discussed in the existing research. This paper investigates how the ranking order of alternatives is determined based on preference information of ordinal interval numbers in GDM problems. When ranking a large quantity of ordinal interval numbers, the efficiency and accuracy of the ranking process are critical. A new approach is proposed to rank alternatives using ordinal interval numbers when every ranking ordinal in an ordinal interval number is thought to be uniformly and independently distributed in its interval. First, we give the definition of possibility degree on comparing two ordinal interval numbers and the related theory analysis. Then, to rank alternatives, by comparing multiple ordinal interval numbers, a collective expectation possibility degree matrix on pairwise comparisons of alternatives is built, and an optimization model based on this matrix is constructed. Furthermore, an algorithm is also presented to rank alternatives by solving the model. Finally, two examples are used to illustrate the use of the proposed approach.

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

Energy Technology Data Exchange (ETDEWEB)

Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es [Instituto de Física Fundamental (CSIC), Serrano 123, E-28006 Madrid (Spain); Fernández-Perea, Ricardo [Instituto de Estructura de la Materia (CSIC), Serrano 123, E-28006 Madrid (Spain); Madzharova, Fani; Voloshina, Elena, E-mail: elena.voloshina@hu-berlin.de [Humboldt-Universität zu Berlin, Institut für Chemie, Unter den Linden 6, 10099 Berlin (Germany)

2016-06-28

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He–Mg pair potentials is also presented, as an improvement of the approximation using isolated He–Mg pairs.

Enthalpic discrimination of homochiral pairwise interactions: Enantiomers of proline and hydroxyproline in (dimethyl formamide (DMF) + H2O) and (dimethylsulfoxide (DMSO) + H2O) mixtures at 298.15 K

International Nuclear Information System (INIS)

Hu, Xin-Gen; Liu, Jia-Min; Guo, Zheng; Liang, Hong-Yu; Jia, Zhao-Peng; Cheng, Wei-Na; Guo, Ai-Di; Zhang, He-Juan

2013-01-01

Highlights: • The h xx values of each α-amino acids decrease gradually with the mass fractions of cosolvents. • The absolute values of h xx of L-enantiomers are larger than D-enantiomers in the range w COS = 0 to 0.30. • The h xx values of the two proline enantiomers are all positive at each composition of mixed solvents. • When a hydrophilic hydroxyl group is introduced into proline enantiomers, the values of h xx become negative. -- Abstract: Dilution enthalpies of two pairs of α-amino acid enantiomers, namely L-proline vsD-proline, and L-hydroxyproline vsD-hydroxyproline, in water-rich regions of dimethyl formamide (DMF) + H 2 O and dimethylsulfoxide (DMSO) + H 2 O mixtures (mass fractions of cosolvents w COS = 0 to 0.30) have been determined respectively at 298.15 K by isothermal titration calorimetry (ITC). The successive values of dilution enthalpy obtained in a single run of ITC determination were used to calculate homochiral enthalpic pairwise interaction coefficients (h xx ) at the corresponding composition of mixed solvents according to the McMillan–Mayer’ statistical thermodynamic approach. The sign and magnitude of h xx were interpreted in terms of solute–solute interactions mediated by solvent and cosolvent molecules, and preferential configurations of homochiral pairwise interactions (L–L or D–D pairs) in aqueous solutions. The variations of h xx with w COS were considered to be dependent greatly on the competition equilibrium between hydrophobic and hydrophilic interactions, as well as the structural alteration of water caused by the two highly polar aprotic cosolvents (DMF and DMSO). Especially, it was found that when one of the two kinds of interactions (hydrophobic or hydrophilic interactions) preponderates over the other in solutions, enthalpic effect of homochiral pairwise interactions is always remarkable, and is characterized by a large absolute value of h xx , positive or negative, which corresponds respectively to the

Comparison of type 2 diabetes mellitus incidence in different phases of hepatitis B virus infection: A meta-analysis.

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Shen, Yi; Zhang, Sheng; Wang, Xulin; Wang, Yuanyuan; Zhang, Jian; Qin, Gang; Li, Wenchao; Ding, Kun; Zhang, Lei; Liang, Feng

2017-10-01

Because whether hepatitis B virus infection increases the risk of type 2 diabetes mellitus has been a controversial topic, pair-wise and network meta-analyses of published literature were carried out to accurately evaluate the association between different phases of hepatitis B virus infection and the risk of type 2 diabetes mellitus. A comprehensive literature retrieval was conducted from the PubMed, Embase, Cochrane Library and Chinese Database to identify epidemiological studies on the association between hepatitis B virus infection and the risk of type 2 diabetes mellitus that were published from 1999 to 2015. A pair-wise meta-analysis of direct evidence was performed to estimate the pooled odds ratios and 95% confidence intervals. A network meta-analysis was conducted, including the construction of a network plot, inconsistency plot, predictive interval plot, comparison-adjusted funnel plot and rank diagram, to graphically link the direct and indirect comparisons between different hepatitis B virus infective phases. Eighteen publications (n=113 639) describing 32 studies were included in this meta-analysis. In the pair-wise meta-analysis, the pooled odds ratio for type 2 diabetes mellitus in chronic hepatitis B cirrhosis patients was 1.76 (95% confidence interval: 1.44-2.14) when compared with non-cirrhotic chronic hepatitis B patients. In the network meta-analysis, six comparisons of four hepatitis B virus infectious states indicated the following descending order for the risk of type 2 diabetes mellitus: hepatitis B cirrhosis patients, non-cirrhotic chronic hepatitis B patients, hepatitis B virus carriers and non-hepatitis B virus controls. This study suggests that hepatitis B virus infection is not an independent risk factor for type 2 diabetes mellitus, but the development of cirrhosis may increase the incidence of type 2 diabetes mellitus cirrhosis. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A risk based approach for SSTO/TSTO comparisons

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Greenberg, Joel S.

1996-03-01

An approach has been developed for performing early comparisons of transportation architectures explicitly taking into account quantitative measures of uncertainty and resulting risk. Risk considerations are necessary since the transportation systems are likely to have significantly different levels of risk, both because of differing degrees of freedom in achieving desired performance levels and their different states of development and utilization. The approach considers the uncertainty of achievement of technology goals, effect that the achieved technology level will have on transportation system performance and the relationship between system performance/capability and the ability to accommodate variations in payload mass. The consequences of system performance are developed in terms of nonrecurring, recurring, and the present value of transportation system life cycle costs.

An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

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Taneda Akito

2008-12-01

Full Text Available Abstract Background Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA discovery. Results We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%. By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences. Conclusion The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.

Use of an excess variance approach for the certification of reference materials by interlaboratory comparison

International Nuclear Information System (INIS)

Crozet, M.; Rigaux, C.; Roudil, D.; Tuffery, B.; Ruas, A.; Desenfant, M.

2014-01-01

In the nuclear field, the accuracy and comparability of analytical results are crucial to insure correct accountancy, good process control and safe operational conditions. All of these require reliable measurements based on reference materials whose certified values must be obtained by robust metrological approaches according to the requirements of ISO guides 34 and 35. The data processing of the characterization step is one of the key steps of a reference material production process. Among several methods, the use of interlaboratory comparison results for reference material certification is very common. The DerSimonian and Laird excess variance approach, described and implemented in this paper, is a simple and efficient method for the data processing of interlaboratory comparison results for reference material certification. By taking into account not only the laboratory uncertainties but also the spread of the individual results into the calculation of the weighted mean, this approach minimizes the risk to get biased certified values in the case where one or several laboratories either underestimate their measurement uncertainties or do not identify all measurement biases. This statistical method has been applied to a new CETAMA plutonium reference material certified by interlaboratory comparison and has been compared to the classical weighted mean approach described in ISO Guide 35. This paper shows the benefits of using an 'excess variance' approach for the certification of reference material by interlaboratory comparison. (authors)

Data Analysis A Model Comparison Approach, Second Edition

CERN Document Server

Judd, Charles M; Ryan, Carey S

2008-01-01

This completely rewritten classic text features many new examples, insights and topics including mediational, categorical, and multilevel models. Substantially reorganized, this edition provides a briefer, more streamlined examination of data analysis. Noted for its model-comparison approach and unified framework based on the general linear model, the book provides readers with a greater understanding of a variety of statistical procedures. This consistent framework, including consistent vocabulary and notation, is used throughout to develop fewer but more powerful model building techniques. T

Comparison of Human Exploration Architecture and Campaign Approaches

Science.gov (United States)

Goodliff, Kandyce; Cirillo, William; Mattfeld, Bryan; Stromgren, Chel; Shyface, Hilary

2015-01-01

As part of an overall focus on space exploration, National Aeronautics and Space Administration (NASA) continues to evaluate potential approaches for sending humans beyond low Earth orbit (LEO). In addition, various external organizations are studying options for beyond LEO exploration. Recent studies include NASA's Evolvable Mars Campaign and Design Reference Architecture (DRA) 5.0, JPL's Minimal Mars Architecture; the Inspiration Mars mission; the Mars One campaign; and the Global Exploration Roadmap (GER). Each of these potential exploration constructs applies unique methods, architectures, and philosophies for human exploration. It is beneficial to compare potential approaches in order to better understand the range of options available for exploration. Since most of these studies were conducted independently, the approaches, ground rules, and assumptions used to conduct the analysis differ. In addition, the outputs and metrics presented for each construct differ substantially. This paper will describe the results of an effort to compare and contrast the results of these different studies under a common set of metrics. The paper will first present a summary of each of the proposed constructs, including a description of the overall approach and philosophy for exploration. Utilizing a common set of metrics for comparison, the paper will present the results of an evaluation of the potential benefits, critical challenges, and uncertainties associated with each construct. The analysis framework will include a detailed evaluation of key characteristics of each construct. These will include but are not limited to: a description of the technology and capability developments required to enable the construct and the uncertainties associated with these developments; an analysis of significant operational and programmatic risks associated with that construct; and an evaluation of the extent to which exploration is enabled by the construct, including the destinations

Comparison of two Minkowski-space approaches to heavy quarkonia

Energy Technology Data Exchange (ETDEWEB)

Leitao, Sofia; Biernat, Elmar P. [Universidade de Lisboa, CFTP, Instituto Superior Tecnico, Lisbon (Portugal); Li, Yang [Iowa State University, Department of Physics and Astronomy, Ames, IA (United States); College of William and Mary, Department of Physics, Williamsburg, VA (United States); Maris, Pieter; Vary, James P. [Iowa State University, Department of Physics and Astronomy, Ames, IA (United States); Pena, M.T. [Universidade de Lisboa, CFTP, Instituto Superior Tecnico, Lisbon (Portugal); Universidade de Lisboa, Departamento de Fisica, Instituto Superior Tecnico, Lisbon (Portugal); Stadler, Alfred [Universidade de Lisboa, CFTP, Instituto Superior Tecnico, Lisbon (Portugal); Universidade de Evora, Departamento de Fisica, Evora (Portugal)

2017-10-15

In this work we compare mass spectra and decay constants obtained from two recent, independent, and fully relativistic approaches to the quarkonium bound-state problem: the Basis Light-Front Quantization approach, where light-front wave functions are naturally formulated; and, the Covariant Spectator Theory (CST), based on a reorganization of the Bethe-Salpeter equation. Even though conceptually different, both solutions are obtained in Minkowski space. Comparisons of decay constants for more than ten states of charmonium and bottomonium show favorable agreement between the two approaches as well as with experiment where available. We also apply the Brodsky-Huang-Lepage prescription to convert the CST amplitudes into functions of light-front variables. This provides an ideal opportunity to investigate the similarities and differences at the level of the wave functions. Several qualitative features are observed in remarkable agreement between the two approaches even for the rarely addressed excited states. Leading-twist distribution amplitudes as well as parton distribution functions of heavy quarkonia are also analyzed. (orig.)

A Comparison of Microeconomic and Macroeconomic Approaches to Deforestation Analysis

Directory of Open Access Journals (Sweden)

Jeff Felardo

2016-01-01

Full Text Available The economics of deforestation has been explored in detail. Generally, the frame of analysis takes either a microeconomics or macroeconomics approach. The microeconomics approach assumes that individual decision makers are responsible for deforestation as a result of utility maximizing behavior and imperfect property right regimes. The macroeconomics approach explores nationwide trends thought to be associated with forest conversion. This paper investigates the relationship between these two approaches by empirically testing the determinants of deforestation using the same data set from Thailand. The theory for both the microeconomics-based and macroeconomics-based approaches are developed and then tested statistically. The models were constructed using established theoretical frames developed in the literature. The results from both models show statistical significance consistent with prior results in the tropical deforestation literature. A comparison of the two approaches demonstrates that the macro approach is useful in identifying relevant aggregate trends in the deforestation process; the micro approach provides the opportunity to isolate factors of those trends which are necessary for effective policy decisions.

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Torarinsson, Elfar; Gorodkin, Jan

2007-01-01

and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool...... the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained....... Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned...

AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins.

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Hon Cheng Muh

Full Text Available Allergy is a major health problem in industrialized countries. The number of transgenic food crops is growing rapidly creating the need for allergenicity assessment before they are introduced into human food chain. While existing bioinformatic methods have achieved good accuracies for highly conserved sequences, the discrimination of allergens and non-allergens from allergen-like non-allergen sequences remains difficult. We describe AllerHunter, a web-based computational system for the assessment of potential allergenicity and allergic cross-reactivity in proteins. It combines an iterative pairwise sequence similarity encoding scheme with SVM as the discriminating engine. The pairwise vectorization framework allows the system to model essential features in allergens that are involved in cross-reactivity, but not limited to distinct sets of physicochemical properties. The system was rigorously trained and tested using 1,356 known allergen and 13,449 putative non-allergen sequences. Extensive testing was performed for validation of the prediction models. The system is effective for distinguishing allergens and non-allergens from allergen-like non-allergen sequences. Testing results showed that AllerHunter, with a sensitivity of 83.4% and specificity of 96.4% (accuracy = 95.3%, area under the receiver operating characteristic curve AROC = 0.928+/-0.004 and Matthew's correlation coefficient MCC = 0.738, performs significantly better than a number of existing methods using an independent dataset of 1443 protein sequences. AllerHunter is available at (http://tiger.dbs.nus.edu.sg/AllerHunter.

Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms

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Patricia Ortegon

2015-01-01

Full Text Available In order to understand how cellular metabolism has taken its modern form, the conservation and variations between metabolic pathways were evaluated by using a genetic algorithm (GA. The GA approach considered information on the complete metabolism of the bacterium Escherichia coli K-12, as deposited in the KEGG database, and the enzymes belonging to a particular pathway were transformed into enzymatic step sequences by using the breadth-first search algorithm. These sequences represent contiguous enzymes linked to each other, based on their catalytic activities as they are encoded in the Enzyme Commission numbers. In a posterior step, these sequences were compared using a GA in an all-against-all (pairwise comparisons approach. Individual reactions were chosen based on their measure of fitness to act as parents of offspring, which constitute the new generation. The sequences compared were used to construct a similarity matrix (of fitness values that was then considered to be clustered by using a k-medoids algorithm. A total of 34 clusters of conserved reactions were obtained, and their sequences were finally aligned with a multiple-sequence alignment GA optimized to align all the reaction sequences included in each group or cluster. From these comparisons, maps associated with the metabolism of similar compounds also contained similar enzymatic step sequences, reinforcing the Patchwork Model for the evolution of metabolism in E. coli K-12, an observation that can be expanded to other organisms, for which there is metabolism information. Finally, our mapping of these reactions is discussed, with illustrations from a particular case.

An Analytic Hierarchy Process for School Quality and Inspection: Model Development and Application

Science.gov (United States)

Al Qubaisi, Amal; Badri, Masood; Mohaidat, Jihad; Al Dhaheri, Hamad; Yang, Guang; Al Rashedi, Asma; Greer, Kenneth

2016-01-01

Purpose: The purpose of this paper is to develop an analytic hierarchy planning-based framework to establish criteria weights and to develop a school performance system commonly called school inspections. Design/methodology/approach: The analytic hierarchy process (AHP) model uses pairwise comparisons and a measurement scale to generate the…

A density functional approach to ferrogels

Science.gov (United States)

Cremer, P.; Heinen, M.; Menzel, A. M.; Löwen, H.

2017-07-01

Ferrogels consist of magnetic colloidal particles embedded in an elastic polymer matrix. As a consequence, their structural and rheological properties are governed by a competition between magnetic particle-particle interactions and mechanical matrix elasticity. Typically, the particles are permanently fixed within the matrix, which makes them distinguishable by their positions. Over time, particle neighbors do not change due to the fixation by the matrix. Here we present a classical density functional approach for such ferrogels. We map the elastic matrix-induced interactions between neighboring colloidal particles distinguishable by their positions onto effective pairwise interactions between indistinguishable particles similar to a ‘pairwise pseudopotential’. Using Monte-Carlo computer simulations, we demonstrate for one-dimensional dipole-spring models of ferrogels that this mapping is justified. We then use the pseudopotential as an input into classical density functional theory of inhomogeneous fluids and predict the bulk elastic modulus of the ferrogel under various conditions. In addition, we propose the use of an ‘external pseudopotential’ when one switches from the viewpoint of a one-dimensional dipole-spring object to a one-dimensional chain embedded in an infinitely extended bulk matrix. Our mapping approach paves the way to describe various inhomogeneous situations of ferrogels using classical density functional concepts of inhomogeneous fluids.

On the equivalence of generalized least-squares approaches to the evaluation of measurement comparisons

Science.gov (United States)

Koo, A.; Clare, J. F.

2012-06-01

Analysis of CIPM international comparisons is increasingly being carried out using a model-based approach that leads naturally to a generalized least-squares (GLS) solution. While this method offers the advantages of being easier to audit and having general applicability to any form of comparison protocol, there is a lack of consensus over aspects of its implementation. Two significant results are presented that show the equivalence of three differing approaches discussed by or applied in comparisons run by Consultative Committees of the CIPM. Both results depend on a mathematical condition equivalent to the requirement that any two artefacts in the comparison are linked through a sequence of measurements of overlapping pairs of artefacts. The first result is that a GLS estimator excluding all sources of error common to all measurements of a participant is equal to the GLS estimator incorporating all sources of error, including those associated with any bias in the standards or procedures of the measuring laboratory. The second result identifies the component of uncertainty in the estimate of bias that arises from possible systematic effects in the participants' measurement standards and procedures. The expression so obtained is a generalization of an expression previously published for a one-artefact comparison with no inter-participant correlations, to one for a comparison comprising any number of repeat measurements of multiple artefacts and allowing for inter-laboratory correlations.

Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

OpenAIRE

Maddock, Simon T.; Briscoe, Andrew G.; Wilkinson, Mark; Waeschenbach, Andrea; San Mauro, Diego; Day, Julia J.; Littlewood, D. Tim J.; Foster, Peter G.; Nussbaum, Ronald A.; Gower, David J.

2016-01-01

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a ‘traditional’ Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing pla...

GraphAlignment: Bayesian pairwise alignment of biological networks

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Kolář Michal

2012-11-01

Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

T2-weighted liver MRI using the multiVane technique at 3T: Comparison with conventional T2-weighted MRI

Energy Technology Data Exchange (ETDEWEB)

Kang, Kyung A [Dept. of Radiology, Myongji Hospital, Seonam University College of Medicine, Goyang (Korea, Republic of); Kim, Young Kon; Jeong, Woo Kyoung; Choi, Dong Il; Lee, Won Jae [Dept. of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Eun Ju [Philips Healthcare Korea, Philips, Seoul (Korea, Republic of); Jung, Sin Ho; Baek, Sun Young [Biostatistics and Clinical Epidemiology Center, Samsung Medical Center, Seoul (Korea, Republic of)

2015-10-15

To assess the value of applying MultiVane to liver T2-weighted imaging (T2WI) compared with conventional T2WIs with emphasis on detection of focal liver lesions. Seventy-eight patients (43 men and 35 women) with 86 hepatic lesions and 20 pancreatico-biliary diseases underwent MRI including T2WIs acquired using breath-hold (BH), respiratory-triggered (RT), and MultiVane technique at 3T. Two reviewers evaluated each T2WI with respect to artefacts, organ sharpness, and conspicuity of intrahepatic vessels, hilar duct, and main lesion using five-point scales, and made pairwise comparisons between T2WI sequences for these categories. Diagnostic accuracy (Az) and sensitivity for hepatic lesion detection were evaluated using alternative free-response receiver operating characteristic analysis. MultiVane T2WI was significantly better than BH-T2WI or RT-T2WI for organ sharpness and conspicuity of intrahepatic vessels and main lesion in both separate reviews and pairwise comparisons (p < 0.001). With regard to motion artefacts, MultiVane T2WI or BH-T2WI was better than RT-T2WI (p < 0.001). Conspicuity of hilar duct was better with BH-T2WI than with MultiVane T2WI (p = 0.030) or RT-T2WI (p < 0.001). For detection of 86 hepatic lesions, sensitivity (mean, 97.7%) of MultiVane T2WI was significantly higher than that of BH-T2WI (mean, 89.5%) (p = 0.008) or RT-T2WI (mean, 84.9%) (p = 0.001). Applying the MultiVane technique to T2WI of the liver is a promising approach to improving image quality that results in increased detection of focal liver lesions compared with conventional T2WI.

Theory of pairwise coupling embedded in more general local dispersion relations

International Nuclear Information System (INIS)

Fuchs, V.; Bers, A.; Harten, L.

1985-01-01

Earlier work on the mode conversion theory by Fuchs, Ko, and Bers is detailed and expanded upon, and its relation to energy conservation is discussed. Given a local dispersion relation, D(ω; k, z) = 0, describing stable waves excited at an externally imposed frequency ω, a pairwise mode-coupling event embedded therein is extracted by expanding D(k, z) around a contour k = k/sub c/(z) given by partialD/partialk = 0. The branch points of D(k, z) = 0 are the turning points of a second-order differential-equation representation. In obtaining the fraction of mode-converted energy, the connection formula and conservation of energy must be used together. Also, proper attention must be given to distinguish cases for which the coupling disappears or persists upon confluence of the branches, a property which is shown to depend on the forward (v/sub g/v/sub ph/>0) or backward (v/sub g/v/sub ph/<0) nature of the waves. Examples occurring in ion-cyclotron and lower-hybrid heating are presented, illustrating the use of the theory

A note on the statistical analysis of point judgment matrices

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MG Kabera

2013-06-01

Full Text Available The Analytic Hierarchy Process is a multicriteria decision making technique developed by Saaty in the 1970s. The core of the approach is the pairwise comparison of objects according to a single criterion using a 9-point ratio scale and the estimation of weights associated with these objects based on the resultant judgment matrix. In the present paper some statistical approaches to extracting the weights of objects from a judgment matrix are reviewed and new ideas which are rooted in the traditional method of paired comparisons are introduced.

Comparison of potential method in analytic hierarchy process for multi-attribute of catering service companies

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Mamat, Siti Salwana; Ahmad, Tahir; Awang, Siti Rahmah

2017-08-01

Analytic Hierarchy Process (AHP) is a method used in structuring, measuring and synthesizing criteria, in particular ranking of multiple criteria in decision making problems. On the other hand, Potential Method is a ranking procedure in which utilizes preference graph ς (V, A). Two nodes are adjacent if they are compared in a pairwise comparison whereby the assigned arc is oriented towards the more preferred node. In this paper Potential Method is used to solve problem on a catering service selection. The comparison of result by using Potential method is made with Extent Analysis. The Potential Method is found to produce the same rank as Extent Analysis in AHP.

A Comparison of Routing Protocol for WSNs: Redundancy Based Approach A Comparison of Routing Protocol for WSNs: Redundancy Based Approach

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Anand Prakash

2014-03-01

Full Text Available Wireless Sensor Networks (WSNs with their dynamic applications gained a tremendous attention of researchers. Constant monitoring of critical situations attracted researchers to utilize WSNs at vast platforms. The main focus in WSNs is to enhance network localization as much as one could, for efficient and optimal utilization of resources. Different approaches based upon redundancy are proposed for optimum functionality. Localization is always related with redundancy of sensor nodes deployed at remote areas for constant and fault tolerant monitoring. In this work, we propose a comparison of classic flooding and the gossip protocol for homogenous networks which enhances stability and throughput quiet significantly.  

APOLLO: a quality assessment service for single and multiple protein models.

Science.gov (United States)

Wang, Zheng; Eickholt, Jesse; Cheng, Jianlin

2011-06-15

We built a web server named APOLLO, which can evaluate the absolute global and local qualities of a single protein model using machine learning methods or the global and local qualities of a pool of models using a pair-wise comparison approach. Based on our evaluations on 107 CASP9 (Critical Assessment of Techniques for Protein Structure Prediction) targets, the predicted quality scores generated from our machine learning and pair-wise methods have an average per-target correlation of 0.671 and 0.917, respectively, with the true model quality scores. Based on our test on 92 CASP9 targets, our predicted absolute local qualities have an average difference of 2.60 Å with the actual distances to native structure. http://sysbio.rnet.missouri.edu/apollo/. Single and pair-wise global quality assessment software is also available at the site.

Network meta-analysis: a technique to gather evidence from direct and indirect comparisons

Science.gov (United States)

2017-01-01

Systematic reviews and pairwise meta-analyses of randomized controlled trials, at the intersection of clinical medicine, epidemiology and statistics, are positioned at the top of evidence-based practice hierarchy. These are important tools to base drugs approval, clinical protocols and guidelines formulation and for decision-making. However, this traditional technique only partially yield information that clinicians, patients and policy-makers need to make informed decisions, since it usually compares only two interventions at the time. In the market, regardless the clinical condition under evaluation, usually many interventions are available and few of them have been studied in head-to-head studies. This scenario precludes conclusions to be drawn from comparisons of all interventions profile (e.g. efficacy and safety). The recent development and introduction of a new technique – usually referred as network meta-analysis, indirect meta-analysis, multiple or mixed treatment comparisons – has allowed the estimation of metrics for all possible comparisons in the same model, simultaneously gathering direct and indirect evidence. Over the last years this statistical tool has matured as technique with models available for all types of raw data, producing different pooled effect measures, using both Frequentist and Bayesian frameworks, with different software packages. However, the conduction, report and interpretation of network meta-analysis still poses multiple challenges that should be carefully considered, especially because this technique inherits all assumptions from pairwise meta-analysis but with increased complexity. Thus, we aim to provide a basic explanation of network meta-analysis conduction, highlighting its risks and benefits for evidence-based practice, including information on statistical methods evolution, assumptions and steps for performing the analysis. PMID:28503228

Optimal data collection for informative rankings expose well-connected graphs

NARCIS (Netherlands)

Osting, Braxton; Brune, Christoph; Osher, Stanley J.

2014-01-01

Given a graph where vertices represent alternatives and arcs represent pairwise comparison data, the statistical ranking problem is to find a potential function, defined on the vertices, such that the gradient of the potential function agrees with the pairwise comparisons. Our goal in this paper is

Brain without anatomy: construction and comparison of fully network-driven structural MRI connectomes.

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Olga Tymofiyeva

Full Text Available MRI connectomics methods treat the brain as a network and provide new information about its organization, efficiency, and mechanisms of disruption. The most commonly used method of defining network nodes is to register the brain to a standardized anatomical atlas based on the Brodmann areas. This approach is limited by inter-subject variability and can be especially problematic in the context of brain maturation or neuroplasticity (cerebral reorganization after brain damage. In this study, we combined different image processing and network theory methods and created a novel approach that enables atlas-free construction and connection-wise comparison of diffusion MRI-based brain networks. We illustrated the proposed approach in three age groups: neonates, 6-month-old infants, and adults. First, we explored a data-driven method of determining the optimal number of equal-area nodes based on the assumption that all cortical areas of the brain are connected and, thus, no part of the brain is structurally isolated. Second, to enable a connection-wise comparison, alignment to a "reference brain" was performed in the network domain within each group using a matrix alignment algorithm with simulated annealing. The correlation coefficients after pair-wise network alignment ranged from 0.6102 to 0.6673. To test the method's reproducibility, one subject from the 6-month-old group and one from the adult group were scanned twice, resulting in correlation coefficients of 0.7443 and 0.7037, respectively. While being less than 1 due to parcellation and noise, statistically, these values were significantly higher than inter-subject values. Rotation of the parcellation largely explained the variability. Through the abstraction from anatomy, the developed framework allows for a fully network-driven analysis of structural MRI connectomes and can be applied to subjects at any stage of development and with substantial differences in cortical anatomy.

A Comparison of Swedish and U.S. Fathers' Self-Reported Use of Parental Discipline.

Science.gov (United States)

Jutengren, Goran; Palmerus, Kerstin

2002-01-01

Interviewed two samples (pairwise matched on sex and age of child and fathers' education) of fathers from Sweden and the United States about parental discipline with their 38- to 66-5month-olds. Found that, compared with U.S. fathers, Swedish fathers displayed a range of disciplining approaches from punitive reprimands to restrictive control…

Comparison of two approaches for establishing performance criteria related to Maintenance Rule

International Nuclear Information System (INIS)

Jerng, Dong-Wook; Kim, Man Cheol

2015-01-01

Probabilistic safety assessment (PSA) serves as a tool for systemically analyzing the safety of nuclear power plants. This paper explains and compares two approaches for the establishment of performance criteria related to the Maintenance Rule: (1) the individual reliability-based approach, and (2) the PSA importance measure-based approach. Different characteristics of the two approaches were compared in a qualitative manner, while a quantitative comparison was performed through application of the two approaches to a nuclear power plant. It was observed that the individual reliability-based approach resulted in more conservative performance criteria, compared to the PSA importance measure-based approach. It is thus expected that the PSA importance measure-based approach will allow for more flexible maintenance policy under conditions of limited resources, while providing for a macroscopic view of overall plant safety. Based on insights derived through this analysis, we emphasize the importance of a balance between reliability and safety significance, and propose a balance measure accordingly. The conclusions of this analysis are likely to be applicable to other types of nuclear power plants. (author)

Optimal definition of inter-residual contact in globular proteins based on pairwise interaction energy calculations, its robustness, and applications.

Science.gov (United States)

Fačkovec, Boris; Vondrášek, Jiří

2012-10-25

Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between "productive" and "non-productive" contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.

Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.

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Ankita Chaurasia

Full Text Available A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi. An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann's factor was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼ 40% to ∼ 90%, in each pairwise comparison. The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from <1% to ∼ 10%, in each pairwise comparison. The results further support the hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes.

pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.

Science.gov (United States)

Gil, Víctor A; Guallar, Víctor

2013-09-15

We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms. The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section. victor.guallar@bsc.es Supplementary data are available at Bioinformatics online.

The pairwise phase consistency in cortical network and its relationship with neuronal activation

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Wang Daming

2017-01-01

Full Text Available Gamma-band neuronal oscillation and synchronization with the range of 30-90 Hz are ubiquitous phenomenon across numerous brain areas and various species, and correlated with plenty of cognitive functions. The phase of the oscillation, as one aspect of CTC (Communication through Coherence hypothesis, underlies various functions for feature coding, memory processing and behaviour performing. The PPC (Pairwise Phase Consistency, an improved coherence measure, statistically quantifies the strength of phase synchronization. In order to evaluate the PPC and its relationships with input stimulus, neuronal activation and firing rate, a simplified spiking neuronal network is constructed to simulate orientation columns in primary visual cortex. If the input orientation stimulus is preferred for a certain orientation column, neurons within this corresponding column will obtain higher firing rate and stronger neuronal activation, which consequently engender higher PPC values, with higher PPC corresponding to higher firing rate. In addition, we investigate the PPC in time resolved analysis with a sliding window.

Video-based depression detection using local Curvelet binary patterns in pairwise orthogonal planes.

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Pampouchidou, Anastasia; Marias, Kostas; Tsiknakis, Manolis; Simos, Panagiotis; Fan Yang; Lemaitre, Guillaume; Meriaudeau, Fabrice

2016-08-01

Depression is an increasingly prevalent mood disorder. This is the reason why the field of computer-based depression assessment has been gaining the attention of the research community during the past couple of years. The present work proposes two algorithms for depression detection, one Frame-based and the second Video-based, both employing Curvelet transform and Local Binary Patterns. The main advantage of these methods is that they have significantly lower computational requirements, as the extracted features are of very low dimensionality. This is achieved by modifying the previously proposed algorithm which considers Three-Orthogonal-Planes, to only Pairwise-Orthogonal-Planes. Performance of the algorithms was tested on the benchmark dataset provided by the Audio/Visual Emotion Challenge 2014, with the person-specific system achieving 97.6% classification accuracy, and the person-independed one yielding promising preliminary results of 74.5% accuracy. The paper concludes with open issues, proposed solutions, and future plans.

Integrating remote sensing with GIS-based multi-criteria evaluation approach for Karst rocky desertification assessment in Southwest of China

International Nuclear Information System (INIS)

Zhang, Z; Xu, W; Zhou, W; Zhang, L; Xiao, Y; Ouyang, Z; Ou, X

2014-01-01

The increasing exploitation of Karst resources is leading to severe environmental impacts, as Karst frequently occurs in the most fragile and vulnerable environments. This paper presents a multi-criteria evaluation (MCE) approach in a spatial context to support Karst rocky desertification (KRD) assessment by integrating remote sensing data with GIS. The study area is located in Wenshan Prefecture, Yunnan Province, Southwest of China. Criteria and impact factors for KRD first were identified and weighted through pairwise comparison method. A GIS fuzzy set membership function was then used to generate gradient effects of each criterion, and a clustering method based on K-mean algorithms was used to classify KRD into several descending rank zones (or levels). Both ROC and error matrix assessments indicated that the MCE approach is better than the NDVI approach. In addition, we found it is useful to integrate the topographic and human disturbance factors into KRD mapping and assessment, compared with most of the previous KRD assessment studies mainly focused on developing vegetation or land cover information in karst regions by using remote sensing alone. Furthermore, the integrated MCE approach is robust, flexible, and easy to be implemented. It also explicitly includes the quantitative and qualitative information, for instance, opinions of decision makers and experts as well as characteristics of the landscape

A comparison of approaches in fitting continuum SEDs

International Nuclear Information System (INIS)

Liu Yao; Wang Hong-Chi; Madlener David; Wolf Sebastian

2013-01-01

We present a detailed comparison of two approaches, the use of a pre-calculated database and simulated annealing (SA), for fitting the continuum spectral energy distribution (SED) of astrophysical objects whose appearance is dominated by surrounding dust. While pre-calculated databases are commonly used to model SED data, only a few studies to date employed SA due to its unclear accuracy and convergence time for this specific problem. From a methodological point of view, different approaches lead to different fitting quality, demand on computational resources and calculation time. We compare the fitting quality and computational costs of these two approaches for the task of SED fitting to provide a guide to the practitioner to find a compromise between desired accuracy and available resources. To reduce uncertainties inherent to real datasets, we introduce a reference model resembling a typical circumstellar system with 10 free parameters. We derive the SED of the reference model with our code MC3 D at 78 logarithmically distributed wavelengths in the range [0.3 μm, 1.3 mm] and use this setup to simulate SEDs for the database and SA. Our result directly demonstrates the applicability of SA in the field of SED modeling, since the algorithm regularly finds better solutions to the optimization problem than a pre-calculated database. As both methods have advantages and shortcomings, a hybrid approach is preferable. While the database provides an approximate fit and overall probability distributions for all parameters deduced using Bayesian analysis, SA can be used to improve upon the results returned by the model grid.

Evaluating the Quality of Evidence from a Network Meta-Analysis

Science.gov (United States)

Salanti, Georgia; Del Giovane, Cinzia; Chaimani, Anna; Caldwell, Deborah M.; Higgins, Julian P. T.

2014-01-01

Systematic reviews that collate data about the relative effects of multiple interventions via network meta-analysis are highly informative for decision-making purposes. A network meta-analysis provides two types of findings for a specific outcome: the relative treatment effect for all pairwise comparisons, and a ranking of the treatments. It is important to consider the confidence with which these two types of results can enable clinicians, policy makers and patients to make informed decisions. We propose an approach to determining confidence in the output of a network meta-analysis. Our proposed approach is based on methodology developed by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) Working Group for pairwise meta-analyses. The suggested framework for evaluating a network meta-analysis acknowledges (i) the key role of indirect comparisons (ii) the contributions of each piece of direct evidence to the network meta-analysis estimates of effect size; (iii) the importance of the transitivity assumption to the validity of network meta-analysis; and (iv) the possibility of disagreement between direct evidence and indirect evidence. We apply our proposed strategy to a systematic review comparing topical antibiotics without steroids for chronically discharging ears with underlying eardrum perforations. The proposed framework can be used to determine confidence in the results from a network meta-analysis. Judgements about evidence from a network meta-analysis can be different from those made about evidence from pairwise meta-analyses. PMID:24992266

Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

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Raphaël Mourad

Full Text Available Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

Dynamical pairwise entanglement and two-point correlations in the three-ligand spin-star structure

Science.gov (United States)

Motamedifar, M.

2017-10-01

We consider the three-ligand spin-star structure through homogeneous Heisenberg interactions (XXX-3LSSS) in the framework of dynamical pairwise entanglement. It is shown that the time evolution of the central qubit ;one-particle; state (COPS) brings about the generation of quantum W states at periodical time instants. On the contrary, W states cannot be generated from the time evolution of a ligand ;one-particle; state (LOPS). We also investigate the dynamical behavior of two-point quantum correlations as well as the expectation values of the different spin-components for each element in the XXX-3LSSS. It is found that when a W state is generated, the same value of the concurrence between any two arbitrary qubits arises from the xx and yy two-point quantum correlations. On the opposite, zz quantum correlation between any two qubits vanishes at these time instants.

Self-Regulatory Behaviors and Approaches to Learning of Arts Students: A Comparison between Professional Training and English Learning

Science.gov (United States)

Tseng, Min-chen; Chen, Chia-cheng

2017-01-01

This study investigated the self-regulatory behaviors of arts students, namely memory strategy, goal-setting, self-evaluation, seeking assistance, environmental structuring, learning responsibility, and planning and organizing. We also explored approaches to learning, including deep approach (DA) and surface approach (SA), in a comparison between…

A Comparison of Machine Learning Approaches for Corn Yield Estimation

Science.gov (United States)

Kim, N.; Lee, Y. W.

2017-12-01

Machine learning is an efficient empirical method for classification and prediction, and it is another approach to crop yield estimation. The objective of this study is to estimate corn yield in the Midwestern United States by employing the machine learning approaches such as the support vector machine (SVM), random forest (RF), and deep neural networks (DNN), and to perform the comprehensive comparison for their results. We constructed the database using satellite images from MODIS, the climate data of PRISM climate group, and GLDAS soil moisture data. In addition, to examine the seasonal sensitivities of corn yields, two period groups were set up: May to September (MJJAS) and July and August (JA). In overall, the DNN showed the highest accuracies in term of the correlation coefficient for the two period groups. The differences between our predictions and USDA yield statistics were about 10-11 %.

Sexual risk attitudes and intentions of youth aged 12-14 years: survey comparisons of parent-teen prevention and control groups.

Science.gov (United States)

Lederman, Regina P; Chan, Wenyaw; Roberts-Gray, Cynthia

2004-01-01

In this study, the authors compared differences in sexual risk attitudes and intentions for three groups of youth (experimental program, n = 90; attention control, n = 80; and nonparticipant control, n = 634) aged 12-14 years. Two student groups participated with their parents in programs focused on strengthening family interaction and prevention of sexual risks, HIV, and adolescent pregnancy. Surveys assessed students' attitudes and intentions regarding early sexual and other health-risk behaviors, family interactions, and perceived parental disapproval of risk behaviors. The authors used general linear modeling to compare results. The experimental prevention program differentiated the total scores of the 3 groups (p < .05). A similar result was obtained for student intentions to avoid sex (p < .01). Pairwise comparisons showed the experimental program group scored higher than the nonparticipant group on total scores (p < .01) and on students' intention to avoid sex (p < .01). The results suggest this novel educational program involving both parents and students offers a promising approach to HIV and teen pregnancy prevention.

On Solving Intransitivities in Repeated Pairwise Choices

NARCIS (Netherlands)

A. Maas (Arne); Th.G.G. Bezembinder (Thom); P.P. Wakker (Peter)

1995-01-01

textabstractAn operational method is presented for deriving a linear ranking of alternatives from repeated paired comparisons of the alternatives. Intransitivities in the observed preferences are cleared away by the introduction of decision errors of varying importance. An observed preference

Which percentile-based approach should be preferred for calculating normalized citation impact values? An empirical comparison of five approaches including a newly developed citation-rank approach (P100)

NARCIS (Netherlands)

Bornmann, L.; Leydesdorff, L.; Wang, J.

2013-01-01

For comparisons of citation impacts across fields and over time, bibliometricians normalize the observed citation counts with reference to an expected citation value. Percentile-based approaches have been proposed as a non-parametric alternative to parametric central-tendency statistics. Percentiles

Synchronization of pairwise-coupled, identical, relaxation oscillators based on metal-insulator phase transition devices: A model study

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Parihar, Abhinav; Shukla, Nikhil; Datta, Suman; Raychowdhury, Arijit

2015-02-01

Computing with networks of synchronous oscillators has attracted wide-spread attention as novel materials and device topologies have enabled realization of compact, scalable and low-power coupled oscillatory systems. Of particular interest are compact and low-power relaxation oscillators that have been recently demonstrated using MIT (metal-insulator-transition) devices using properties of correlated oxides. Further the computational capability of pairwise coupled relaxation oscillators has also been shown to outperform traditional Boolean digital logic circuits. This paper presents an analysis of the dynamics and synchronization of a system of two such identical coupled relaxation oscillators implemented with MIT devices. We focus on two implementations of the oscillator: (a) a D-D configuration where complementary MIT devices (D) are connected in series to provide oscillations and (b) a D-R configuration where it is composed of a resistor (R) in series with a voltage-triggered state changing MIT device (D). The MIT device acts like a hysteresis resistor with different resistances in the two different states. The synchronization dynamics of such a system has been analyzed with purely charge based coupling using a resistive (RC) and a capacitive (CC) element in parallel. It is shown that in a D-D configuration symmetric, identical and capacitively coupled relaxation oscillator system synchronizes to an anti-phase locking state, whereas when coupled resistively the system locks in phase. Further, we demonstrate that for certain range of values of RC and CC, a bistable system is possible which can have potential applications in associative computing. In D-R configuration, we demonstrate the existence of rich dynamics including non-monotonic flows and complex phase relationship governed by the ratios of the coupling impedance. Finally, the developed theoretical formulations have been shown to explain experimentally measured waveforms of such pairwise coupled

Prediction of microsleeps using pairwise joint entropy and mutual information between EEG channels.

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Baseer, Abdul; Weddell, Stephen J; Jones, Richard D

2017-07-01

Microsleeps are involuntary and brief instances of complete loss of responsiveness, typically of 0.5-15 s duration. They adversely affect performance in extended attention-driven jobs and can be fatal. Our aim was to predict microsleeps from 16 channel EEG signals. Two information theoretic concepts - pairwise joint entropy and mutual information - were independently used to continuously extract features from EEG signals. k-nearest neighbor (kNN) with k = 3 was used to calculate both joint entropy and mutual information. Highly correlated features were discarded and the rest were ranked using Fisher score followed by an average of 3-fold cross-validation area under the curve of the receiver operating characteristic (AUC ROC ). Leave-one-out method (LOOM) was performed to test the performance of microsleep prediction system on independent data. The best prediction for 0.25 s ahead was AUCROC, sensitivity, precision, geometric mean (GM), and φ of 0.93, 0.68, 0.33, 0.75, and 0.38 respectively with joint entropy using single linear discriminant analysis (LDA) classifier.

Solution to urn models of pairwise interaction with application to social, physical, and biological sciences

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Pickering, William; Lim, Chjan

2017-07-01

We investigate a family of urn models that correspond to one-dimensional random walks with quadratic transition probabilities that have highly diverse applications. Well-known instances of these two-urn models are the Ehrenfest model of molecular diffusion, the voter model of social influence, and the Moran model of population genetics. We also provide a generating function method for diagonalizing the corresponding transition matrix that is valid if and only if the underlying mean density satisfies a linear differential equation and express the eigenvector components as terms of ordinary hypergeometric functions. The nature of the models lead to a natural extension to interaction between agents in a general network topology. We analyze the dynamics on uncorrelated heterogeneous degree sequence networks and relate the convergence times to the moments of the degree sequences for various pairwise interaction mechanisms.

An integrative approach to inferring biologically meaningful gene modules

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Wang Kai

2011-07-01

Full Text Available Abstract Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

Enthalpic pairwise self-association of L-carnitine in aqueous solutions of some alkali halides at T = 298.15 K

International Nuclear Information System (INIS)

Wang, Hua-Qin; Cheng, Wei-Na; Zhu, Li-Yuan; Hu, Xin-Gen

2016-01-01

Highlights: • Dilution enthalpies of L-carnitine in aqueous alkali halide solutions by ITC. • The second virial coefficients of enthalpy (h_2) have been calculated. • The values of h_2 increase with increasing molalities of aqueous salt solutions. • The signs of h_2 turn from negative in pure water to positive in salt solutions. • The trends is ascribed to the salt effects on pairwise self-associations. - Abstract: Knowledge of the influence of ions of various nature on intermolecular hydrophilic and hydrophobic interactions in solutions is required in many research fields. In this paper, dilution enthalpies of zwitterion L-carnitine in aqueous NaCl, KCl and NaBr solutions of various molalities (b = 0 to 3.0 mol · kg"−"1) have been determined respectively at T = (298.15 ± 0.01) K and p = (0.100 ± 0.005) MPa by isothermal titration calorimetry (ITC). In light of the MacMillan–Mayer theory, the 2nd virial enthalpic coefficients (h_2) have been calculated. The h_2 coefficients increase gradually with increasing molality (b) of the three aqueous alkali halides solutions, from small negative values in pure water to relatively larger positive values in solution. The trends of h_2 coefficients are ascribed to the salt effects on the balance between hydrophilic and hydrophobic interactions in pairwise self-associations. It is considered that the size of cations and anions exert influences on h_2 coefficients through their surface charge densities and hydration (or dehydration) abilities.

BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis.

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Allen W Bryan

2009-03-01

Full Text Available Amyloids and prion proteins are clinically and biologically important beta-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Recent work has indicated the utility of pairwise probabilistic statistics in beta-structure prediction. We develop here a new strategy for beta-structure prediction, emphasizing the determination of beta-strands and pairs of beta-strands as fundamental units of beta-structure. Our program, BETASCAN, calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence's potential beta-structures. BETASCAN suggests multiple alternate folding patterns and assigns relative a priori probabilities based solely on amino acid sequence, probability tables, and pre-chosen parameters. The algorithm compares favorably with the results of previous algorithms (BETAPRO, PASTA, SALSA, TANGO, and Zyggregator in beta-structure prediction and amyloid propensity prediction. Accurate prediction is demonstrated for experimentally determined amyloid beta-structures, for a set of known beta-aggregates, and for the parallel beta-strands of beta-helices, amyloid-like globular proteins. BETASCAN is able both to detect beta-strands with higher sensitivity and to detect the edges of beta-strands in a richly beta-like sequence. For two proteins (Abeta and Het-s, there exist multiple sets of experimental data implying contradictory structures; BETASCAN is able to detect each competing structure as a potential structure variant. The ability to correlate multiple alternate beta-structures to experiment opens the possibility of computational investigation of prion strains and structural heterogeneity of amyloid

Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis

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Kaur Parminder

2012-08-01

Full Text Available Abstract Background An approach to molecular classification based on the comparative expression of protein pairs is presented. The method overcomes some of the present limitations in using peptide intensity data for class prediction for problems such as the detection of a disease, disease prognosis, or for predicting treatment response. Data analysis is particularly challenging in these situations due to sample size (typically tens being much smaller than the large number of peptides (typically thousands. Methods based upon high dimensional statistical models, machine learning or other complex classifiers generate decisions which may be very accurate but can be complex and difficult to interpret in simple or biologically meaningful terms. A classification scheme, called ProtPair, is presented that generates simple decision rules leading to accurate classification which is based on measurement of very few proteins and requires only relative expression values, providing specific targeted hypotheses suitable for straightforward validation. Results ProtPair has been tested against clinical data from 21 patients following a bone marrow transplant, 13 of which progress to idiopathic pneumonia syndrome (IPS. The approach combines multiple peptide pairs originating from the same set of proteins, with each unique peptide pair providing an independent measure of discriminatory power. The prediction rate of the ProtPair for IPS study as measured by leave-one-out CV is 69.1%, which can be very beneficial for clinical diagnosis as it may flag patients in need of closer monitoring. The “top ranked” proteins provided by ProtPair are known to be associated with the biological processes and pathways intimately associated with known IPS biology based on mouse models. Conclusions An approach to biomarker discovery, called ProtPair, is presented. ProtPair is based on the differential expression of pairs of peptides and the associated proteins. Using mass

The Asian crisis contagion: A dynamic correlation approach analysis

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Essaadi Essahbi

2009-01-01

Full Text Available In this paper we are testing for contagion caused by the Thai baht collapse of July 1997. In line with earlier work, shift-contagion is defined as a structural change within the international propagation mechanisms of financial shocks. We adopt Bai and Perron's (1998 structural break approach in order to detect the endogenous break points of the pair-wise time-varying correlations between Thailand and seven Asian stock market returns. Our approach enables us to solve the misspecification problem of the crisis window. Our results illustrate the existence of shift-contagion in the Asian crisis caused by the crisis in Thailand.

Distinguishing between forensic science and forensic pseudoscience: testing of validity and reliability, and approaches to forensic voice comparison.

Science.gov (United States)

Morrison, Geoffrey Stewart

2014-05-01

In this paper it is argued that one should not attempt to directly assess whether a forensic analysis technique is scientifically acceptable. Rather one should first specify what one considers to be appropriate principles governing acceptable practice, then consider any particular approach in light of those principles. This paper focuses on one principle: the validity and reliability of an approach should be empirically tested under conditions reflecting those of the case under investigation using test data drawn from the relevant population. Versions of this principle have been key elements in several reports on forensic science, including forensic voice comparison, published over the last four-and-a-half decades. The aural-spectrographic approach to forensic voice comparison (also known as "voiceprint" or "voicegram" examination) and the currently widely practiced auditory-acoustic-phonetic approach are considered in light of this principle (these two approaches do not appear to be mutually exclusive). Approaches based on data, quantitative measurements, and statistical models are also considered in light of this principle. © 2013.

Effectiveness of fenugreek as a galactagogue: A network meta-analysis.

Science.gov (United States)

Khan, Tahir Mehmood; Wu, David Bin-Chia; Dolzhenko, Anton V

2018-03-01

A systematic review and network-meta analysis (NMA) were performed to test significance of the galactagogue effect of fenugreek administrated to lactating women versus other comparators (i.e., placebo/control/other galactagogues). A pairwise comparison for the treatment effect was carried out to generate the forest plot for the NMA. League tables were generated using treatment effect, weighted mean difference (WMD; 95% confidence interval, CI) for all pairwise comparisons, where WMD > 0 favors the column-defining treatment. Five studies were identified with 122 participants receiving treatment with fenugreek. The NMA results of 4 studies indicated that consumption of fenugreek significantly increased amount of the produced breast milk [11.11, CI 95% 6.77, 15.46] versus placebo. The pairwise comparison revealed that fenugreek was effective as a galactagogue compared to placebo, control, and reference groups WMD 17.79 [CI 11.71, 23.88]. However, the effect of fenugreek was substantially inferior to Coleus amboinicus Lour and palm date. The NMA using pairwise comparison demonstrated the effect of C. amboinicus and palm date in the stimulation of the breast milk production was comparable and superior to all comparators. Copyright © 2017 John Wiley & Sons, Ltd.

Hierarchical structure of biological systems: a bioengineering approach.

Science.gov (United States)

Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

2014-01-01

A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

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Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

2015-09-01

The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

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Manolakos, Elias S.

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub. PMID:26605332

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures.

Science.gov (United States)

Sharma, Anuj; Manolakos, Elias S

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub.

PENILAIAN TEKNOLOGI UNTUK MENENTUKAN POSISI INDUSTRI PESAING

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Wahyu Susihono

2013-02-01

Corporation is one of handicraft companies supplied by five small industry of its trainee. Since the company will be privet in a short time, the head office manager wanted one of small industries take over its management. Therefore the company needs to determine one of small industry which is the best. The management intends to make an assessment of technology to five small industries of its trainee internally and externally as the basic of decision making. This research will be held by making an assessment to all of handicraft suppliers by using technometric model approach. In this approach assessment conducted by determining degree of technology component sophistication, valuing state-of-the-art, determining contribution of technology component, making the map of relation between the components, and valuing intensity of contribution components. The questioners spreading to five small industries analyzed by pairwise comparison Analytic Hierarchy Process (AHP then concluded by the calculation of TCC (Technology Contribution Coefficient. The company made internal assessment by using DEA (data envelopment analysis model then compare the result of TCC white DEA quantitatively. TCC result showed that the values of the industry in a row are Maharani by 52.23%, Bestari by 52.23%, Priyo by 41.51%, Rizky 32.66%, and Teguh by 31.93%. The greatest contribution for Maharani came from organware while the rest companies came from humanware. In the future, all of small industries expected to develop technology known by technoware. The Result of internal assessment of Sumiati Export International Corporation by DEA model showed that Maharani in the first position and Rizky in the last position. Technometric model with combination of pairwise comparison AHP aids big companies to make technology assessment to small industries. Keywords: assessment of technology, technometric model, pairwise comparison AHP, DEA

Quasi-chemical approach for adsorption of mixtures with non-additive lateral interactions

Energy Technology Data Exchange (ETDEWEB)

Pinto, O.A. [Instituto de Bionanotecnología (INBIONATEC-CONICET), Universidad Nacional de Santiago de Estero, RN 9 Km 1125 Villa el Zanjón, Santiago del Estero G4206XCP (Argentina); Pasinetti, P.M., E-mail: pmp@unsl.edu.ar [Departamento de Física, Instituto de Física Aplicada (INFAP), Universidad Nacional de San Luis—CONICET, Ejército de los Andes 950, D5700BWS San Luis (Argentina); Ramirez-Pastor, A.J. [Departamento de Física, Instituto de Física Aplicada (INFAP), Universidad Nacional de San Luis—CONICET, Ejército de los Andes 950, D5700BWS San Luis (Argentina)

2017-01-15

Highlights: • The classical quasi-chemical approach is generalized to model non-additive mixtures. • The formalism allows to obtain the partial isotherms and the differential heat of adsorption. • A rich variety of low-temperature phases is observed in the adsorbed layer. • Theoretical results show a good agreement with Monte Carlo simulations. - Abstract: The statistical thermodynamics of binary mixtures with non-additive lateral interactions was developed on a generalization in the spirit of the lattice-gas model and the classical quasi-chemical approximation (QCA). The traditional assumption of a strictly pairwise additive nearest-neighbors interaction is replaced by a more general one, namely that the bond linking a certain atom with any of its neighbors depends considerably on how many of them are actually present (or absent) on the sites in the first coordination shell of the atom. The total and partial adsorption isotherms are given for both attractive and repulsive lateral interactions between the adsorbed species. Interesting behaviors are observed and discussed in terms of the low-temperature phases formed in the system. Comparisons with Monte Carlo simulations are performed in order to test the validity of the theoretical model.

On the non-convergence of energy intensities: evidence from a pair-wise econometric approach

International Nuclear Information System (INIS)

Le Pen, Yannick; Sevi, Benoit

2008-01-01

This paper evaluates convergence of energy intensities for a group of 97 countries in the period 1971-2003. Convergence is tested using a recent method proposed by Pesaran (2007) [M.H. Pesaran. A pair- wise approach to testing for output and growth convergence. Journal of Econometrics 138, 312-355.] based on the stochastic convergence criterion. Main advantages of this method are that results do not depend on a benchmark against which convergence is assessed, and that it is more robust. Applications of several unit-root tests as well as a stationarity test uniformly reject the global convergence hypothesis. Locally, for Middle- East, OECD and Europe sub-groups, non-convergence is less strongly rejected. The introduction of possible structural breaks in the analysis only marginally provides more support to the convergence hypothesis. (authors)

Benefits of Using Pairwise Trajectory Management in the Central East Pacific

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Chartrand, Ryan; Ballard, Kathryn

2016-01-01

Pairwise Trajectory Management (PTM) is a concept that utilizes airborne and ground-based capabilities to enable airborne spacing operations in oceanic regions. The goal of PTM is to use enhanced surveillance, along with airborne tools, to manage the spacing between aircraft. Due to the enhanced airborne surveillance of Automatic Dependent Surveillance-Broadcast (ADS-B) information and reduced communication, the PTM minimum spacing distance will be less than distances currently required of an air traffic controller. Reduced minimum distance will increase the capacity of aircraft operations at a given altitude or volume of airspace, thereby increasing time on desired trajectory and overall flight efficiency. PTM is designed to allow a flight crew to resolve a specific traffic conflict (or conflicts), identified by the air traffic controller, while maintaining the flight crew's desired altitude. The air traffic controller issues a PTM clearance to a flight crew authorized to conduct PTM operations in order to resolve a conflict for the pair (or pairs) of aircraft (i.e., the PTM aircraft and a designated target aircraft). This clearance requires the flight crew of the PTM aircraft to use their ADS-B-enabled onboard equipment to manage their spacing relative to the designated target aircraft to ensure spacing distances that are no closer than the PTM minimum distance. When the air traffic controller determines that PTM is no longer required, the controller issues a clearance to cancel the PTM operation.

A discrete model of Ostwald ripening based on multiple pairwise interactions

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Di Nunzio, Paolo Emilio

2018-06-01

A discrete multi-particle model of Ostwald ripening based on direct pairwise interactions is developed for particles with incoherent interfaces as an alternative to the classical LSW mean field theory. The rate of matter exchange depends on the average surface-to-surface interparticle distance, a characteristic feature of the system which naturally incorporates the effect of volume fraction of second phase. The multi-particle diffusion is described through the definition of an interaction volume containing all the particles involved in the exchange of solute. At small volume fractions this is proportional to the size of the central particle, at higher volume fractions it gradually reduces as a consequence of diffusion screening described on a geometrical basis. The topological noise present in real systems is also included. For volume fractions below about 0.1 the model predicts broad and right-skewed stationary size distributions resembling a lognormal function. Above this value, a transition to sharper, more symmetrical but still right-skewed shapes occurs. An excellent agreement with experiments is obtained for 3D particle size distributions of solid-solid and solid-liquid systems with volume fraction 0.07, 0.30, 0.52 and 0.74. The kinetic constant of the model depends on the cube root of volume fraction up to about 0.1, then increases rapidly with an upward concavity. It is in good agreement with the available literature data on solid-liquid mixtures in the volume fraction range from 0.20 to about 0.75.

A preliminary comparison of hydrodynamic approaches for flood inundation modeling of urban areas in Jakarta Ciliwung river basin

Science.gov (United States)

Rojali, Aditia; Budiaji, Abdul Somat; Pribadi, Yudhistira Satya; Fatria, Dita; Hadi, Tri Wahyu

2017-07-01

This paper addresses on the numerical modeling approaches for flood inundation in urban areas. Decisive strategy to choose between 1D, 2D or even a hybrid 1D-2D model is more than important to optimize flood inundation analyses. To find cost effective yet robust and accurate model has been our priority and motivation in the absence of available High Performance Computing facilities. The application of 1D, 1D/2D and full 2D modeling approach to river flood study in Jakarta Ciliwung river basin, and a comparison of approaches benchmarked for the inundation study are presented. This study demonstrate the successful use of 1D/2D and 2D system to model Jakarta Ciliwung river basin in terms of inundation results and computational aspect. The findings of the study provide an interesting comparison between modeling approaches, HEC-RAS 1D, 1D-2D, 2D, and ANUGA when benchmarked to the Manggarai water level measurement.

Towards Predicting Expressed Emotion in Music from Pairwise Comparisons

DEFF Research Database (Denmark)

Madsen, Jens; Jensen, Bjørn Sand; Larsen, Jan

2012-01-01

We introduce five regression models for the modeling of expressed emotion in music using data obtained in a two alternative forced choice listening experiment. The predictive performance of the proposed models is compared using learning curves, showing that all models converge to produce a similar...

Parent-Child Similarity in Environmental Attitudes: A Pairwise Comparison

Science.gov (United States)

Leppanen, Jaana M.; Haahla, Anu E.; Lensu, Anssi M.; Kuitunen, Markku T.

2012-01-01

Are adolescents' environmental attitudes similar to their parents' attitudes? The main objective of this study is to examine what quantitative associations, if any, exist in parent-child environmental attitudes within the family. The survey data was collected assessing attitudes toward the environment and nature from 15-year-old students (n = 237)…

Energetics of Brazilian ethanol: Comparison between assessment approaches

International Nuclear Information System (INIS)

Ramirez Triana, Carlos Ariel

2011-01-01

As with any other bioenergy product, bioethanol production requires fossil fuel inputs; hence the alleged benefits of energy security and carbon mitigation depend on the extent to which these inputs are capable of drawing a substantive bioenergetic yield. Brazilian ethanol, made out of sugarcane, has been reported as the most efficient gasoline substitute that is commercially available nowadays. For that reason it has been the object of several analyses on the energetics, i.e. energy balances. These studies surprisingly vary widely according with the scholar approach and are not fully comparable among them due to divergences in the assessment method. This paper standardises results of the four most prominent authors in the field, establishing a point of comparison and drawing some light on the energetics studies on biofuels. The main result is shown in , which homogenises the outcomes for referred studies in terms of unit of assessment in the energy input analysis. Subsequently, this information is also charted () explaining the source of divergence among authors. This work ends with a short reference and comparison to some energy balance studies carried out on feedstocks of diverse nature, highlighting the potential that sugarcane-based bioethanol represents nowadays. - Highlights: → Distribution stage could reduce energy ratio but its contribution is not significant. → In Pimentel and Patzek there is an evident impact of the industrial stage. → A coincidence across the studies was the major impact of the agricultural stage. → Brazilian technology to produce ethanol was proved the most energy efficient one.

Statistical comparison of a hybrid approach with approximate and exact inference models for Fusion 2+

Science.gov (United States)

Lee, K. David; Wiesenfeld, Eric; Gelfand, Andrew

2007-04-01

One of the greatest challenges in modern combat is maintaining a high level of timely Situational Awareness (SA). In many situations, computational complexity and accuracy considerations make the development and deployment of real-time, high-level inference tools very difficult. An innovative hybrid framework that combines Bayesian inference, in the form of Bayesian Networks, and Possibility Theory, in the form of Fuzzy Logic systems, has recently been introduced to provide a rigorous framework for high-level inference. In previous research, the theoretical basis and benefits of the hybrid approach have been developed. However, lacking is a concrete experimental comparison of the hybrid framework with traditional fusion methods, to demonstrate and quantify this benefit. The goal of this research, therefore, is to provide a statistical analysis on the comparison of the accuracy and performance of hybrid network theory, with pure Bayesian and Fuzzy systems and an inexact Bayesian system approximated using Particle Filtering. To accomplish this task, domain specific models will be developed under these different theoretical approaches and then evaluated, via Monte Carlo Simulation, in comparison to situational ground truth to measure accuracy and fidelity. Following this, a rigorous statistical analysis of the performance results will be performed, to quantify the benefit of hybrid inference to other fusion tools.

Time-History Seismic Analysis of Masonry Buildings: A Comparison between Two Non-Linear Modelling Approaches

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Michele Betti

2015-05-01

Full Text Available The paper presents a comparison between two numerical modelling approaches employed to investigate the seismic behavior of unreinforced masonry buildings with flexible diaphragms. The comparison is performed analyzing a two-story prototype tested on a shaking table at the CNR-ENEA research center of Casaccia (Italy. The first numerical model was built by using the finite element (FE technique, while the second one was built by a simplified macro-element (ME approach. Both models were employed to perform non-linear dynamic analyses, integrating the equations of motion by step-by-step procedures. The shaking table tests were simulated to analyze the behavior of the prototype from the initial elastic state until the development of extensive damage. The main results of the analyses are discussed and critically compared in terms of engineering parameters, such as accelerations, displacements and base shears. The effectiveness of both models within the investigated typology of buildings is then evaluated in depth.

Computer-aided detection of masses in digital tomosynthesis mammography: Comparison of three approaches

International Nuclear Information System (INIS)

Chan Heangping; Wei Jun; Zhang Yiheng; Helvie, Mark A.; Moore, Richard H.; Sahiner, Berkman; Hadjiiski, Lubomir; Kopans, Daniel B.

2008-01-01

The authors are developing a computer-aided detection (CAD) system for masses on digital breast tomosynthesis mammograms (DBT). Three approaches were evaluated in this study. In the first approach, mass candidate identification and feature analysis are performed in the reconstructed three-dimensional (3D) DBT volume. A mass likelihood score is estimated for each mass candidate using a linear discriminant analysis (LDA) classifier. Mass detection is determined by a decision threshold applied to the mass likelihood score. A free response receiver operating characteristic (FROC) curve that describes the detection sensitivity as a function of the number of false positives (FPs) per breast is generated by varying the decision threshold over a range. In the second approach, prescreening of mass candidate and feature analysis are first performed on the individual two-dimensional (2D) projection view (PV) images. A mass likelihood score is estimated for each mass candidate using an LDA classifier trained for the 2D features. The mass likelihood images derived from the PVs are backprojected to the breast volume to estimate the 3D spatial distribution of the mass likelihood scores. The FROC curve for mass detection can again be generated by varying the decision threshold on the 3D mass likelihood scores merged by backprojection. In the third approach, the mass likelihood scores estimated by the 3D and 2D approaches, described above, at the corresponding 3D location are combined and evaluated using FROC analysis. A data set of 100 DBT cases acquired with a GE prototype system at the Breast Imaging Laboratory in the Massachusetts General Hospital was used for comparison of the three approaches. The LDA classifiers with stepwise feature selection were designed with leave-one-case-out resampling. In FROC analysis, the CAD system for detection in the DBT volume alone achieved test sensitivities of 80% and 90% at average FP rates of 1.94 and 3.40 per breast, respectively. With the

Entropy-optimal weight constraint elicitation with additive multi-attribute utility models

NARCIS (Netherlands)

Valkenhoef , van Gert; Tervonen, Tommi

2016-01-01

We consider the elicitation of incomplete preference information for the additive utility model in terms of linear constraints on the weights. Eliciting incomplete preferences using holistic pair-wise judgments is convenient for the decision maker, but selecting the best pair-wise comparison is

Determining an Estimate of an Equivalence Relation for Moderate and Large Sized Sets

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Leszek Klukowski

2017-01-01

Full Text Available This paper presents two approaches to determining estimates of an equivalence relation on the basis of pairwise comparisons with random errors. Obtaining such an estimate requires the solution of a discrete programming problem which minimizes the sum of the differences between the form of the relation and the comparisons. The problem is NP hard and can be solved with the use of exact algorithms for sets of moderate size, i.e. about 50 elements. In the case of larger sets, i.e. at least 200 comparisons for each element, it is necessary to apply heuristic algorithms. The paper presents results (a statistical preprocessing, which enable us to determine the optimal or a near-optimal solution with acceptable computational cost. They include: the development of a statistical procedure producing comparisons with low probabilities of errors and a heuristic algorithm based on such comparisons. The proposed approach guarantees the applicability of such estimators for any size of set. (original abstract

Partnership Selection Involving Mixed Types of Uncertain Preferences

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Li-Ching Ma

2013-01-01

Full Text Available Partnership selection is an important issue in management science. This study proposes a general model based on mixed integer programming and goal-programming analytic hierarchy process (GP-AHP to solve partnership selection problems involving mixed types of uncertain or inconsistent preferences. The proposed approach is designed to deal with crisp, interval, step, fuzzy, or mixed comparison preferences, derive crisp priorities, and improve multiple solution problems. The degree of fulfillment of a decision maker’s preferences is also taken into account. The results show that the proposed approach keeps more solution ratios within the given preferred intervals and yields less deviation. In addition, the proposed approach can treat incomplete preference matrices with flexibility in reducing the number of pairwise comparisons required and can also be conveniently developed into a decision support system.

Information systems development of analysis company financial state based on the expert-statistical approach

Directory of Open Access Journals (Sweden)

M. N. Ivliev

2016-01-01

Full Text Available The work is devoted to methods of analysis the company financial condition, including aggregated ratings. It is proposed to use the generalized solvency and liquidity indicator and the capital structure composite index. Mathematically, the generalized index is a sum of variables-characteristics and weighting factors characterizing the relative importance of individual characteristics composition. It is offered to select the significant features from a set of standard financial ratios, calculated according to enterprises balance sheets. To obtain the weighting factors values it is proposed to use one of the expert statistical approaches, the analytic hierarchy process. The method is as follows: we choose the most important characteristic and after the experts determine the degree of preference for the main feature based on the linguistic scale. Further, matrix of pairwise comparisons based on the assigned ranks is compiled, which characterizes the relative importance of attributes. The required coefficients are determined as elements of a vector of priorities, which is the first vector of the matrix of paired comparisons. The paper proposes a mechanism for finding the fields for rating numbers analysis. In addition, the paper proposes a method for the statistical evaluation of the balance sheets of various companies by calculating the mutual correlation matrices. Based on the considered mathematical methods to determine quantitative characteristics of technical objects financial and economic activities, was developed algorithms, information and software allowing to realize of different systems economic analysis.

Preference learning with evolutionary Multivariate Adaptive Regression Spline model

DEFF Research Database (Denmark)

Abou-Zleikha, Mohamed; Shaker, Noor; Christensen, Mads Græsbøll

2015-01-01

This paper introduces a novel approach for pairwise preference learning through combining an evolutionary method with Multivariate Adaptive Regression Spline (MARS). Collecting users' feedback through pairwise preferences is recommended over other ranking approaches as this method is more appealing...... for function approximation as well as being relatively easy to interpret. MARS models are evolved based on their efficiency in learning pairwise data. The method is tested on two datasets that collectively provide pairwise preference data of five cognitive states expressed by users. The method is analysed...

Coulomb-Fourier representation approach to three-body scattering with charged particles

International Nuclear Information System (INIS)

Alt, E.O.; Levin, S.B.; Yakovlev, S.L.

2004-01-01

We present a novel approach for calculating charged-composite particle scattering. It consists in eliminating by means of a suitably chosen representation that part of the interaction which is of longest range and, hence, gives rise to all the troublesome features which plague charged particle scattering theories. In this paper only the simplest case is considered, namely that of two charged and one neutral particles which interact via pairwise strong potentials, and a repulsive Coulomb potential between the charged particles

Assessing the Accuracy of Generalized Inferences From Comparison Group Studies Using a Within-Study Comparison Approach: The Methodology.

Science.gov (United States)

Jaciw, Andrew P

2016-06-01

Various studies have examined bias in impact estimates from comparison group studies (CGSs) of job training programs, and in education, where results are benchmarked against experimental results. Such within-study comparison (WSC) approaches investigate levels of bias in CGS-based impact estimates, as well as the success of various design and analytic strategies for reducing bias. This article reviews past literature and summarizes conditions under which CGSs replicate experimental benchmark results. It extends the framework to, and develops the methodology for, situations where results from CGSs are generalized to untreated inference populations. Past research is summarized; methods are developed to examine bias in program impact estimates based on cross-site comparisons in a multisite trial that are evaluated against site-specific experimental benchmarks. Students in Grades K-3 in 79 schools in Tennessee; students in Grades 4-8 in 82 schools in Alabama. Grades K-3 Stanford Achievement Test (SAT) in reading and math scores; Grades 4-8 SAT10 reading scores. Past studies show that bias in CGS-based estimates can be limited through strong design, with local matching, and appropriate analysis involving pretest covariates and variables that represent selection processes. Extension of the methodology to investigate accuracy of generalized estimates from CGSs shows bias from confounders and effect moderators. CGS results, when extrapolated to untreated inference populations, may be biased due to variation in outcomes and impact. Accounting for effects of confounders or moderators may reduce bias. © The Author(s) 2016.

A study of brain networks associated with swallowing using graph-theoretical approaches.

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Bo Luan

Full Text Available Functional connectivity between brain regions during swallowing tasks is still not well understood. Understanding these complex interactions is of great interest from both a scientific and a clinical perspective. In this study, functional magnetic resonance imaging (fMRI was utilized to study brain functional networks during voluntary saliva swallowing in twenty-two adult healthy subjects (all females, [Formula: see text] years of age. To construct these functional connections, we computed mean partial correlation matrices over ninety brain regions for each participant. Two regions were determined to be functionally connected if their correlation was above a certain threshold. These correlation matrices were then analyzed using graph-theoretical approaches. In particular, we considered several network measures for the whole brain and for swallowing-related brain regions. The results have shown that significant pairwise functional connections were, mostly, either local and intra-hemispheric or symmetrically inter-hemispheric. Furthermore, we showed that all human brain functional network, although varying in some degree, had typical small-world properties as compared to regular networks and random networks. These properties allow information transfer within the network at a relatively high efficiency. Swallowing-related brain regions also had higher values for some of the network measures in comparison to when these measures were calculated for the whole brain. The current results warrant further investigation of graph-theoretical approaches as a potential tool for understanding the neural basis of dysphagia.

Comparison of spectroscopically measured tissue alcohol concentration to blood and breath alcohol measurements

Science.gov (United States)

Ridder, Trent D.; Ver Steeg, Benjamin J.; Laaksonen, Bentley D.

2009-09-01

Alcohol testing is an expanding area of interest due to the impacts of alcohol abuse that extend well beyond drunk driving. However, existing approaches such as blood and urine assays are hampered in some testing environments by biohazard risks. A noninvasive, in vivo spectroscopic technique offers a promising alternative, as no body fluids are required. The purpose of this work is to report the results of a 36-subject clinical study designed to characterize tissue alcohol measured using near-infrared spectroscopy relative to venous blood, capillary blood, and breath alcohol. Comparison of blood and breath alcohol concentrations demonstrated significant differences in alcohol concentration [root mean square of 9.0 to 13.5 mg/dL] that were attributable to both assay accuracy and precision as well as alcohol pharmacokinetics. A first-order kinetic model was used to estimate the contribution of alcohol pharmacokinetics to the differences in concentration observed between the blood, breath, and tissue assays. All pair-wise combinations of alcohol assays were investigated, and the fraction of the alcohol concentration variance explained by pharmacokinetics ranged from 41.0% to 83.5%. Accounting for pharmacokinetic concentration differences, the accuracy and precision of the spectroscopic tissue assay were found to be comparable to those of the blood and breath assays.

Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs.

Science.gov (United States)

Lin, Chun-Yuan; Wang, Chung-Hung; Hung, Che-Lun; Lin, Yu-Shiang

2015-01-01

Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is O(n (2)), where n is the maximal length of compounds. In general, the length of compounds is tens to hundreds, and the computation time is small. However, more and more compounds have been synthesized and extracted now, even more than tens of millions. Therefore, it still will be time-consuming when comparing with a large amount of compounds (seen as a multiple compound comparison problem, abbreviated to MCC). The intrinsic time complexity of MCC problem is O(k (2) n (2)) with k compounds of maximal length n. In this paper, we propose a GPU-based algorithm for MCC problem, called CUDA-MCC, on single- and multi-GPUs. Four LINGO-based load-balancing strategies are considered in CUDA-MCC in order to accelerate the computation speed among thread blocks on GPUs. CUDA-MCC was implemented by C+OpenMP+CUDA. CUDA-MCC achieved 45 times and 391 times faster than its CPU version on a single NVIDIA Tesla K20m GPU card and a dual-NVIDIA Tesla K20m GPU card, respectively, under the experimental results.

constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints.

Science.gov (United States)

Matsen, Frederick A

2010-06-01

This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints.

Surface feeding and aggressive behaviour of diploid and triploid brown trout Salmo trutta during allopatric pair-wise matchings.

Science.gov (United States)

Preston, A C; Taylor, J F; Adams, C E; Migaud, H

2014-09-01

Diploid and triploid brown trout Salmo trutta were acclimated for 6 weeks on two feeding regimes (floating and sinking). Thereafter, aggression and surface feeding response were compared between pairs of all diploid, all triploid and diploid and triploid S. trutta in an experimental stream. In each pair-wise matching, fish of similar size were placed in allopatry and rank was determined by the total number of aggressive interactions recorded. Dominant individuals initiated more aggression than subordinates, spent more time defending a territory and positioned themselves closer to the surface food source (Gammarus pulex), whereas subordinates occupied the peripheries. In cross ploidy trials, diploid S. trutta were more aggressive than triploid, and dominated their sibling when placed in pair-wise matchings. Surface feeding, however, did not differ statistically between ploidy irrespective of feeding regime. Triploids adopted a sneak feeding strategy while diploids expended more time defending a territory. In addition, we also tested whether triploids exhibit a similar social dominance to diploids when placed in allopatry. Although aggression was lower in triploid pairs than in the diploid and triploid pairs, a dominance hierarchy was also observed between individuals of the same ploidy. Dominant triploid fish were more aggressive and consumed more feed items than subordinate individuals. Subordinate fish displayed a darker colour index than dominant fish suggesting increased stress levels. Dominant triploid fish, however, appeared to be more tolerant of subordinate individuals and did not display the same degree of invasive aggression as seen in the diploid and diploid or diploid and triploid matchings. These novel findings suggest that sterile triploid S. trutta feed similarly but are less aggressive than diploid trout. Future studies should determine the habitat choice of triploid S. trutta after release and the interaction between wild fish and triploids during

Plant lock and ant key: pairwise coevolution of an exclusion filter in an ant-plant mutualism.

Science.gov (United States)

Brouat, C; Garcia, N; Andary, C; McKey, D

2001-10-22

Although observations suggest pairwise coevolution in specific ant-plant symbioses, coevolutionary processes have rarely been demonstrated. We report on, what is to the authors' knowledge, the strongest evidence yet for reciprocal adaptation of morphological characters in a species-specific ant-plant mutualism. The plant character is the prostoma, which is a small unlignified organ at the apex of the domatia in which symbiotic ants excavate an entrance hole. Each myrmecophyte in the genus Leonardoxa has evolved a prostoma with a different shape. By performing precise measurements on the prostomata of three related myrmecophytes, on their specific associated ants and on the entrance holes excavated by symbiotic ants at the prostomata, we showed that correspondence of the plant and ant traits forms a morphological and behavioural filter. We have strong evidence for coevolution between the dimensions and shape of the symbiotic ants and the prostoma in one of the three ant-Leonardoxa associations.

Within-culture variations of uniqueness: towards an integrative approach based on social status, gender, life contexts, and interpersonal comparison.

Science.gov (United States)

Causse, Elsa; Félonneau, Marie-Line

2014-01-01

Research on uniqueness is widely focused on cross-cultural comparisons and tends to postulate a certain form of within-culture homogeneity. Taking the opposite course of this classic posture, we aimed at testing an integrative approach enabling the study of within-culture variations of uniqueness. This approach considered different sources of variation: social status, gender, life contexts, and interpersonal comparison. Four hundred seventy-nine participants completed a measure based on descriptions of "self" and "other." Results showed important variations of uniqueness. An interaction between social status and life contexts revealed the expression of uniqueness in the low-status group. This study highlights the complexity of uniqueness that appears to be related to both cultural ideology and social hierarchy.

Comparison of High, Intermediate, and Low Frequency Shock Wave Lithotripsy for Urinary Tract Stone Disease: Systematic Review and Network Meta-Analysis.

Science.gov (United States)

Kang, Dong Hyuk; Cho, Kang Su; Ham, Won Sik; Lee, Hyungmin; Kwon, Jong Kyou; Choi, Young Deuk; Lee, Joo Yong

2016-01-01

To perform a systematic review and network meta-analysis of randomized controlled trials (RCTs) to determine the optimal shock wave lithotripsy (SWL) frequency range for treating urinary stones, i.e., high-frequency (100-120 waves/minute), intermediate-frequency (80-90 waves/minute), and low-frequency (60-70 waves/minute) lithotripsy. Relevant RCTs were identified from electronic databases for meta-analysis of SWL success and complication rates. Using pairwise and network meta-analyses, comparisons were made by qualitative and quantitative syntheses. Outcome variables are provided as odds ratios (ORs) with 95% confidence intervals (CIs). Thirteen articles were included in the qualitative and quantitative synthesis using pairwise and network meta-analyses. On pairwise meta-analyses, comparable inter-study heterogeneity was observed for the success rate. On network meta-analyses, the success rates of low- (OR 2.2; 95% CI 1.5-2.6) and intermediate-frequency SWL (OR 2.5; 95% CI 1.3-4.6) were higher than high-frequency SWL. Forest plots from the network meta-analysis showed no significant differences in the success rate between low-frequency SWL versus intermediate-frequency SWL (OR 0.87; 95% CI 0.51-1.7). There were no differences in complication rate across different SWL frequency ranges. By rank-probability testing, intermediate-frequency SWL was ranked highest for success rate, followed by low-frequency and high-frequency SWL. Low-frequency SWL was also ranked highest for low complication rate, with high- and intermediate-frequency SWL ranked lower. Intermediate- and low-frequency SWL have better treatment outcomes than high-frequency SWL when considering both efficacy and complication.

Comparison of different approaches of modelling in a masonry building

Science.gov (United States)

Saba, M.; Meloni, D.

2017-12-01

The present work has the objective to model a simple masonry building, through two different modelling methods in order to assess their validity in terms of evaluation of static stresses. Have been chosen two of the most commercial software used to address this kind of problem, which are of S.T.A. Data S.r.l. and Sismicad12 of Concrete S.r.l. While the 3Muri software adopts the Frame by Macro Elements Method (FME), which should be more schematic and more efficient, Sismicad12 software uses the Finite Element Method (FEM), which guarantees accurate results, with greater computational burden. Remarkably differences of the static stresses, for such a simple structure between the two approaches have been found, and an interesting comparison and analysis of the reasons is proposed.

A Generic multi-dimensional feature extraction method using multiobjective genetic programming.

Science.gov (United States)

Zhang, Yang; Rockett, Peter I

2009-01-01

In this paper, we present a generic feature extraction method for pattern classification using multiobjective genetic programming. This not only evolves the (near-)optimal set of mappings from a pattern space to a multi-dimensional decision space, but also simultaneously optimizes the dimensionality of that decision space. The presented framework evolves vector-to-vector feature extractors that maximize class separability. We demonstrate the efficacy of our approach by making statistically-founded comparisons with a wide variety of established classifier paradigms over a range of datasets and find that for most of the pairwise comparisons, our evolutionary method delivers statistically smaller misclassification errors. At very worst, our method displays no statistical difference in a few pairwise comparisons with established classifier/dataset combinations; crucially, none of the misclassification results produced by our method is worse than any comparator classifier. Although principally focused on feature extraction, feature selection is also performed as an implicit side effect; we show that both feature extraction and selection are important to the success of our technique. The presented method has the practical consequence of obviating the need to exhaustively evaluate a large family of conventional classifiers when faced with a new pattern recognition problem in order to attain a good classification accuracy.

Propensity-score matching in economic analyses: comparison with regression models, instrumental variables, residual inclusion, differences-in-differences, and decomposition methods.

Science.gov (United States)

Crown, William H

2014-02-01

This paper examines the use of propensity score matching in economic analyses of observational data. Several excellent papers have previously reviewed practical aspects of propensity score estimation and other aspects of the propensity score literature. The purpose of this paper is to compare the conceptual foundation of propensity score models with alternative estimators of treatment effects. References are provided to empirical comparisons among methods that have appeared in the literature. These comparisons are available for a subset of the methods considered in this paper. However, in some cases, no pairwise comparisons of particular methods are yet available, and there are no examples of comparisons across all of the methods surveyed here. Irrespective of the availability of empirical comparisons, the goal of this paper is to provide some intuition about the relative merits of alternative estimators in health economic evaluations where nonlinearity, sample size, availability of pre/post data, heterogeneity, and missing variables can have important implications for choice of methodology. Also considered is the potential combination of propensity score matching with alternative methods such as differences-in-differences and decomposition methods that have not yet appeared in the empirical literature.

Pairwise Sequence Alignment Library

Energy Technology Data Exchange (ETDEWEB)

2015-05-20

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny.

Science.gov (United States)

Maddock, Simon T; Briscoe, Andrew G; Wilkinson, Mark; Waeschenbach, Andrea; San Mauro, Diego; Day, Julia J; Littlewood, D Tim J; Foster, Peter G; Nussbaum, Ronald A; Gower, David J

2016-01-01

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina's HiSeq and MiSeq, Roche's 454 GS FLX, and Life Technologies' Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case.

Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny.

Directory of Open Access Journals (Sweden)

Simon T Maddock

Full Text Available Mitochondrial genome (mitogenome sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing on four different sequencing platforms (Illumina's HiSeq and MiSeq, Roche's 454 GS FLX, and Life Technologies' Ion Torrent to produce seven (near- complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case.

Multiple Score Comparison: a network meta-analysis approach to comparison and external validation of prognostic scores

Directory of Open Access Journals (Sweden)

Sarah R. Haile

2017-12-01

Full Text Available Abstract Background Prediction models and prognostic scores have been increasingly popular in both clinical practice and clinical research settings, for example to aid in risk-based decision making or control for confounding. In many medical fields, a large number of prognostic scores are available, but practitioners may find it difficult to choose between them due to lack of external validation as well as lack of comparisons between them. Methods Borrowing methodology from network meta-analysis, we describe an approach to Multiple Score Comparison meta-analysis (MSC which permits concurrent external validation and comparisons of prognostic scores using individual patient data (IPD arising from a large-scale international collaboration. We describe the challenges in adapting network meta-analysis to the MSC setting, for instance the need to explicitly include correlations between the scores on a cohort level, and how to deal with many multi-score studies. We propose first using IPD to make cohort-level aggregate discrimination or calibration scores, comparing all to a common comparator. Then, standard network meta-analysis techniques can be applied, taking care to consider correlation structures in cohorts with multiple scores. Transitivity, consistency and heterogeneity are also examined. Results We provide a clinical application, comparing prognostic scores for 3-year mortality in patients with chronic obstructive pulmonary disease using data from a large-scale collaborative initiative. We focus on the discriminative properties of the prognostic scores. Our results show clear differences in performance, with ADO and eBODE showing higher discrimination with respect to mortality than other considered scores. The assumptions of transitivity and local and global consistency were not violated. Heterogeneity was small. Conclusions We applied a network meta-analytic methodology to externally validate and concurrently compare the prognostic properties

PSA data base, comparison of the German and French approach

International Nuclear Information System (INIS)

Kreuser, A.; Tirira, J.

2001-01-01

The results of probabilistic safety assessments (PSA) of nuclear power plants strongly depend on the reliability data used. This report describes coarsely the general process to generate reliability data for components and resumes the differences between the German and French approaches. As has been shown in former studies which compared international PSA data, PSA data are closely related to the model definitions of the PSA. Therefore single PSA data cannot be compared directly without regard e.g. to the corresponding fault trees. These findings are confirmed by this study. The comparison of German and French methods shows a lot of differences concerning various details of the data generation process. Some differences between single reliability data should be eliminated when taking into account the complete fault tree analysis. But there are some other differences which have a direct impact on the obtained results of a PSA. In view of the all differences between both approaches concerning the definition of data and the data collection process, it is not possible to compare directly German and French PSA data. However, the database differences give no indication on the influence on the PSA results. Therefore, it is a need to perform a common IPSN/GRS assessment on how the different databases impact the PSA results. (orig.)

Urban pavement surface temperature. Comparison of numerical and statistical approach

Science.gov (United States)

Marchetti, Mario; Khalifa, Abderrahmen; Bues, Michel; Bouilloud, Ludovic; Martin, Eric; Chancibaut, Katia

2015-04-01

The forecast of pavement surface temperature is very specific in the context of urban winter maintenance. to manage snow plowing and salting of roads. Such forecast mainly relies on numerical models based on a description of the energy balance between the atmosphere, the buildings and the pavement, with a canyon configuration. Nevertheless, there is a specific need in the physical description and the numerical implementation of the traffic in the energy flux balance. This traffic was originally considered as a constant. Many changes were performed in a numerical model to describe as accurately as possible the traffic effects on this urban energy balance, such as tires friction, pavement-air exchange coefficient, and infrared flux neat balance. Some experiments based on infrared thermography and radiometry were then conducted to quantify the effect fo traffic on urban pavement surface. Based on meteorological data, corresponding pavement temperature forecast were calculated and were compared with fiels measurements. Results indicated a good agreement between the forecast from the numerical model based on this energy balance approach. A complementary forecast approach based on principal component analysis (PCA) and partial least-square regression (PLS) was also developed, with data from thermal mapping usng infrared radiometry. The forecast of pavement surface temperature with air temperature was obtained in the specific case of urban configurtation, and considering traffic into measurements used for the statistical analysis. A comparison between results from the numerical model based on energy balance, and PCA/PLS was then conducted, indicating the advantages and limits of each approach.

Heisenberg coupling constant predicted for molecular magnets with pairwise spin-contamination correction

Energy Technology Data Exchange (ETDEWEB)

Masunov, Artëm E., E-mail: amasunov@ucf.edu [NanoScience Technology Center, Department of Chemistry, and Department of Physics, University of Central Florida, Orlando, FL 32826 (United States); Photochemistry Center RAS, ul. Novatorov 7a, Moscow 119421 (Russian Federation); Gangopadhyay, Shruba [Department of Physics, University of California, Davis, CA 95616 (United States); IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120 (United States)

2015-12-15

New method to eliminate the spin-contamination in broken symmetry density functional theory (BS DFT) calculations is introduced. Unlike conventional spin-purification correction, this method is based on canonical Natural Orbitals (NO) for each high/low spin coupled electron pair. We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher spin state built on these bonding and antibonding NOs (not self-consistent Kohn–Sham orbitals of the high spin state). Compared to the other spin-contamination correction schemes, spin-correction is applied to each correlated electron pair individually. We investigate two binuclear Mn(IV) molecular magnets using this pairwise correction. While one of the molecules is described by magnetic orbitals strongly localized on the metal centers, and spin gap is accurately predicted by Noodleman and Yamaguchi schemes, for the other one the gap is predicted poorly by these schemes due to strong delocalization of the magnetic orbitals onto the ligands. We show our new correction to yield more accurate results in both cases. - Highlights: • Magnetic orbitails obtained for high and low spin states are not related. • Spin-purification correction becomes inaccurate for delocalized magnetic orbitals. • We use the natural orbitals of the broken symmetry state to build high spin state. • This new correction is made separately for each electron pair. • Our spin-purification correction is more accurate for delocalised magnetic orbitals.

Galaxy and Mass Assembly (GAMA): small-scale anisotropic galaxy clustering and the pairwise velocity dispersion of galaxies

Science.gov (United States)

Loveday, J.; Christodoulou, L.; Norberg, P.; Peacock, J. A.; Baldry, I. K.; Bland-Hawthorn, J.; Brown, M. J. I.; Colless, M.; Driver, S. P.; Holwerda, B. W.; Hopkins, A. M.; Kafle, P. R.; Liske, J.; Lopez-Sanchez, A. R.; Taylor, E. N.

2018-03-01

The galaxy pairwise velocity dispersion (PVD) can provide important tests of non-standard gravity and galaxy formation models. We describe measurements of the PVD of galaxies in the Galaxy and Mass Assembly (GAMA) survey as a function of projected separation and galaxy luminosity. Due to the faint magnitude limit (r PVD to smaller scales (r⊥ = 0.01 h - 1 Mpc) than previous work. The measured PVD at projected separations r⊥ ≲ 1 h - 1 Mpc increases near monotonically with increasing luminosity from σ12 ≈ 200 km s - 1 at Mr = -17 mag to σ12 ≈ 600 km s - 1 at Mr ≈ -22 mag. Analysis of the Gonzalez-Perez et al. (2014) GALFORM semi-analytic model yields no such trend of PVD with luminosity: the model overpredicts the PVD for faint galaxies. This is most likely a result of the model placing too many low-luminosity galaxies in massive haloes.

Integration of fuzzy reasoning approach (FRA and fuzzy analytic hierarchy process (FAHP for risk assessment in mining industry

Directory of Open Access Journals (Sweden)

Shikha Verma

2014-10-01

Full Text Available Purpose: Mining industry has always been known for its unsafe working environment. This industry is one of the most hazard prone industries. To maintain safety in workplace timely assessment of risk associated with different operations performed to extract ore from the ore body has become necessity. To serve the said purpose, present work demonstrates a robust hybrid risk assessment approach for mining industry.Design/Methodology: Accident data from 1995 to 2012 is reviewed to identify hazards contributed to negative outcomes. The FRA approach is implemented to evaluate the risk levels associated with identified hazard factors. Thereafter AHP pairwise comparison matrix is developed to obtain priority weights for the hazard factors. Final priority of hazards based on severity of level of risk associated with them is obtained considering the outcome of FRA approach in terms of risk score for the hazards, combined with the priority weights obtained from AHP technique.Findings: Defuzzified FAHP weight of hazard factors, this weight gives priority sequence of hazards to be considered for development of plan of mitigation.Originality/Value: Risk assessment is a requirement of the Occupational Health and Safety Act 2000 (Section 7& 8. The data required to assess the risk is uncertain, and in such case fuzzy approach is well suited to process the data and get the crisp output. The output of fuzzy approach is made robust with its integration to AHP. In this way FAHP can be used as robust technique for risk assessment in this industry and this technique develops an efficient safety management system for the achievement of goal to develop the workplace with zero accident, which many other countries have already achieved.

Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs

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Chun-Yuan Lin

2015-01-01

Full Text Available Compound comparison is an important task for the computational chemistry. By the comparison results, potential inhibitors can be found and then used for the pharmacy experiments. The time complexity of a pairwise compound comparison is O(n2, where n is the maximal length of compounds. In general, the length of compounds is tens to hundreds, and the computation time is small. However, more and more compounds have been synthesized and extracted now, even more than tens of millions. Therefore, it still will be time-consuming when comparing with a large amount of compounds (seen as a multiple compound comparison problem, abbreviated to MCC. The intrinsic time complexity of MCC problem is O(k2n2 with k compounds of maximal length n. In this paper, we propose a GPU-based algorithm for MCC problem, called CUDA-MCC, on single- and multi-GPUs. Four LINGO-based load-balancing strategies are considered in CUDA-MCC in order to accelerate the computation speed among thread blocks on GPUs. CUDA-MCC was implemented by C+OpenMP+CUDA. CUDA-MCC achieved 45 times and 391 times faster than its CPU version on a single NVIDIA Tesla K20m GPU card and a dual-NVIDIA Tesla K20m GPU card, respectively, under the experimental results.

Discovery of resources using MADM approaches for parallel and distributed computing

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Mandeep Kaur

2017-06-01

Full Text Available Grid, a form of parallel and distributed computing, allows the sharing of data and computational resources among its users from various geographical locations. The grid resources are diverse in terms of their underlying attributes. The majority of the state-of-the-art resource discovery techniques rely on the static resource attributes during resource selection. However, the matching resources based on the static resource attributes may not be the most appropriate resources for the execution of user applications because they may have heavy job loads, less storage space or less working memory (RAM. Hence, there is a need to consider the current state of the resources in order to find the most suitable resources. In this paper, we have proposed a two-phased multi-attribute decision making (MADM approach for discovery of grid resources by using P2P formalism. The proposed approach considers multiple resource attributes for decision making of resource selection and provides the best suitable resource(s to grid users. The first phase describes a mechanism to discover all matching resources and applies SAW method to shortlist the top ranked resources, which are communicated to the requesting super-peer. The second phase of our proposed methodology applies integrated MADM approach (AHP enriched PROMETHEE-II on the list of selected resources received from different super-peers. The pairwise comparison of the resources with respect to their attributes is made and the rank of each resource is determined. The top ranked resource is then communicated to the grid user by the grid scheduler. Our proposed methodology enables the grid scheduler to allocate the most suitable resource to the user application and also reduces the search complexity by filtering out the less suitable resources during resource discovery.

Technical note: Comparison of methane ebullition modelling approaches used in terrestrial wetland models

Science.gov (United States)

Peltola, Olli; Raivonen, Maarit; Li, Xuefei; Vesala, Timo

2018-02-01

Emission via bubbling, i.e. ebullition, is one of the main methane (CH4) emission pathways from wetlands to the atmosphere. Direct measurement of gas bubble formation, growth and release in the peat-water matrix is challenging and in consequence these processes are relatively unknown and are coarsely represented in current wetland CH4 emission models. In this study we aimed to evaluate three ebullition modelling approaches and their effect on model performance. This was achieved by implementing the three approaches in one process-based CH4 emission model. All the approaches were based on some kind of threshold: either on CH4 pore water concentration (ECT), pressure (EPT) or free-phase gas volume (EBG) threshold. The model was run using 4 years of data from a boreal sedge fen and the results were compared with eddy covariance measurements of CH4 fluxes.Modelled annual CH4 emissions were largely unaffected by the different ebullition modelling approaches; however, temporal variability in CH4 emissions varied an order of magnitude between the approaches. Hence the ebullition modelling approach drives the temporal variability in modelled CH4 emissions and therefore significantly impacts, for instance, high-frequency (daily scale) model comparison and calibration against measurements. The modelling approach based on the most recent knowledge of the ebullition process (volume threshold, EBG) agreed the best with the measured fluxes (R2 = 0.63) and hence produced the most reasonable results, although there was a scale mismatch between the measurements (ecosystem scale with heterogeneous ebullition locations) and model results (single horizontally homogeneous peat column). The approach should be favoured over the two other more widely used ebullition modelling approaches and researchers are encouraged to implement it into their CH4 emission models.

Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.

Science.gov (United States)

Aeschbacher, S; Futschik, A; Beaumont, M A

2013-02-01

We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction. © 2013 Blackwell Publishing Ltd.

Pairwise NMR experiments for the determination of protein backbone dihedral angle Φ based on cross-correlated spin relaxation

International Nuclear Information System (INIS)

Takahashi, Hideo; Shimada, Ichio

2007-01-01

Novel cross-correlated spin relaxation (CCR) experiments are described, which measure pairwise CCR rates for obtaining peptide dihedral angles Φ. The experiments utilize intra-HNCA type coherence transfer to refocus 2-bond J NCα coupling evolution and generate the N (i)-C α (i) or C'(i-1)-C α (i) multiple quantum coherences which are required for measuring the desired CCR rates. The contribution from other coherences is also discussed and an appropriate setting of the evolution delays is presented. These CCR experiments were applied to 15 N- and 13 C-labeled human ubiquitin. The relevant CCR rates showed a high degree of correlation with the Φ angles observed in the X-ray structure. By utilizing these CCR experiments in combination with those previously established for obtaining dihedral angle Ψ, we can determine high resolution structures of peptides that bind weakly to large target molecules

An Integrated model for Product Quality Development—A case study on Quality functions deployment and AHP based approach

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Maitra, Subrata; Banerjee, Debamalya

2010-10-01

Present article is based on application of the product quality and improvement of design related with the nature of failure of machineries and plant operational problems of an industrial blower fan Company. The project aims at developing the product on the basis of standardized production parameters for selling its products in the market. Special attention is also being paid to the blower fans which have been ordered directly by the customer on the basis of installed capacity of air to be provided by the fan. Application of quality function deployment is primarily a customer oriented approach. Proposed model of QFD integrated with AHP to select and rank the decision criterions on the commercial and technical factors and the measurement of the decision parameters for selection of best product in the compettitive environment. The present AHP-QFD model justifies the selection of a blower fan with the help of the group of experts' opinion by pairwise comparison of the customer's and ergonomy based technical design requirements. The steps invoved in implementation of the QFD—AHP and selection of weighted criterion may be helpful for all similar purpose industries maintaining cost and utility for competitive product.

Verification and validation of decision support software: Expert Choice{trademark} and PCM{trademark}

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Q.H.; Martin, J.D.

1994-11-04

This report documents the verification and validation of two decision support programs: EXPERT CHOICE{trademark} and PCM{trademark}. Both programs use the Analytic Hierarchy Process (AHP) -- or pairwise comparison technique -- developed by Dr. Thomas L. Saaty. In order to provide an independent method for the validating the two programs, the pairwise comparison algorithm was developed for a standard mathematical program. A standard data set -- selecting a car to purchase -- was used with each of the three programs for validation. The results show that both commercial programs performed correctly.

Biotic interactions in the face of climate change: a comparison of three modelling approaches.

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Anja Jaeschke

Full Text Available Climate change is expected to alter biotic interactions, and may lead to temporal and spatial mismatches of interacting species. Although the importance of interactions for climate change risk assessments is increasingly acknowledged in observational and experimental studies, biotic interactions are still rarely incorporated in species distribution models. We assessed the potential impacts of climate change on the obligate interaction between Aeshna viridis and its egg-laying plant Stratiotes aloides in Europe, based on an ensemble modelling technique. We compared three different approaches for incorporating biotic interactions in distribution models: (1 We separately modelled each species based on climatic information, and intersected the future range overlap ('overlap approach'. (2 We modelled the potential future distribution of A. viridis with the projected occurrence probability of S. aloides as further predictor in addition to climate ('explanatory variable approach'. (3 We calibrated the model of A. viridis in the current range of S. aloides and multiplied the future occurrence probabilities of both species ('reference area approach'. Subsequently, all approaches were compared to a single species model of A. viridis without interactions. All approaches projected a range expansion for A. viridis. Model performance on test data and amount of range gain differed depending on the biotic interaction approach. All interaction approaches yielded lower range gains (up to 667% lower than the model without interaction. Regarding the contribution of algorithm and approach to the overall uncertainty, the main part of explained variation stems from the modelling algorithm, and only a small part is attributed to the modelling approach. The comparison of the no-interaction model with the three interaction approaches emphasizes the importance of including obligate biotic interactions in projective species distribution modelling. We recommend the use of

Climate change convention : reallocation of carbon dioxide emissions; Convenzione sui cambiamenti climatici: ipotesi per una assegnazione di quote di emissioni di anidride carbonica

Energy Technology Data Exchange (ETDEWEB)

Turchetti, P; Venanzi, M [ENEA, Centro Ricerche Casaccia, Rome (Italy). Dip. Ambiente

1995-07-01

In 1992, during the United Nation`s Conference on Environment and Development, held in Rio de Janeiro, the Framework Convention on Climate Change was signed. The ultimate objective of this Convention is the control and the reduction of greenhouse gas releases from human activities, to achieve stabilization of greenhouse gas concentrations in the atmosphere. The purpose of this research is to provide a reallocation of carbon dioxide important greenhouse gas, among nine countries representing the different geopolitical worldwide situations. Demographic, socioeconomic and environmental criteria have been taken into account. Some of these issues have been proposed in the international negotiating context. In order to apportion emissions the Analytic Hierarchy Process (AHP) has been used. The AHP is a multi objective decision-making technique employing a method of pairwise comparisons to rank order alternatives of a problem formulated in a hierarchic structure by computing the largest eigenvalue of the pairwise comparisons matrix. Moreover, the AHP approach enables one to deal with both quantitative and qualitative factors in a logical fashion. The findings summarize the different indicators considered representing the proposals of the parties involved in the international debate.

Entropy production rate as a criterion for inconsistency in decision theory

Science.gov (United States)

Dixit, Purushottam D.

2018-05-01

Individual and group decisions are complex, often involving choosing an apt alternative from a multitude of options. Evaluating pairwise comparisons breaks down such complex decision problems into tractable ones. Pairwise comparison matrices (PCMs) are regularly used to solve multiple-criteria decision-making problems, for example, using Saaty’s analytic hierarchy process (AHP) framework. However, there are two significant drawbacks of using PCMs. First, humans evaluate PCMs in an inconsistent manner. Second, not all entries of a large PCM can be reliably filled by human decision makers. We address these two issues by first establishing a novel connection between PCMs and time-irreversible Markov processes. Specifically, we show that every PCM induces a family of dissipative maximum path entropy random walks (MERW) over the set of alternatives. We show that only ‘consistent’ PCMs correspond to detailed balanced MERWs. We identify the non-equilibrium entropy production in the induced MERWs as a metric of inconsistency of the underlying PCMs. Notably, the entropy production satisfies all of the recently laid out criteria for reasonable consistency indices. We also propose an approach to use incompletely filled PCMs in AHP. Potential future avenues are discussed as well.

Understanding students' motivation in project work: a 2 x 2 achievement goal approach.

Science.gov (United States)

Liu, Woon Chia; Wang, C K John; Tan, Oon Seng; Ee, Jessie; Koh, Caroline

2009-03-01

The project work (PW) initiative was launched in 2000 by the Ministry of Education, Singapore, to encourage application of knowledge across disciplines, and to develop thinking, communication, collaboration, and metacognitive skills. Although PW has been introduced for a few years, few studies have examined the motivation of students in PW, especially with the use of the recently proposed 2 x 2 achievement goal framework. To use a cluster analytic approach to identify students' achievement goal profiles at an intra-individual level, and to examine their links to various psychological characteristics and perceived outcomes in PW. Participants were 491 Secondary 2 students (mean age = 13.78, SD = 0.77) from two government coeducational schools. Cluster analysis was performed to identify distinct subgroups of students with similar achievement goal profiles. One-way MANOVAs, followed by post hoc Tukey HSD tests for pairwise comparisons were used to determine whether there was any significant difference amongst clusters in terms of the psychological characteristics and perceived outcomes in PW. Four distinct clusters of students were identified. The cluster with high achievement goals and the cluster with moderately high goals had the most positive psychological characteristics and perceived outcomes. In contrast, the cluster with very low scores for all four achievement goals had the most maladaptive profile. The study provides support for the 2 x 2 achievement goal framework, and demonstrates that multiple goals can operate simultaneously. However, it highlights the need for cross-cultural studies to look into the approach-avoidance dimension in the 2 x 2 achievement goal framework.

Evaluating the effect of corridors and landscape heterogeneity on dispersal probability: a comparison of three spatially explicit modelling approaches

DEFF Research Database (Denmark)

Jepsen, J. U.; Baveco, J. M.; Topping, C. J.

2004-01-01

preferences of the modeller, rather than by a critical evaluation of model performance. We present a comparison of three common spatial simulation approaches (patch-based incidence-function model (IFM), individual-based movement model (IBMM), individual-based population model including detailed behaviour...

Primary total hip arthroplasty: a comparison of the lateral Hardinge approach to an anterior mini-invasive approach

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Nathan Wayne

2009-11-01

Full Text Available The anterior mini-invasive (MI approach to performing total hip arthroplasty (THA is associated with less soft tissue damage and shorter postoperative recovery than other methods. Our hospital recently abandoned the traditional lateral Hardinge (LH approach in favour of this new method. We compared the first 100 patients operated after the changeover to the new method (MI group to the last 100 patients operated using the traditional method (LH group. Clinical and radiological parameters and complications were recorded pre- and postoperatively and the collected data of the two groups were statistically compared. There were no statistically significant differences between either group with regard to patient demographics or procedural data, placement of the femur component, postoperative leg discrepancy, prosthesis dislocation, blood transfusion, or postoperative dislocation of the components. The MI group had a significantly longer operating time, more bleeding, higher rate of nerve damage, and a higher percentage of acetabular component malposition whilst having a significantly shorter hospital stay and significantly fewer infections of the operative site in comparison to the LH group. Additionally, and perhaps most worrying was the clinically significant increase in intraoperative femur fractures in the MI group. The changeover to the anterior mini-invasive approach, which was the surgeons' initial experience with the MI technique, resulted in a drastic increase in the number of overall complications accompanied by less soft tissue damage and a shorter period of rehabilitation. Our results suggest that further analysis of this surgical MI technique will be needed before it can be recommended for widespread adoption.

Comparison of gimbal approaches to decrease drag force and radar cross sectional area in missile application

Science.gov (United States)

Sakarya, Doǧan Uǧur

2017-05-01

Drag force effect is an important aspect of range performance in missile applications especially for long flight time. However, old fashioned gimbal approaches force to increase missile diameter. This increase has negative aspect of rising in both drag force and radar cross sectional area. A new gimbal approach was proposed recently. It uses a beam steering optical arrangement. Therefore, it needs less volume envelope for same field of regard and same optomechanical assembly than the old fashioned gimbal approaches. In addition to longer range performance achieved with same fuel in the new gimbal approach, this method provides smaller cross sectional area which can be more invisible in enemies' radar. In this paper, the two gimbal approaches - the old fashioned one and the new one- are compared in order to decrease drag force and radar cross sectional area in missile application. In this study; missile parameters are assumed to generate gimbal and optical design parameters. Optical design is performed according to these missile criteria. Two gimbal configurations are designed with respect to modeled missile parameters. Also analyzes are performed to show decreased drag force and radar cross sectional area in the new approach for comparison.

Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut.

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Vincent Raquin

2017-12-01

Full Text Available Dengue virus (DENV causes more human infections than any other mosquito-borne virus. The current lack of antiviral strategies has prompted genome-wide screens for host genes that are required for DENV infectivity. Earlier transcriptomic studies that identified DENV host factors in the primary vector Aedes aegypti used inbred laboratory colonies and/or pools of mosquitoes that erase individual variation. Here, we performed transcriptome sequencing on individual midguts in a field-derived Ae. aegypti population to identify new candidate host factors modulating DENV replication. We analyzed the transcriptomic data using an approach that accounts for individual co-variation between viral RNA load and gene expression. This approach generates a prediction about the agonist or antagonist effect of candidate genes on DENV replication based on the sign of the correlation between gene expression and viral RNA load. Using this method, we identified 39 candidate genes that went undetected by conventional pairwise comparison of gene expression levels between DENV-infected midguts and uninfected controls. Only four candidate genes were detected by both methods, emphasizing their complementarity. We demonstrated the value of our approach by functional validation of a candidate agonist gene encoding a sterol regulatory element-binding protein (SREBP, which was identified by correlation analysis but not by pairwise comparison. We confirmed that SREBP promotes DENV infection in the midgut by RNAi-mediated gene knockdown in vivo. We suggest that our approach for transcriptomic analysis can empower genome-wide screens for potential agonist or antagonist factors by leveraging inter-individual variation in gene expression. More generally, this method is applicable to a wide range of phenotypic traits displaying inter-individual variation.

Enabling task-based information prioritization via semantic web encodings

Science.gov (United States)

Michaelis, James R.

2016-05-01

Modern Soldiers rely upon accurate and actionable information technology to achieve mission objectives. While increasingly rich sensor networks for Areas of Operation (AO) can offer many directions for aiding Soldiers, limitations are imposed by current tactical edge systems on the rate that content can be transmitted. Furthermore, mission tasks will often require very specific sets of information which may easily be drowned out by other content sources. Prior research on Quality and Value of Information (QoI/VoI) has aimed to define ways to prioritize information objects based on their intrinsic attributes (QoI) and perceived value to a consumer (VoI). As part of this effort, established ranking approaches for obtaining Subject Matter Expert (SME) recommendations, such as the Analytic Hierarchy Process (AHP) have been considered. However, limited work has been done to tie Soldier context - such as descriptions of their mission and tasks - back to intrinsic attributes of information objects. As a first step toward addressing the above challenges, this work introduces an ontology-backed approach - rooted in Semantic Web publication practices - for expressing both AHP decision hierarchies and corresponding SME feedback. Following a short discussion on related QoI/VoI research, an ontology-based data structure is introduced for supporting evaluation of Information Objects, using AHP rankings designed to facilitate information object prioritization. Consistent with alternate AHP approaches, prioritization in this approach is based on pairwise comparisons between Information Objects with respect to established criteria, as well as on pairwise comparison of the criteria to assess their relative importance. The paper concludes with a discussion of both ongoing and future work.

A hybrid fuzzy MCDM approach to maintenance Quality Function Deployment

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Davy George Valavi

2015-01-01

Full Text Available Maintenance Quality Function Deployment (MQFD is a model, which enhances the synergic power of Quality Function Deployment (QFD and Total Productive Maintenance (TPM. One of the crucial and important steps during the implementation of MQFD is the determination of the importance or weightages of the critical factors (CF and sub factors (SF. The CFs and SFs have to be compared precisely for the successful implementation of MQFD. The crisp pair-wise comparison in the conventional Analytical Hierarchy Process (AHP may be insufficient to determine the degree of weightage of CFs and SFs where vagueness and uncetainties are associated. In this paper, a modification of AHP based MQFD by incorporating fuzzy operations is proposed, which can improve the accuracy of determination of the weightages. A case study showing the applicability of this method is illustrated in this paper.

A comparison of trans-cranial and trans-sphenoidal approaches for vision improvement due to pitutary adenomas

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Fakhr Tabatabai SA

1997-07-01

Full Text Available To improve visual disturbance, optic nerve decompression can be performed via transcranial or tran-sphenoidal approaches. Although the surgical exposure in transcranial approach is favourable, yet the optic nerve's presence in the field may make it vulnerable to damage. Of fighty patients with different types of pituitary adenomas, 35 cases with medium-sized (1-3 cm tumors have been studied in a randomized clinical trial during a three year period, to compare the applicability of these approaches. While short hospital stay with better visual outcome was observed in fifteen trans-sphenoidal cases, in comparison to 20 trans-cranial cases, however the preoperative visual status and underlying disorders were similar in both groups. Decompressing the optic apparatus, trans-sphenoidally, seems beneficial, where there are no contraindications for the procedure in medium-sized pituitary adenomas

Market-based approaches to tree valuation

Science.gov (United States)

Geoffrey H. Donovan; David T. Butry

2008-01-01

A recent four-part series in Arborist News outlined different appraisal processes used to value urban trees. The final article in the series described the three generally accepted approaches to tree valuation: the sales comparison approach, the cost approach, and the income capitalization approach. The author, D. Logan Nelson, noted that the sales comparison approach...

Comparison of Exposure in the Kaplan Versus the Kocher Approach in the Treatment of Radial Head Fractures.

Science.gov (United States)

Barnes, Leslie Fink; Lombardi, Joseph; Gardner, Thomas R; Strauch, Robert J; Rosenwasser, Melvin P

2018-01-01

The aim of this study was to compare the complete visible surface area of the radial head, neck, and coronoid in the Kaplan and Kocher approaches to the lateral elbow. The hypothesis was that the Kaplan approach would afford greater visibility due to the differential anatomy of the intermuscular planes. Ten cadavers were dissected with the Kaplan and Kocher approaches, and the visible surface area was measured in situ using a 3-dimensional digitizer. Six measurements were taken for each approach by 2 surgeons, and the mean of these measurements were analyzed. The mean surface area visible with the lateral collateral ligament (LCL) preserved in the Kaplan approach was 616.6 mm 2 in comparison with the surface area of 136.2 mm 2 visible in the Kocher approach when the LCL was preserved. Using a 2-way analysis of variance, the difference between these 2 approaches was statistically significant. When the LCL complex was incised in the Kocher approach, the average visible surface area of the Kocher approach was 456.1 mm 2 and was statistically less than the Kaplan approach. The average surface area of the coronoid visible using a proximally extended Kaplan approach was 197.8 mm 2 . The Kaplan approach affords significantly greater visible surface area of the proximal radius than the Kocher approach.

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.

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Jakob H Havgaard

2007-10-01

Full Text Available It has become clear that noncoding RNAs (ncRNA play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist computational methods that can be used to search for ncRNAs by comparing sequences from different genomes. One main problem with these methods is their computational complexity, and heuristics are therefore employed. Two heuristics are currently very popular: pre-folding and pre-aligning. However, these heuristics are not ideal, as pre-aligning is dependent on sequence similarity that may not be present and pre-folding ignores the comparative information. Here, pruning of the dynamical programming matrix is presented as an alternative novel heuristic constraint. All subalignments that do not exceed a length-dependent minimum score are discarded as the matrix is filled out, thus giving the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained. Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool for searching for new ncRNAs. The software package is available for download at http://foldalign.ku.dk.

A Two-Stage Penalized Logistic Regression Approach to Case-Control Genome-Wide Association Studies

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Jingyuan Zhao

2012-01-01

Full Text Available We propose a two-stage penalized logistic regression approach to case-control genome-wide association studies. This approach consists of a screening stage and a selection stage. In the screening stage, main-effect and interaction-effect features are screened by using L1-penalized logistic like-lihoods. In the selection stage, the retained features are ranked by the logistic likelihood with the smoothly clipped absolute deviation (SCAD penalty (Fan and Li, 2001 and Jeffrey’s Prior penalty (Firth, 1993, a sequence of nested candidate models are formed, and the models are assessed by a family of extended Bayesian information criteria (J. Chen and Z. Chen, 2008. The proposed approach is applied to the analysis of the prostate cancer data of the Cancer Genetic Markers of Susceptibility (CGEMS project in the National Cancer Institute, USA. Simulation studies are carried out to compare the approach with the pair-wise multiple testing approach (Marchini et al. 2005 and the LASSO-patternsearch algorithm (Shi et al. 2007.

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

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Morozov Alexandre V

2009-08-01

Full Text Available Abstract Background The reaction of HIV protease to inhibitor therapy is characterized by the emergence of complex mutational patterns which confer drug resistance. The response of HIV protease to drugs often involves both primary mutations that directly inhibit the action of the drug, and a host of accessory resistance mutations that may occur far from the active site but may contribute to restoring the fitness or stability of the enzyme. Here we develop a probabilistic approach based on connected information that allows us to study residue, pair level and higher-order correlations within the same framework. Results We apply our methodology to a database of approximately 13,000 sequences which have been annotated by the treatment history of the patients from which the samples were obtained. We show that including pair interactions is essential for agreement with the mutational data, since neglect of these interactions results in order-of-magnitude errors in the probabilities of the simultaneous occurence of many mutations. The magnitude of these pair correlations changes dramatically between sequences obtained from patients that were or were not exposed to drugs. Higher-order effects make a contribution of as much as 10% for residues taken three at a time, but increase to more than twice that for 10 to 15-residue groups. The sequence data is insufficient to determine the higher-order effects for larger groups. We find that higher-order interactions have a significant effect on the predicted frequencies of sequences with large numbers of mutations. While relatively rare, such sequences are more prevalent after multi-drug therapy. The relative importance of these higher-order interactions increases with the number of drugs the patient had been exposed to. Conclusion Correlations are critical for the understanding of mutation patterns in HIV protease. Pair interactions have substantial qualitative effects, while higher-order interactions are

Applicability of the cost-effectiveness approach for comparison of waste management options

International Nuclear Information System (INIS)

Vuori, S.; Peltonen, E.; Vieno, T.; Vira, J.

1984-01-01

There is an obvious need to consider the achievable level of safety of waste management in view of the costs involved. The feasibility of the cost-effectiveness approach for this purpose is discussed in the framework of practical case studies. The analysis indicates that such an approach has clear benefits, but it also reveals several issues and ambiguities in its application. The waste management alternatives considered include various concepts for the disposal of low- and intermediate-level reactor wastes as well as of the unreprocessed spent fuel. The employed impact indicators describe both the individual and collective risks. In addition, indicators simultaneously giving a perspective into other risks in the society and a means to make a rank ordering of the alternative options are proposed. The cost-effectiveness ratios for collective risks vary in the range of ten to hundreds of millions US $ per man.Sv. The examples considered also indicate that increased costs do not necessarily improve safety. Furthermore, the comparison of the safety of different options requires more sophisticated and realistic models than those employed in the present analyses, because an unbalanced degree of conservatism could result in misleading conclusions. (author)

Comparison of Two Probabilistic Fatigue Damage Assessment Approaches Using Prognostic Performance Metrics

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Xuefei Guan

2011-01-01

Full Text Available In this paper, two probabilistic prognosis updating schemes are compared. One is based on the classical Bayesian approach and the other is based on newly developed maximum relative entropy (MRE approach. The algorithm performance of the two models is evaluated using a set of recently developed prognostics-based metrics. Various uncertainties from measurements, modeling, and parameter estimations are integrated into the prognosis framework as random input variables for fatigue damage of materials. Measures of response variables are then used to update the statistical distributions of random variables and the prognosis results are updated using posterior distributions. Markov Chain Monte Carlo (MCMC technique is employed to provide the posterior samples for model updating in the framework. Experimental data are used to demonstrate the operation of the proposed probabilistic prognosis methodology. A set of prognostics-based metrics are employed to quantitatively evaluate the prognosis performance and compare the proposed entropy method with the classical Bayesian updating algorithm. In particular, model accuracy, precision, robustness and convergence are rigorously evaluated in addition to the qualitative visual comparison. Following this, potential development and improvement for the prognostics-based metrics are discussed in detail.

Many-body dispersion effects in the binding of adsorbates on metal surfaces

Energy Technology Data Exchange (ETDEWEB)

Maurer, Reinhard J. [Department of Chemistry, Yale University, New Haven, Connecticut 06520 (United States); Ruiz, Victor G.; Tkatchenko, Alexandre [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Germany)

2015-09-14

A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we demonstrate the importance of collective van der Waals dispersion effects beyond the pairwise approximation for organic–inorganic systems on the example of atoms, molecules, and nanostructures adsorbed on metals. We use the recently developed many-body dispersion (MBD) approach in the context of density-functional theory [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012) and Ambrosetti et al., J. Chem. Phys. 140, 18A508 (2014)] and assess its ability to correctly describe the binding of adsorbates on metal surfaces. We briefly review the MBD method and highlight its similarities to quantum-chemical approaches to electron correlation in a quasiparticle picture. In particular, we study the binding properties of xenon, 3,4,9,10-perylene-tetracarboxylic acid, and a graphene sheet adsorbed on the Ag(111) surface. Accounting for MBD effects, we are able to describe changes in the anisotropic polarizability tensor, improve the description of adsorbate vibrations, and correctly capture the adsorbate–surface interaction screening. Comparison to other methods and experiment reveals that inclusion of MBD effects improves adsorption energies and geometries, by reducing the overbinding typically found in pairwise additive dispersion-correction approaches.

Comparison of co-expression measures: mutual information, correlation, and model based indices.

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Song, Lin; Langfelder, Peter; Horvath, Steve

2012-12-09

Co-expression measures are often used to define networks among genes. Mutual information (MI) is often used as a generalized correlation measure. It is not clear how much MI adds beyond standard (robust) correlation measures or regression model based association measures. Further, it is important to assess what transformations of these and other co-expression measures lead to biologically meaningful modules (clusters of genes). We provide a comprehensive comparison between mutual information and several correlation measures in 8 empirical data sets and in simulations. We also study different approaches for transforming an adjacency matrix, e.g. using the topological overlap measure. Overall, we confirm close relationships between MI and correlation in all data sets which reflects the fact that most gene pairs satisfy linear or monotonic relationships. We discuss rare situations when the two measures disagree. We also compare correlation and MI based approaches when it comes to defining co-expression network modules. We show that a robust measure of correlation (the biweight midcorrelation transformed via the topological overlap transformation) leads to modules that are superior to MI based modules and maximal information coefficient (MIC) based modules in terms of gene ontology enrichment. We present a function that relates correlation to mutual information which can be used to approximate the mutual information from the corresponding correlation coefficient. We propose the use of polynomial or spline regression models as an alternative to MI for capturing non-linear relationships between quantitative variables. The biweight midcorrelation outperforms MI in terms of elucidating gene pairwise relationships. Coupled with the topological overlap matrix transformation, it often leads to more significantly enriched co-expression modules. Spline and polynomial networks form attractive alternatives to MI in case of non-linear relationships. Our results indicate that MI

Testing statistical significance scores of sequence comparison methods with structure similarity

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Leunissen Jack AM

2006-10-01

Full Text Available Abstract Background In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. Results All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. Conclusion The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons.

CoCoNUT: an efficient system for the comparison and analysis of genomes

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Kurtz Stefan

2008-11-01

Full Text Available Abstract Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit that allows solving several different tasks in a unified framework: (1 finding regions of high similarity among multiple genomic sequences and aligning them, (2 comparing two draft or multi-chromosomal genomes, (3 locating large segmental duplications in large genomic sequences, and (4 mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component, CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics.

Pharmacological treatments in asthma-affected horses: A pair-wise and network meta-analysis.

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Calzetta, L; Roncada, P; di Cave, D; Bonizzi, L; Urbani, A; Pistocchini, E; Rogliani, P; Matera, M G

2017-11-01

Equine asthma is a disease characterised by reversible airflow obstruction, bronchial hyper-responsiveness and airway inflammation following exposure of susceptible horses to specific airborne agents. Although clinical remission can be achieved in a low-airborne dust environment, repeated exacerbations may lead to irreversible airway remodelling. The available data on the pharmacotherapy of equine asthma result from several small studies, and no head-to-head clinical trials have been conducted among the available medications. To assess the impact of the pharmacological interventions in equine asthma and compare the effect of different classes of drugs on lung function. Pair-wise and network meta-analysis. Literature searches for clinical trials on the pharmacotherapy of equine asthma were performed. The risk of publication bias was assessed by funnel plots and Egger's test. Changes in maximum transpulmonary or pleural pressure, pulmonary resistance and dynamic lung compliance vs. control were analysed via random-effects models and Bayesian networks. The results obtained from 319 equine asthma-affected horses were extracted from 32 studies. Bronchodilators, corticosteroids and chromones improved maximum transpulmonary or pleural pressure (range: -8.0 to -21.4 cmH 2 O; Ptherapies. Long-term treatments were more effective than short-term treatments. Weak publication bias was detected. This study demonstrates that long-term treatments with inhaled corticosteroids and long-acting β 2 -AR agonists may represent the first choice for treating equine asthma. Further high quality clinical trials are needed to clarify whether inhaled bronchodilators should be preferred to inhaled corticosteroids or vice versa, and to investigate the potential superiority of combination therapy in equine asthma. © 2017 EVJ Ltd.

Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

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Xin Yi Ng

2015-01-01

Full Text Available This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM- LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity.

Modeling Temporal Structure in Music for Emotion Prediction using Pairwise Comparisons

DEFF Research Database (Denmark)

Madsen, Jens; Jensen, Bjørn Sand; Larsen, Jan

2014-01-01

such as emotions, genre, and similarity. This paper addresses the specific hypothesis whether temporal information is essential for predicting expressed emotions in music, as a prototypical example of a cognitive aspect of music. We propose to test this hypothesis using a novel processing pipeline: 1) Extracting...

Comparison of ductile-to-brittle transition curve fitting approaches

International Nuclear Information System (INIS)

Cao, L.W.; Wu, S.J.; Flewitt, P.E.J.

2012-01-01

Ductile-to-brittle transition (DBT) curve fitting approaches are compared over the transition temperature range for reactor pressure vessel steels with different kinds of data, including Charpy-V notch impact energy data and fracture toughness data. Three DBT curve fitting methods have been frequently used in the past, including the Burr S-Weibull and tanh distributions. In general there is greater scatter associated with test data obtained within the transition region. Therefore these methods give results with different accuracies, especially when fitting to small quantities of data. The comparison shows that the Burr distribution and tanh distribution can almost equally fit well distributed and large data sets extending across the test temperature range to include the upper and lower shelves. The S-Weibull distribution fit is poor for the lower shelf of the DBT curve. Overall for both large and small quantities of measured data the Burr distribution provides the best description. - Highlights: ► Burr distribution offers a better fit than that of a S-Weibull and tanh fit. ► Burr and tanh methods show similar fitting ability for a large data set. ► Burr method can fit sparse data well distributed across the test temperature. ► S-Weibull method cannot fit the lower shelf well and show poor fitting quality.

A heuristic approach to possibilistic clustering algorithms and applications

CERN Document Server

Viattchenin, Dmitri A

2013-01-01

The present book outlines a new approach to possibilistic clustering in which the sought clustering structure of the set of objects is based directly on the formal definition of fuzzy cluster and the possibilistic memberships are determined directly from the values of the pairwise similarity of objects.   The proposed approach can be used for solving different classification problems. Here, some techniques that might be useful at this purpose are outlined, including a methodology for constructing a set of labeled objects for a semi-supervised clustering algorithm, a methodology for reducing analyzed attribute space dimensionality and a methods for asymmetric data processing. Moreover,  a technique for constructing a subset of the most appropriate alternatives for a set of weak fuzzy preference relations, which are defined on a universe of alternatives, is described in detail, and a method for rapidly prototyping the Mamdani’s fuzzy inference systems is introduced. This book addresses engineers, scientist...

Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.

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Chaurasia, Ankita; Tarallo, Andrea; Bernà, Luisa; Yagi, Mitsuharu; Agnisola, Claudio; D'Onofrio, Giuseppe

2014-01-01

A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi). An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann's factor) was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼ 40% to ∼ 90%, in each pairwise comparison). The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes.

A comparison of HK-CONWIP and BK-CONWIP control strategies in a multi-product manufacturing system

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Chukwunonyelum Emmanuel Onyeocha

2015-12-01

Full Text Available This paper evaluates the performance of the Hybrid Kanban Constant Work-In-Process control strategy and Basestock Kanban Constant Work-In-Process control strategy operating Shared Kanban Allocation Policy (S-KAP and Dedicated Kanban Allocation Policy (D-KAP in a multi-product serial flow line. We explored the effect of an increase of product types on the WIP inventory in the system. A simulation-based optimisation technique was used in determining the optimal settings for the strategies. The strategies were compared via pairwise comparison technique and Nelson’s ranking and selection procedure. S-KAP responds quicker to demand than D-KAP. BK-CONWIP outperforms HK-CONWIP in a serial manufacturing system. It was shown that an increase in the number of product-type increases the number of PAC and WIP inventory.

Neurons the decision makers, Part I: The firing function of a single neuron.

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Saaty, Thomas

2017-02-01

This paper is concerned with understanding synthesis of electric signals in the neural system based on making pairwise comparisons. Fundamentally, every person and every animal are born with the talent to compare stimuli from things that share properties in space or over time. Comparisons always need experience to distinguish among things. Pairwise comparisons are numerically reciprocal. If a value is assigned to the larger of two elements that have a given property when compared with the smaller one, then the smaller has the reciprocal of that value when compared with the larger. Because making comparisons requires the reciprocal property, we need mathematics that can cope with division. There are four division algebras that would allow us to use our reciprocals arising from comparisons: The real numbers, the complex numbers, the non-commutative quaternions and the non-associative octonions. Rather than inferring function as from electric flow in a network, in this paper we infer the flow from function. Neurons fire in response to stimuli and their firings vary relative to the intensities of the stimuli. We believe neurons use some kind of pairwise comparison mechanism to determine when to fire based on the stimuli they receive. The ideas we develop here about flows are used to deduce how a system based on this kind of firing determination works and can be described. Furthermore the firing of neurons requires continuous comparisons. To develop a formula describing the output of these pairwise comparisons requires solving Fredholm's equation of the second kind which is satisfied if and only if a simple functional equation has solutions. The Fourier transform of the real solution of this equation leads to inverse square laws like those that are common in physics. The Fourier transform applied to a complex valued solution leads to Dirac type of firings. Such firings are dense in the very general fields of functions known as Sobolev spaces and thus can be used to

Comparison of lipid and calorie loss from donor human milk among 3 methods of simulated gavage feeding: one-hour, 2-hour, and intermittent gravity feedings.

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Brooks, Christine; Vickers, Amy Manning; Aryal, Subhash

2013-04-01

The objective of this study was to compare the differences in lipid loss from 24 samples of banked donor human milk (DHM) among 3 feeding methods: DHM given by syringe pump over 1 hour, 2 hours, and by bolus/gravity gavage. Comparative, descriptive. There were no human subjects. Twenty-four samples of 8 oz of DHM were divided into four 60-mL aliquots. Timed feedings were given by Medfusion 2001 syringe pumps with syringes connected to narrow-lumened extension sets designed for enteral feedings and connected to standard silastic enteral feeding tubes. Gravity feedings were given using the identical syringes connected to the same silastic feeding tubes. All aliquots were analyzed with the York Dairy Analyzer. Univariate repeated-measures analyses of variance were used for the omnibus testing for overall differences between the feeding methods. Lipid content expressed as grams per deciliter at the end of each feeding method was compared with the prefed control samples using the Dunnett's test. The Tukey correction was used for other pairwise multiple comparisons. The univariate repeated-measures analysis of variance conducted to test for overall differences between feeding methods showed a significant difference between the methods (F = 58.57, df = 3, 69, P gravity feeding methods (P = .3296). Pairwise comparison using the Tukey correction revealed a significant difference between both gravity and 1-hour feeding methods (P gravity and 2-hour feeding method (P gravity feedings, the timed feedings resulted in a statistically significant loss of fat as compared with their controls. These findings should raise questions about how those infants in the neonatal intensive care unit are routinely gavage fed.

A participatory approach for selecting cost-effective measures in the WFD context: the Mar Menor (SE Spain).

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Perni, Angel; Martínez-Paz, José M

2013-08-01

Achieving a good ecological status in water bodies by 2015 is one of the objectives established in the European Water Framework Directive. Cost-effective analysis (CEA) has been applied for selecting measures to achieve this goal, but this appraisal technique requires technical and economic information that is not always available. In addition, there are often local insights that can only be identified by engaging multiple stakeholders in a participatory process. This paper proposes to combine CEA with the active involvement of stakeholders for selecting cost-effective measures. This approach has been applied to the case study of one of the main coastal lagoons in the European Mediterranean Sea, the Mar Menor, which presents eutrophication problems. Firstly, face-to-face interviews were conducted to estimate relative effectiveness and relative impacts of a set of measures by means of the pairwise comparison technique. Secondly, relative effectiveness was used to estimate cost-effectiveness ratios. The most cost-effective measures were the restoration of watercourses that drain into the lagoon and the treatment of polluted groundwater. Although in general the stakeholders approved the former, most of them stated that the latter involved some uncertainties, which must be addressed before implementing it. Stakeholders pointed out that the PoM would have a positive impact not only on water quality, but also on fishing, agriculture and tourism in the area. This approach can be useful to evaluate other programmes, plans or projects related to other European environmental strategies. Copyright © 2013 Elsevier B.V. All rights reserved.

Comparison of Different Approaches to Predict the Performance of Pumps As Turbines (PATs

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Mauro Venturini

2018-04-01

Full Text Available This paper deals with the comparison of different methods which can be used for the prediction of the performance curves of pumps as turbines (PATs. The considered approaches are four, i.e., one physics-based simulation model (“white box” model, two “gray box” models, which integrate theory on turbomachines with specific data correlations, and one “black box” model. More in detail, the modeling approaches are: (1 a physics-based simulation model developed by the same authors, which includes the equations for estimating head, power, and efficiency and uses loss coefficients and specific parameters; (2 a model developed by Derakhshan and Nourbakhsh, which first predicts the best efficiency point of a PAT and then reconstructs their complete characteristic curves by means of two ad hoc equations; (3 the prediction model developed by Singh and Nestmann, which predicts the complete turbine characteristics based on pump shape and size; (4 an Evolutionary Polynomial Regression model, which represents a data-driven hybrid scheme which can be used for identifying the explicit mathematical relationship between PAT and pump curves. All approaches are applied to literature data, relying on both pump and PAT performance curves of head, power, and efficiency over the entire range of operation. The experimental data were provided by Derakhshan and Nourbakhsh for four different turbomachines, working in both pump and PAT mode with specific speed values in the range 1.53–5.82. This paper provides a quantitative assessment of the predictions made by means of the considered approaches and also analyzes consistency from a physical point of view. Advantages and drawbacks of each method are also analyzed and discussed.

K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

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Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

2018-05-15

Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

SU-E-T-608: Performance Comparison of Four Commercial Treatment Planning Systems Applied to Intensity-Modulated Radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Cao, Y; Li, R; Chi, Z [The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, CN, Shijiazhuang, Hebei (China)

2014-06-01

Purpose: To compare the performances of four commercial treatment planning systems (TPS) used for the intensity-modulated radiotherapy (IMRT). Methods: Ten patients of nasopharyngeal (4 cases), esophageal (3 cases) and cervical (3 cases) cancer were randomly selected from a 3-month IMRT plan pool at one radiotherapy center. For each patient, four IMRT plans were newly generated by using four commercial TPS (Corvus, Monaco, Pinnacle and Xio), and then verified with Matrixx (two-dimensional array/IBA Company) on Varian23EX accelerator. A pass rate (PR) calculated from the Gamma index by OminiPro IMRT 1.5 software was evaluated at four plan verification standards (1%/1mm, 2%/2mm, 3%/3mm, 4%/4mm and 5%/5mm) for each treatment plan. Overall and multiple pairwise comparisons of PRs were statistically conducted by analysis of covariance (ANOVA) F and LSD tests among four TPSs. Results: Overall significant (p>0.05) differences of PRs were found among four TPSs with F test values of 3.8 (p=0.02), 21.1(>0.01), 14.0 (>0.01), 8.3(>0.01) at standards of 1%/1mm to 4%/4mm respectively, except at 5%/5mm standard with 2.6 (p=0.06). All means (standard deviation) of PRs at 3%/3mm of 94.3 ± 3.3 (Corvus), 98.8 ± 0.8 (Monaco), 97.5± 1.7 (Pinnacle), 98.4 ± 1.0 (Xio) were above 90% and met clinical requirement. Multiple pairwise comparisons had not demonstrated a consistent low or high pattern on either TPS. Conclusion: Matrixx dose verification results show that the validation pass rates of Monaco and Xio plans are relatively higher than those of the other two; Pinnacle plan shows slight higher pass rate than Corvus plan; lowest pass rate was achieved by the Corvus plan among these four kinds of TPS.

Support vector methods for survival analysis: a comparison between ranking and regression approaches.

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Van Belle, Vanya; Pelckmans, Kristiaan; Van Huffel, Sabine; Suykens, Johan A K

2011-10-01

To compare and evaluate ranking, regression and combined machine learning approaches for the analysis of survival data. The literature describes two approaches based on support vector machines to deal with censored observations. In the first approach the key idea is to rephrase the task as a ranking problem via the concordance index, a problem which can be solved efficiently in a context of structural risk minimization and convex optimization techniques. In a second approach, one uses a regression approach, dealing with censoring by means of inequality constraints. The goal of this paper is then twofold: (i) introducing a new model combining the ranking and regression strategy, which retains the link with existing survival models such as the proportional hazards model via transformation models; and (ii) comparison of the three techniques on 6 clinical and 3 high-dimensional datasets and discussing the relevance of these techniques over classical approaches fur survival data. We compare svm-based survival models based on ranking constraints, based on regression constraints and models based on both ranking and regression constraints. The performance of the models is compared by means of three different measures: (i) the concordance index, measuring the model's discriminating ability; (ii) the logrank test statistic, indicating whether patients with a prognostic index lower than the median prognostic index have a significant different survival than patients with a prognostic index higher than the median; and (iii) the hazard ratio after normalization to restrict the prognostic index between 0 and 1. Our results indicate a significantly better performance for models including regression constraints above models only based on ranking constraints. This work gives empirical evidence that svm-based models using regression constraints perform significantly better than svm-based models based on ranking constraints. Our experiments show a comparable performance for methods

Testing process predictions of models of risky choice: a quantitative model comparison approach

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Pachur, Thorsten; Hertwig, Ralph; Gigerenzer, Gerd; Brandstätter, Eduard

2013-01-01

This article presents a quantitative model comparison contrasting the process predictions of two prominent views on risky choice. One view assumes a trade-off between probabilities and outcomes (or non-linear functions thereof) and the separate evaluation of risky options (expectation models). Another view assumes that risky choice is based on comparative evaluation, limited search, aspiration levels, and the forgoing of trade-offs (heuristic models). We derived quantitative process predictions for a generic expectation model and for a specific heuristic model, namely the priority heuristic (Brandstätter et al., 2006), and tested them in two experiments. The focus was on two key features of the cognitive process: acquisition frequencies (i.e., how frequently individual reasons are looked up) and direction of search (i.e., gamble-wise vs. reason-wise). In Experiment 1, the priority heuristic predicted direction of search better than the expectation model (although neither model predicted the acquisition process perfectly); acquisition frequencies, however, were inconsistent with both models. Additional analyses revealed that these frequencies were primarily a function of what Rubinstein (1988) called “similarity.” In Experiment 2, the quantitative model comparison approach showed that people seemed to rely more on the priority heuristic in difficult problems, but to make more trade-offs in easy problems. This finding suggests that risky choice may be based on a mental toolbox of strategies. PMID:24151472

Testing Process Predictions of Models of Risky Choice: A Quantitative Model Comparison Approach

Directory of Open Access Journals (Sweden)

Thorsten ePachur

2013-09-01

Full Text Available This article presents a quantitative model comparison contrasting the process predictions of two prominent views on risky choice. One view assumes a trade-off between probabilities and outcomes (or nonlinear functions thereof and the separate evaluation of risky options (expectation models. Another view assumes that risky choice is based on comparative evaluation, limited search, aspiration levels, and the forgoing of trade-offs (heuristic models. We derived quantitative process predictions for a generic expectation model and for a specific heuristic model, namely the priority heuristic (Brandstätter, Gigerenzer, & Hertwig, 2006, and tested them in two experiments. The focus was on two key features of the cognitive process: acquisition frequencies (i.e., how frequently individual reasons are looked up and direction of search (i.e., gamble-wise vs. reason-wise. In Experiment 1, the priority heuristic predicted direction of search better than the expectation model (although neither model predicted the acquisition process perfectly; acquisition frequencies, however, were inconsistent with both models. Additional analyses revealed that these frequencies were primarily a function of what Rubinstein (1988 called similarity. In Experiment 2, the quantitative model comparison approach showed that people seemed to rely more on the priority heuristic in difficult problems, but to make more trade-offs in easy problems. This finding suggests that risky choice may be based on a mental toolbox of strategies.

Accuracy evaluation of automatic quantification of the articular cartilage surface curvature from MRI

DEFF Research Database (Denmark)

Folkesson, Jenny; Dam, Erik B; Olsen, Ole F

2007-01-01

for intersubject comparisons. Digital phantoms were created to establish the accuracy of the curvature estimation methods. RESULTS: A comparison of the two curvature estimation methods to ground truth yielded absolute pairwise differences of 1.1%, and 4.8%, respectively. The interscan reproducibility for the two...

Comparison of approaches to Total Quality Management. Including an examination of the Department of Energy`s position on quality management

Energy Technology Data Exchange (ETDEWEB)

Bennett, C.T.

1994-03-01

This paper presents a comparison of several qualitatively different approaches to Total Quality Management (TQM). The continuum ranges from management approaches that are primarily standards -- with specific guidelines, but few theoretical concepts -- to approaches that are primarily philosophical, with few specific guidelines. The approaches to TQM discussed in this paper include the International Organization for Standardization (ISO) 9000 Standard, the Malcolm Baldrige National Quality Award, Senge`s the Learning Organization, Watkins and Marsick`s approach to organizational learning, Covey`s Seven Habits of Highly Successful People, and Deming`s Fourteen Points for Management. Some of these approaches (Deming and ISO 9000) are then compared to the DOE`s official position on quality management and conduct of operations (DOE Orders 5700.6C and 5480.19). Using a tabular format, it is shown that while 5700.6C (Quality Assurance) maps well to many of the current approaches to TQM, DOE`s principle guide to management Order 5419.80 (Conduct of Operations) has many significant conflicts with some of the modern approaches to continuous quality improvement.

An Integrated Approach of Fuzzy Linguistic Preference Based AHP and Fuzzy COPRAS for Machine Tool Evaluation.

Directory of Open Access Journals (Sweden)

Huu-Tho Nguyen

Full Text Available Globalization of business and competitiveness in manufacturing has forced companies to improve their manufacturing facilities to respond to market requirements. Machine tool evaluation involves an essential decision using imprecise and vague information, and plays a major role to improve the productivity and flexibility in manufacturing. The aim of this study is to present an integrated approach for decision-making in machine tool selection. This paper is focused on the integration of a consistent fuzzy AHP (Analytic Hierarchy Process and a fuzzy COmplex PRoportional ASsessment (COPRAS for multi-attribute decision-making in selecting the most suitable machine tool. In this method, the fuzzy linguistic reference relation is integrated into AHP to handle the imprecise and vague information, and to simplify the data collection for the pair-wise comparison matrix of the AHP which determines the weights of attributes. The output of the fuzzy AHP is imported into the fuzzy COPRAS method for ranking alternatives through the closeness coefficient. Presentation of the proposed model application is provided by a numerical example based on the collection of data by questionnaire and from the literature. The results highlight the integration of the improved fuzzy AHP and the fuzzy COPRAS as a precise tool and provide effective multi-attribute decision-making for evaluating the machine tool in the uncertain environment.

Dimensional comparison theory.

Science.gov (United States)

Möller, Jens; Marsh, Herb W

2013-07-01

Although social comparison (Festinger, 1954) and temporal comparison (Albert, 1977) theories are well established, dimensional comparison is a largely neglected yet influential process in self-evaluation. Dimensional comparison entails a single individual comparing his or her ability in a (target) domain with his or her ability in a standard domain (e.g., "How good am I in math compared with English?"). This article reviews empirical findings from introspective, path-analytic, and experimental studies on dimensional comparisons, categorized into 3 groups according to whether they address the "why," "with what," or "with what effect" question. As the corresponding research shows, dimensional comparisons are made in everyday life situations. They impact on domain-specific self-evaluations of abilities in both domains: Dimensional comparisons reduce self-concept in the worse off domain and increase self-concept in the better off domain. The motivational basis for dimensional comparisons, their integration with recent social cognitive approaches, and the interdependence of dimensional, temporal, and social comparisons are discussed. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Comparison of Australian and US Cost-Benefit Approaches to MEPS

Energy Technology Data Exchange (ETDEWEB)

McMahon, James E.

2004-03-12

The Australian Greenhouse Office contracted with the Collaborative Labeling and Appliance Standards Program (CLASP) for LBNL to compare US and Australian approaches to analyzing costs and benefits of minimum energy performance standards (MEPS). This report compares the approaches for three types of products: household refrigerators and freezers, small electric storage water heaters, and commercial/industrial air conditioners. This report presents the findings of similarities and differences between the approaches of the two countries and suggests changes to consider in the approach taken in Australia. The purpose of the Australian program is to reduce greenhouse gas emissions, while the US program is intended to increase energy efficiency; each program is thus subject to specific constraints. The market and policy contexts are different, with the USA producing most of its own products and conducting pioneering engineering-economic studies to identify maximum energy efficiency levels that are technologically feasible and economically justified. In contrast, Australia imports a large share of its products and adopts MEPS already in place elsewhere. With these differences in circumstances, Australia's analysis approach could be expected to have less analytical detail and still result in MEPS levels that are appropriate for their policy and market context. In practice, the analysis required to meet these different objectives is quite similar. To date, Australia's cost-benefit analysis has served the goals and philosophies of the program well and been highly effective in successfully identifying MEPS that are significantly reducing greenhouse gas emissions while providing economic benefits to consumers. In some cases, however, the experience of the USA--using more extensive data sets and more detailed analysis--suggests possible improvements to Australia's cost-benefit analysis. The principal findings of the comparison are: (1) The Technology and Market

A Comparison of Online, Video Synchronous, and Traditional Learning Modes for an Introductory Undergraduate Physics Course

Science.gov (United States)

Faulconer, E. K.; Griffith, J.; Wood, B.; Acharyya, S.; Roberts, D.

2018-05-01

While the equivalence between online and traditional classrooms has been well-researched, very little of this includes college-level introductory Physics. Only one study explored Physics at the whole-class level rather than specific course components such as a single lab or a homework platform. In this work, we compared the failure rate, grade distribution, and withdrawal rates in an introductory undergraduate Physics course across several learning modes including traditional face-to-face instruction, synchronous video instruction, and online classes. Statistically significant differences were found for student failure rates, grade distribution, and withdrawal rates but yielded small effect sizes. Post-hoc pair-wise test was run to determine differences between learning modes. Online students had a significantly lower failure rate than students who took the class via synchronous video classroom. While statistically significant differences were found for grade distributions, the pair-wise comparison yielded no statistically significance differences between learning modes when using the more conservative Bonferroni correction in post-hoc testing. Finally, in this study, student withdrawal rates were lowest for students who took the class in person (in-person classroom and synchronous video classroom) than online. Students that persist in an online introductory Physics class are more likely to achieve an A than in other modes. However, the withdrawal rate is higher from online Physics courses. Further research is warranted to better understand the reasons for higher withdrawal rates in online courses. Finding the root cause to help eliminate differences in student performance across learning modes should remain a high priority for education researchers and the education community as a whole.

Rigorous approach to the comparison between experiment and theory in Casimir force measurements

International Nuclear Information System (INIS)

Klimchitskaya, G L; Chen, F; Decca, R S; Fischbach, E; Krause, D E; Lopez, D; Mohideen, U; Mostepanenko, V M

2006-01-01

In most experiments on the Casimir force the comparison between measurement data and theory was done using the concept of the root-mean-square deviation, a procedure that has been criticized in the literature. Here we propose a special statistical analysis which should be performed separately for the experimental data and for the results of the theoretical computations. In so doing, the random, systematic and total experimental errors are found as functions of separation, taking into account the distribution laws for each error at 95% confidence. Independently, all theoretical errors are combined to obtain the total theoretical error at the same confidence. Finally, the confidence interval for the differences between theoretical and experimental values is obtained as a function of separation. This rigorous approach is applied to two recent experiments on the Casimir effect

Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.

Science.gov (United States)

Bastien, Olivier; Maréchal, Eric

2008-08-07

Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2) following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory) is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure). Homologous sequences were considered as systems 1) having a high redundancy of information reflected by the magnitude of their alignment scores, 2) which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a constant rate, corresponding to the

Using structural equation modeling for network meta-analysis.

Science.gov (United States)

Tu, Yu-Kang; Wu, Yun-Chun

2017-07-14

Network meta-analysis overcomes the limitations of traditional pair-wise meta-analysis by incorporating all available evidence into a general statistical framework for simultaneous comparisons of several treatments. Currently, network meta-analyses are undertaken either within the Bayesian hierarchical linear models or frequentist generalized linear mixed models. Structural equation modeling (SEM) is a statistical method originally developed for modeling causal relations among observed and latent variables. As random effect is explicitly modeled as a latent variable in SEM, it is very flexible for analysts to specify complex random effect structure and to make linear and nonlinear constraints on parameters. The aim of this article is to show how to undertake a network meta-analysis within the statistical framework of SEM. We used an example dataset to demonstrate the standard fixed and random effect network meta-analysis models can be easily implemented in SEM. It contains results of 26 studies that directly compared three treatment groups A, B and C for prevention of first bleeding in patients with liver cirrhosis. We also showed that a new approach to network meta-analysis based on the technique of unrestricted weighted least squares (UWLS) method can also be undertaken using SEM. For both the fixed and random effect network meta-analysis, SEM yielded similar coefficients and confidence intervals to those reported in the previous literature. The point estimates of two UWLS models were identical to those in the fixed effect model but the confidence intervals were greater. This is consistent with results from the traditional pairwise meta-analyses. Comparing to UWLS model with common variance adjusted factor, UWLS model with unique variance adjusted factor has greater confidence intervals when the heterogeneity was larger in the pairwise comparison. The UWLS model with unique variance adjusted factor reflects the difference in heterogeneity within each comparison

German nuclear codes revised: comparison with approaches used in other countries

International Nuclear Information System (INIS)

Raetzke, C.; Micklinghoff, M.

2005-01-01

The article deals with the plan of the German Federal Ministry for the Environment (BMU) to revise the German set of nuclear codes, and draws a comparison with approaches pursued in other countries in formulating and implementing new requirements imposed upon existing plants. A striking feature of the BMU project is the intention to have the codes reflect the state of the art in an entirely abstract way irrespective of existing plants. This implies new requirements imposed on plant design, among other things. However, the state authorities, which establish the licensing conditions for individual plants in concrete terms, will not be able to apply these new codes for legal reasons (protection of vested rights) to the extent in which they incorporate changes in safety philosophy. Also the procedure adopted has raised considerable concern. The processing time of two years is inordinately short, and participation of the public and of industry does not go beyond the strictly formal framework of general public participation. In the light of this absence of quality assurance, it would be surprising if this new set of codes did not suffer from considerable deficits in its contents. Other countries show that the BMU is embarking on an isolated approach in every respect. Elsewhere, backfitting requirements are developed carefully and over long periods of time; they are discussed in detail with the operators; costs and benefits are weighted, and the consequences are evaluated. These elements are in common to procedures in all countries, irrespective of very different steps in detail. (orig.)

Profiling cellular protein complexes by proximity ligation with dual tag microarray readout.

Science.gov (United States)

Hammond, Maria; Nong, Rachel Yuan; Ericsson, Olle; Pardali, Katerina; Landegren, Ulf

2012-01-01

Patterns of protein interactions provide important insights in basic biology, and their analysis plays an increasing role in drug development and diagnostics of disease. We have established a scalable technique to compare two biological samples for the levels of all pairwise interactions among a set of targeted protein molecules. The technique is a combination of the proximity ligation assay with readout via dual tag microarrays. In the proximity ligation assay protein identities are encoded as DNA sequences by attaching DNA oligonucleotides to antibodies directed against the proteins of interest. Upon binding by pairs of antibodies to proteins present in the same molecular complexes, ligation reactions give rise to reporter DNA molecules that contain the combined sequence information from the two DNA strands. The ligation reactions also serve to incorporate a sample barcode in the reporter molecules to allow for direct comparison between pairs of samples. The samples are evaluated using a dual tag microarray where information is decoded, revealing which pairs of tags that have become joined. As a proof-of-concept we demonstrate that this approach can be used to detect a set of five proteins and their pairwise interactions both in cellular lysates and in fixed tissue culture cells. This paper provides a general strategy to analyze the extent of any pairwise interactions in large sets of molecules by decoding reporter DNA strands that identify the interacting molecules.

Detection and comparison of Selenomonas sputigena in subgingival biofilms in chronic and aggressive periodontitis patients

Directory of Open Access Journals (Sweden)

Disha Nagpal

2016-01-01

Full Text Available Background: With the advent of DNA-based culture-independent techniques, a constantly growing number of Selenomonas phylotypes have been detected in patients with destructive periodontal diseases. However, the prevalence levels that have been determined in different studies vary considerably. Aim: The present study was undertaken to detect and compare the presence of Selenomonas sputigena in the subgingival plaque samples from generalized aggressive periodontitis (GAP, chronic generalized periodontitis, and periodontally healthy patients using conventional polymerase chain reaction (PCR technique. Materials and Methods: A total of 90 patients were categorized as periodontally healthy individuals (Group I, n = 30, chronic generalized periodontitis (Group II, n = 30, and GAP (Group III, n = 30. The clinical parameters were recorded and subgingival plaque samples were collected. These were then subjected to conventional PCR analysis.Statistical Analysis Used: Kruskal–Wallis ANOVA test was used for multiple group comparisons followed by Mann–Whitney U-test for pairwise comparison. Results: On comparison between three groups, all the clinical parameters were found to be statistically highly significant. Comparing Groups I-II and I-III, the difference in detection was found to be statistically highly significant whereas in Groups II-III, it was statistically nonsignificant. On comparison of S. sputigena detected and undetected patients to clinical parameters in various study groups, the difference was found to be nonsignificant. Conclusion:S. sputigena was found to be significantly associated with chronic and aggressive periodontitis. Although the difference in its detection frequency in both groups was statistically nonsignificant when compared clinically, S. sputigena was more closely associated with the GAP.

Stakeholder perceptions in fisheries management - Sectors with benthic impacts

DEFF Research Database (Denmark)

Soma, K.; Nielsen, J. R.; Papadopoulou, N.

2018-01-01

), fisheries stakeholders are encouraged by the Common Fisheries Policy (CFP) reform to contribute to policy formulations. Still, the CFP reform remains unclear about how to possibly incorporate perceptions of specific conservation measures and objectives in practice. Against this background, this article aims...... at exploring a systematic multi-criteria approach that provides information about stakeholder preferences for objectives reflecting on what is more important to aim for (‘what’), mitigation measures as strategies for reaching their objectives (‘how’), and accountability options that can enhance trust...... in the people who carry out management (‘who'). The approach applies a pairwise comparison approach to elucidate the stakeholder preferences, and to estimate the relative importance of the different options. It is conducted in the Black Sea, the Mediterranean Sea, the Baltic Sea, and the North Sea. The outcomes...

An integrative multi-criteria decision making techniques for supplier evaluation problem with its application

Science.gov (United States)

Fatrias, D.; Kamil, I.; Meilani, D.

2018-03-01

Coordinating business operation with suppliers becomes increasingly important to survive and prosper under the dynamic business environment. A good partnership with suppliers not only increase efficiency, but also strengthen corporate competitiveness. Associated with such concern, this study aims to develop a practical approach of multi-criteria supplier evaluation using combined methods of Taguchi loss function (TLF), best-worst method (BWM) and VIse Kriterijumska Optimizacija kompromisno Resenje (VIKOR). A new framework of integrative approach adopting these methods is our main contribution for supplier evaluation in literature. In this integrated approach, a compromised supplier ranking list based on the loss score of suppliers is obtained using efficient steps of a pairwise comparison based decision making process. Implemetation to the case problem with real data from crumb rubber industry shows the usefulness of the proposed approach. Finally, a suitable managerial implication is presented.

Comparison and Contrast in Perceptual Categorization

Science.gov (United States)

Hampton, James A.; Estes, Zachary; Simmons, Claire L.

2005-01-01

People categorized pairs of perceptual stimuli that varied in both category membership and pairwise similarity. Experiments 1 and 2 showed categorization of 1 color of a pair to be reliably contrasted from that of the other. This similarity-based contrast effect occurred only when the context stimulus was relevant for the categorization of the…

Process perspective on image quality evaluation

Science.gov (United States)

Leisti, Tuomas; Halonen, Raisa; Kokkonen, Anna; Weckman, Hanna; Mettänen, Marja; Lensu, Lasse; Ritala, Risto; Oittinen, Pirkko; Nyman, Göte

2008-01-01

The psychological complexity of multivariate image quality evaluation makes it difficult to develop general image quality metrics. Quality evaluation includes several mental processes and ignoring these processes and the use of a few test images can lead to biased results. By using a qualitative/quantitative (Interpretation Based Quality, IBQ) methodology, we examined the process of pair-wise comparison in a setting, where the quality of the images printed by laser printer on different paper grades was evaluated. Test image consisted of a picture of a table covered with several objects. Three other images were also used, photographs of a woman, cityscape and countryside. In addition to the pair-wise comparisons, observers (N=10) were interviewed about the subjective quality attributes they used in making their quality decisions. An examination of the individual pair-wise comparisons revealed serious inconsistencies in observers' evaluations on the test image content, but not on other contexts. The qualitative analysis showed that this inconsistency was due to the observers' focus of attention. The lack of easily recognizable context in the test image may have contributed to this inconsistency. To obtain reliable knowledge of the effect of image context or attention on subjective image quality, a qualitative methodology is needed.

Traction cytometry: regularization in the Fourier approach and comparisons with finite element method.

Science.gov (United States)

Kulkarni, Ankur H; Ghosh, Prasenjit; Seetharaman, Ashwin; Kondaiah, Paturu; Gundiah, Namrata

2018-05-09

Traction forces exerted by adherent cells are quantified using displacements of embedded markers on polyacrylamide substrates due to cell contractility. Fourier Transform Traction Cytometry (FTTC) is widely used to calculate tractions but has inherent limitations due to errors in the displacement fields; these are mitigated through a regularization parameter (γ) in the Reg-FTTC method. An alternate finite element (FE) approach computes tractions on a domain using known boundary conditions. Robust verification and recovery studies are lacking but essential in assessing the accuracy and noise sensitivity of the traction solutions from the different methods. We implemented the L2 regularization method and defined a maximum curvature point in the traction with γ plot as the optimal regularization parameter (γ*) in the Reg-FTTC approach. Traction reconstructions using γ* yield accurate values of low and maximum tractions (Tmax) in the presence of up to 5% noise. Reg-FTTC is hence a clear improvement over the FTTC method but is inadequate to reconstruct low stresses such as those at nascent focal adhesions. FE, implemented using a node-by-node comparison, showed an intermediate reconstruction compared to Reg-FTTC. We performed experiments using mouse embryonic fibroblast (MEF) and compared results between these approaches. Tractions from FTTC and FE showed differences of ∼92% and 22% as compared to Reg-FTTC. Selection of an optimum value of γ for each cell reduced variability in the computed tractions as compared to using a single value of γ for all the MEF cells in this study.

Self-regulatory Behaviors and Approaches to Learning of Arts Students: A Comparison Between Professional Training and English Learning.

Science.gov (United States)

Tseng, Min-Chen; Chen, Chia-Cheng

2017-06-01

This study investigated the self-regulatory behaviors of arts students, namely memory strategy, goal-setting, self-evaluation, seeking assistance, environmental structuring, learning responsibility, and planning and organizing. We also explored approaches to learning, including deep approach (DA) and surface approach (SA), in a comparison between students' professional training and English learning. The participants consisted of 344 arts majors. The Academic Self-Regulation Questionnaire and the Revised Learning Process Questionnaire were adopted to examine students' self-regulatory behaviors and their approaches to learning. The results show that a positive and significant correlation was found in students' self-regulatory behaviors between professional training and English learning. The results indicated that increases in using self-regulatory behaviors in professional training were associated with increases in applying self-regulatory behaviors in learning English. Seeking assistance, self-evaluation, and planning and organizing were significant predictors for learning English. In addition, arts students used the deep approach more often than the surface approach in both their professional training and English learning. A positive correlation was found in DA, whereas a negative correlation was shown in SA between students' self-regulatory behaviors and their approaches to learning. Students with high self-regulation adopted a deep approach, and they applied the surface approach less in professional training and English learning. In addition, a SEM model confirmed that DA had a positive influence; however, SA had a negative influence on self-regulatory behaviors.

Picking Funds with Confidence

DEFF Research Database (Denmark)

Grønborg, Niels Strange; Lunde, Asger; Timmermann, Allan

We present a new approach to selecting active mutual funds that uses both holdings and return information to eliminate funds with predicted inferior performance through a sequence of pair-wise comparisons. Our methodology determines both the number of skilled funds and their identity, funds...... identified ex-ante as being superior earn substantially higher risk-adjusted returns than top funds identified by conventional alpha ranking methods. Importantly, we find strong evidence of variation in the breadth of the set of funds identified as superior, as well as fluctuations in the style and industry...... exposures of such funds over time and across different volatility states....

Multi-criteria analysis of potential recovery facilities in a reverse supply chain

Science.gov (United States)

Nukala, Satish; Gupta, Surendra M.

2005-11-01

Analytic Hierarchy Process (AHP) has been employed by researchers for solving multi-criteria analysis problems. However, AHP is often criticized for its unbalanced scale of judgments and failure to precisely handle the inherent uncertainty and vagueness in carrying out the pair-wise comparisons. With an objective to address these drawbacks, in this paper, we employ a fuzzy approach in selecting potential recovery facilities in the strategic planning of a reverse supply chain network that addresses the decision maker's level of confidence in the fuzzy assessments and his/her attitude towards risk. A numerical example is considered to illustrate the methodology.

Comparative effects of different dietary approaches on blood pressure in hypertensive and pre-hypertensive patients: A systematic review and network meta-analysis.

Science.gov (United States)

Schwingshackl, Lukas; Chaimani, Anna; Schwedhelm, Carolina; Toledo, Estefania; Pünsch, Marina; Hoffmann, Georg; Boeing, Heiner

2018-05-02

Pairwise meta-analyses have shown beneficial effects of individual dietary approaches on blood pressure but their comparative effects have not been established. Therefore we performed a systematic review of different dietary intervention trials and estimated the aggregate blood pressure effects through network meta-analysis including hypertensive and pre-hypertensive patients. PubMed, Cochrane CENTRAL, and Google Scholar were searched until June 2017. The inclusion criteria were defined as follows: i) Randomized trial with a dietary approach; ii) hypertensive and pre-hypertensive adult patients; and iii) minimum intervention period of 12 weeks. In order to determine the pooled effect of each intervention relative to each of the other intervention for both diastolic and systolic blood pressure (SBP and DBP), random effects network meta-analysis was performed. A total of 67 trials comparing 13 dietary approaches (DASH, low-fat, moderate-carbohydrate, high-protein, low-carbohydrate, Mediterranean, Palaeolithic, vegetarian, low-GI/GL, low-sodium, Nordic, Tibetan, and control) enrolling 17,230 participants were included. In the network meta-analysis, the DASH, Mediterranean, low-carbohydrate, Palaeolithic, high-protein, low-glycaemic index, low-sodium, and low-fat dietary approaches were significantly more effective in reducing SBP (-8.73 to -2.32 mmHg) and DBP (-4.85 to -1.27 mmHg) compared to a control diet. According to the SUCRAs, the DASH diet was ranked the most effective dietary approach in reducing SBP (90%) and DBP (91%), followed by the Palaeolithic, and the low-carbohydrate diet (ranked 3rd for SBP) or the Mediterranean diet (ranked 3rd for DBP). For most comparisons, the credibility of evidence was rated very low to moderate, with the exception for the DASH vs. the low-fat dietary approach for which the quality of evidence was rated high. The present network meta-analysis suggests that the DASH dietary approach might be the most effective dietary measure

Pluralism and Objectivism: Cornerstones for Interpersonal Comparisons

DEFF Research Database (Denmark)

Nielsen, Lasse

2012-01-01

comparison, and between a subjectivist and objectivist standard of interpersonal comparison. The paper provides a normative argument for pluralism and objectivism with regard to interpersonal comparison, and it suggests that the Capability Approach as developed by Amartya Sen and Martha Nussbaum fits...

Learning Preference Models from Data: On the Problem of Label Ranking and Its Variants

Science.gov (United States)

Hüllermeier, Eyke; Fürnkranz, Johannes

The term “preference learning” refers to the application of machine learning methods for inducing preference models from empirical data. In the recent literature, corresponding problems appear in various guises. After a brief overview of the field, this work focuses on a particular learning scenario called label ranking where the problem is to learn a mapping from instances to rankings over a finite number of labels. Our approach for learning such a ranking function, called ranking by pairwise comparison (RPC), first induces a binary preference relation from suitable training data, using a natural extension of pairwise classification. A ranking is then derived from this relation by means of a ranking procedure. This paper elaborates on a key advantage of such an approach, namely the fact that our learner can be adapted to different loss functions by using different ranking procedures on the same underlying order relations. In particular, the Spearman rank correlation is minimized by using a simple weighted voting procedure. Moreover, we discuss a loss function suitable for settings where candidate labels must be tested successively until a target label is found. In this context, we propose the idea of “empirical conditioning” of class probabilities. A related ranking procedure, called “ranking through iterated choice”, is investigated experimentally.

Parameter sampling capabilities of sequential and simultaneous data assimilation: I. Analytical comparison

International Nuclear Information System (INIS)

Fossum, Kristian; Mannseth, Trond

2014-01-01

We assess the parameter sampling capabilities of some Bayesian, ensemble-based, joint state-parameter (JS) estimation methods. The forward model is assumed to be non-chaotic and have nonlinear components, and the emphasis is on results obtained for the parameters in the state-parameter vector. A variety of approximate sampling methods exist, and a number of numerical comparisons between such methods have been performed. Often, more than one of the defining characteristics vary from one method to another, so it can be difficult to point out which characteristic of the more successful method in such a comparison was decisive. In this study, we single out one defining characteristic for comparison; whether or not data are assimilated sequentially or simultaneously. The current paper is concerned with analytical investigations into this issue. We carefully select one sequential and one simultaneous JS method for the comparison. We also design a corresponding pair of pure parameter estimation methods, and we show how the JS methods and the parameter estimation methods are pairwise related. It is shown that the sequential and the simultaneous parameter estimation methods are equivalent for one particular combination of observations with different degrees of nonlinearity. Strong indications are presented for why one may expect the sequential parameter estimation method to outperform the simultaneous parameter estimation method for all other combinations of observations. Finally, the conditions for when similar relations can be expected to hold between the corresponding JS methods are discussed. A companion paper, part II (Fossum and Mannseth 2014 Inverse Problems 30 114003), is concerned with statistical analysis of results from a range of numerical experiments involving sequential and simultaneous JS estimation, where the design of the numerical investigation is motivated by our findings in the current paper. (paper)

Renewables in residential development. An integrated GIS-based multicriteria approach for decentralized micro renewable energy production in new settlement development. A case study of the eastern metropolitan area of Cagliari, Sardinia, Italy

Energy Technology Data Exchange (ETDEWEB)

Palmas, Claudia [Cagliari Univ. (Italy). Dept. of Land Engineering; Abis, Emanuela [Cagliari Univ. (Italy). Dept. of Architecture; Haaren, Christina von [Leibniz Univ. of Hannover (Germany). Dept. of Environmental Planning; Lovett, Andrew [East Anglia Univ., Norwich (United Kingdom). School of Environmental Sciences

2011-07-01

In recent years there has been an increasing interest in using micro renewable energy sources to heat and power homes. However, planning has not yet developed methodological approaches for integrating such objectives of optimized energy efficiency with other environmental requirements and concerns of sustainable residential development. This study addresses such integration by first presenting an approach to assess the different potentials of the landscape for generating renewable energy (solar, wind, geothermic, biomass). Subsequently, optimized locations for residential development according to other sustainability criteria are identified and the two sets of results integrated by systematic GIS operations. The methodological approach for evaluating spatial variations in energy potential and producing the energy potential maps was based on existing methods for assessing the energy potential of the landscape which were adapted to the local scale and data availability. In the case of bioenergy potential a new method was developed. Other environmental criteria for deciding about sustainable locations for residential areas with different types of micro generation were identified through a survey of more than 100 expert respondents. This survey involved pairwise comparisons of relevant factors, which were then translated using the Analytical Hierarchy Process into relative weights. Subsequently these weights were applied to factor maps in a GIS via a weighted linear combination method to obtain suitable areas for new settlements and preferred locations for micro renewable technologies in the eastern metropolitan area of Cagliari, Sardinia. (orig.)

Derringer desirability and kinetic plot LC-column comparison approach for MS-compatible lipopeptide analysis.

Science.gov (United States)

D'Hondt, Matthias; Verbeke, Frederick; Stalmans, Sofie; Gevaert, Bert; Wynendaele, Evelien; De Spiegeleer, Bart

2014-06-01

Lipopeptides are currently re-emerging as an interesting subgroup in the peptide research field, having historical applications as antibacterial and antifungal agents and new potential applications as antiviral, antitumor, immune-modulating and cell-penetrating compounds. However, due to their specific structure, chromatographic analysis often requires special buffer systems or the use of trifluoroacetic acid, limiting mass spectrometry detection. Therefore, we used a traditional aqueous/acetonitrile based gradient system, containing 0.1% (m/v) formic acid, to separate four pharmaceutically relevant lipopeptides (polymyxin B 1 , caspofungin, daptomycin and gramicidin A 1 ), which were selected based upon hierarchical cluster analysis (HCA) and principal component analysis (PCA). In total, the performance of four different C18 columns, including one UPLC column, were evaluated using two parallel approaches. First, a Derringer desirability function was used, whereby six single and multiple chromatographic response values were rescaled into one overall D -value per column. Using this approach, the YMC Pack Pro C18 column was ranked as the best column for general MS-compatible lipopeptide separation. Secondly, the kinetic plot approach was used to compare the different columns at different flow rate ranges. As the optimal kinetic column performance is obtained at its maximal pressure, the length elongation factor λ ( P max / P exp ) was used to transform the obtained experimental data (retention times and peak capacities) and construct kinetic performance limit (KPL) curves, allowing a direct visual and unbiased comparison of the selected columns, whereby the YMC Triart C18 UPLC and ACE C18 columns performed as best. Finally, differences in column performance and the (dis)advantages of both approaches are discussed.

A novel combined approach of diffuse reflectance UV-Vis-NIR spectroscopy and multivariate analysis for non-destructive examination of blue ballpoint pen inks in forensic application.

Science.gov (United States)

Kumar, Raj; Sharma, Vishal

2017-03-15

The present research is focused on the analysis of writing inks using destructive UV-Vis spectroscopy (dissolution of ink by the solvent) and non-destructive diffuse reflectance UV-Vis-NIR spectroscopy along with Chemometrics. Fifty seven samples of blue ballpoint pen inks were analyzed under optimum conditions to determine the differences in spectral features of inks among same and different manufacturers. Normalization was performed on the spectroscopic data before chemometric analysis. Principal Component Analysis (PCA) and K-mean cluster analysis were used on the data to ascertain whether the blue ballpoint pen inks could be differentiated by their UV-Vis/UV-Vis NIR spectra. The discriminating power is calculated by qualitative analysis by the visual comparison of the spectra (absorbance peaks), produced by the destructive and non-destructive methods. In the latter two methods, the pairwise comparison is made by incorporating the clustering method. It is found that chemometric method provides better discriminating power (98.72% and 99.46%, in destructive and non-destructive, respectively) in comparison to the qualitative analysis (69.67%). Copyright © 2016 Elsevier B.V. All rights reserved.

Social Comparison and Body Image in Adolescence: A Grounded Theory Approach

Science.gov (United States)

Krayer, A.; Ingledew, D. K.; Iphofen, R.

2008-01-01

This study explored the use of social comparison appraisals in adolescents' lives with particular reference to enhancement appraisals which can be used to counter threats to the self. Social comparison theory has been increasingly used in quantitative research to understand the processes through which societal messages about appearance influence…

Domain similarity based orthology detection

OpenAIRE

Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

2015-01-01

Background Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationa...

A Fiducial Approach to Extremes and Multiple Comparisons

Science.gov (United States)

Wandler, Damian V.

2010-01-01

Generalized fiducial inference is a powerful tool for many difficult problems. Based on an extension of R. A. Fisher's work, we used generalized fiducial inference for two extreme value problems and a multiple comparison procedure. The first extreme value problem is dealing with the generalized Pareto distribution. The generalized Pareto…

Comparison between Fisherian and Bayesian approach to ...

African Journals Online (AJOL)

... of its simplicity and optimality properties is normally used for two group cases. However, Bayesian approach is found to be better than Fisher's approach because of its low misclassification error rate. Keywords: variance-covariance matrices, centroids, prior probability, mahalanobis distance, probability of misclassification ...

A comparison of image restoration approaches applied to three-dimensional confocal and wide-field fluorescence microscopy.

Science.gov (United States)

Verveer, P. J; Gemkow, M. J; Jovin, T. M

1999-01-01

We have compared different image restoration approaches for fluorescence microscopy. The most widely used algorithms were classified with a Bayesian theory according to the assumed noise model and the type of regularization imposed. We considered both Gaussian and Poisson models for the noise in combination with Tikhonov regularization, entropy regularization, Good's roughness and without regularization (maximum likelihood estimation). Simulations of fluorescence confocal imaging were used to examine the different noise models and regularization approaches using the mean squared error criterion. The assumption of a Gaussian noise model yielded only slightly higher errors than the Poisson model. Good's roughness was the best choice for the regularization. Furthermore, we compared simulated confocal and wide-field data. In general, restored confocal data are superior to restored wide-field data, but given sufficient higher signal level for the wide-field data the restoration result may rival confocal data in quality. Finally, a visual comparison of experimental confocal and wide-field data is presented.

Simulation of imaging in tapping-mode atomic-force microscopy: a comparison amongst a variety of approaches

Energy Technology Data Exchange (ETDEWEB)

Pishkenari, H N; Mahboobi, S H; Meghdari, A, E-mail: mahboobi@sharif.edu [Center of Excellence in Design, Robotics and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran (Iran, Islamic Republic of)

2011-02-23

Models capable of accurate simulation of microcantilever dynamics coupled with complex tip-sample interactions are essential for interpretation and prediction of the imaging results in amplitude modulation or tapping-mode atomic-force microscopy (AM-AFM or TM-AFM). In this paper, four approaches based on combinations of lumped and finite element methods for modelling of cantilever dynamics, and van der Waals and molecular dynamics for modelling of tip-sample interactions, are used to simulate the precise imaging by AM-AFM. Based on the simulated imaging and force determination, the efficiency of different modelling schemes is evaluated. This comparison is performed considering their coincidence with the realistic behaviour of AM-AFM in imaging of nanoscale features. In the conducted simulations, a diamond tip is used to scan a C60 molecule absorbed on a graphite substrate. The effects of amplitude set-point, cantilever stiffness and quality factor on the accuracy of different modelling approaches are studied.

Project on Alternative Systems Study - PASS. Comparison of technology of KBS-3, MLH, VLH and VDH concepts by using an expert group

International Nuclear Information System (INIS)

Olsson, Lars; Sandstedt, H.

1992-09-01

This report constitutes a technical comparison and ranking of four repository concepts for final disposal of spent nuclear fuel, that have been studied by SKB: KBS-3, Medium Long Holes (MLH), Very Long Holes (VLH) and Very Deep Holes (VDH). The technical comparison is part of the project 'Project on Alternative Systems Study, PASS', which was initiated by SKB. With the objective of presenting a ranking of the four concepts. Besides this comparison of Technology the ranking is separately made for Long-term Performance and Safety, and Costs before the merging into one verdict. The ranking regarding Technology was carried out in accordance with the method Analytical Hierarchy Process, AHP, and by the aid of expert judgement in the form of a group consisting of six experts. The AHP method implies that the criteria for comparison are ordered in a hierarchy and that the ranking is carried out by pairwise comparison of the criteria. In the evaluation process a measure of the relative importance of each criterion is obtained. The result of the expert judgement exercise was that each expert individually ranked the four concepts in the following order with the top ranked alternative first: KBS-3, MLH, VLH and VDH. The common opinion among the experts was that the top ranking of KBS-3 is significant and the the major criteria used in the study could change substantially without changing the top ranking of KBS-3

CCM key comparison CCM.D-K4 'Hydrometer'

Science.gov (United States)

Lorefice, S.; Becerra, L. O.; Lenard, E.; Lee, Y. J.; Lee, W. G.; Madec, T.; Meury, P. A.; Caceres, J.; Santos, C.; Vamossy, C.; Man, J.; Fen, K.; Toda, K.; Wright, J.; Bettin, H.; Toth, H.

2016-01-01

This report presents the comparison philosophy, methodology, analysis and the results of the designed CCM.D-K4 key comparison that covered the calibration of high resolution hydrometers for liquid and alcoholometers in the density range 600 kg/m3 to 2000 kg/m3 at the temperature of 20°C. The main purpose of this comparison was not only to evaluate the degree of equivalence in the calibration of high accuracy hydrometers between NMI participants, but also to link, were it is possible, the results of previous comparisons to Key Comparison Reference Values (KCRVs) of CCM.D-K4. Eleven NMI laboratories took part in the CCM.D-K4 divided in two groups (petals). With the CCM.D-K4 purpose, two similar sets consisting of three hydrometers for liquid density determinations and an alcoholometer were circulated to the NMI participants as a travelling standard in the time interval from January 2011 to April 2012. Twelve Key Comparison Reference Values (KCRVs) for each petal have been obtained at the density values related to the tested density marks of the transfer standards by the results of participants. The KCRVs and corresponding uncertainties were calculated by the weighted mean in the case of consistent results, otherwise the median was used. The degree of equivalence (DoE) with respect to the corresponding KCRV was determined for each participant and, in this particular comparison, the Weighted Least Squares (WLS) method was used to link the individual DoE of each participant by a continuous function. Significant drift of the transfer standards was not detected. This report also gives instructions on calculating pair-wise degrees of equivalence, with the addition of any information on correlations that may be necessary to estimate more accurately as well as the procedure for linking international comparisons to the CCM.D-K4. Finally an example of linkage to the CCM.D-K4 is given by dealing with the results of the bilateral comparison between INRiM and NMIA, which was

Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

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Jiang Wei

2008-08-01

Full Text Available Abstract Background With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. Results The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8 (p ≈ 0, desmin (DES (p = 2.71 × 10-6 and enolase 1 (ENO1 (p = 4.19 × 10-5], while two novel hub genes [RNA binding motif protein 9 (RBM9 (p = 1.50 × 10-4 and ribosomal protein L30 (RPL30 (p = 1.50 × 10-4] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO based analysis of the colon cancer-specific gene network and

Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements.

Science.gov (United States)

Jiang, Wei; Li, Xia; Rao, Shaoqi; Wang, Lihong; Du, Lei; Li, Chuanxing; Wu, Chao; Wang, Hongzhi; Wang, Yadong; Yang, Baofeng

2008-08-10

With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8) (p approximately 0), desmin (DES) (p = 2.71 x 10(-6)) and enolase 1 (ENO1) (p = 4.19 x 10(-5))], while two novel hub genes [RNA binding motif protein 9 (RBM9) (p = 1.50 x 10(-4)) and ribosomal protein L30 (RPL30) (p = 1.50 x 10(-4))] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO) based analysis of the colon cancer-specific gene network and the sub-network that

A Comparison of Proliferation Resistance Measures of Misuse Scenarios Using a Markov Approach

International Nuclear Information System (INIS)

Yue, M.; Cheng, L.-Y.; Bari, R.

2008-01-01

Misuse of declared nuclear facilities is one of the important proliferation threats. The robustness of a facility against these threats is characterized by a number of proliferation resistance (PR) measures. This paper evaluates and compares PR measures for several misuse scenarios using a Markov model approach to implement the pathway analysis methodology being developed by the PR and PP (Proliferation Resistance and Physical Protection) Expert Group. Different misue strategies can be adopted by a proliferator and each strategy is expected to have different impacts on the proliferator's success. Selected as the probabilistic measure to represent proliferation resistance, the probabilities of the proliferator's success of misusing a hypothetical ESFR (Example Sodium Fast Reactor) facility system are calculated using the Markov model based on the pathways constructed for individual misuse scenarios. Insights from a comparison of strategies that are likely to be adopted by the proliferator are discussed in this paper.

Comparison of posterior retroperitoneal and transabdominal lateral approaches in robotic adrenalectomy: an analysis of 200 cases.

Science.gov (United States)

Kahramangil, Bora; Berber, Eren

2018-04-01

Although numerous studies have been published on robotic adrenalectomy (RA) in the literature, none has done a comparison of posterior retroperitoneal (PR) and transabdominal lateral (TL) approaches. The aim of this study was to compare the outcomes of robotic PR and TL adrenalectomy. This is a retrospective analysis of a prospectively maintained database. Between September 2008 and January 2017, perioperative outcomes of patients undergoing RA through PR and TL approaches were recorded into an IRB-approved database. Clinical and perioperative parameters were compared using Student's t test, Wilcoxon rank-sum test, and χ 2 test. Multivariate regression analysis was performed to determine factors associated with total operative time. 188 patients underwent 200 RAs. 110 patients were operated through TL and 78 patients through PR approach. Overall, conversion rate to open was 2.5% and 90-day morbidity 4.8%. The perioperative outcomes of TL and PR approaches were similar regarding estimated blood loss, rate of conversion to open, length of hospital stay, and 90-day morbidity. PR approach resulted in a shorter mean ± SD total operative time (136.3 ± 38.7 vs. 154.6 ± 48.4 min; p = 0.005) and lower visual analog scale pain score on postoperative day #1 (4.3 ± 2.5 vs. 5.4 ± 2.4; p = 0.001). After excluding tumors larger than 6 cm operated through TL approach, the difference in operative times persisted (136.3 ± 38.7 vs. 153.7 ± 45.7 min; p = 0.009). On multivariate regression analysis, increasing BMI and TL approaches were associated with longer total operative time. This study shows that robotic PR and TL approaches are equally safe and efficacious. With experience, shorter operative time and less postoperative pain can be achieved with PR technique. This supports the preferential utilization of PR approach in high-volume centers with enough experience.

Comparison of different modeling approaches to simulate contaminant transport in a fractured limestone aquifer

DEFF Research Database (Denmark)

Mosthaf, Klaus; Rosenberg, L.; Balbarini, Nicola

. Given available field data and model purpose, this paper therefore aims to develop, examine and compare modeling approaches for transport of contaminants in fractured limestone aquifers. The model comparison was conducted for a contaminated site in Denmark, where a plume of a dissolved contaminant (PCE...... was combined with an analysis of heterogeneities and fractures from a nearby excavation (analog site). Methods for translating the geological information and fracture mapping into each of the model concepts were examined. Each model was compared with available field data, considering both model fit...... of field data is the determination of relevant hydraulic properties and interpretation of aqueous and solid phase contaminant concentration sampling data. Traditional water sampling has a bias towards fracture sampling, however concentrations in the limestone matrix are needed for assessing contaminant...

Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores

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Maréchal Eric

2008-08-01

Full Text Available Abstract Background Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2 following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. Results We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure. Homologous sequences were considered as systems 1 having a high redundancy of information reflected by the magnitude of their alignment scores, 2 which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a

Comparison of beta-binomial regression model approaches to analyze health-related quality of life data.

Science.gov (United States)

Najera-Zuloaga, Josu; Lee, Dae-Jin; Arostegui, Inmaculada

2017-01-01

Health-related quality of life has become an increasingly important indicator of health status in clinical trials and epidemiological research. Moreover, the study of the relationship of health-related quality of life with patients and disease characteristics has become one of the primary aims of many health-related quality of life studies. Health-related quality of life scores are usually assumed to be distributed as binomial random variables and often highly skewed. The use of the beta-binomial distribution in the regression context has been proposed to model such data; however, the beta-binomial regression has been performed by means of two different approaches in the literature: (i) beta-binomial distribution with a logistic link; and (ii) hierarchical generalized linear models. None of the existing literature in the analysis of health-related quality of life survey data has performed a comparison of both approaches in terms of adequacy and regression parameter interpretation context. This paper is motivated by the analysis of a real data application of health-related quality of life outcomes in patients with Chronic Obstructive Pulmonary Disease, where the use of both approaches yields to contradictory results in terms of covariate effects significance and consequently the interpretation of the most relevant factors in health-related quality of life. We present an explanation of the results in both methodologies through a simulation study and address the need to apply the proper approach in the analysis of health-related quality of life survey data for practitioners, providing an R package.

Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach

Science.gov (United States)

2012-01-01

Background Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim’s epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim’s DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim’s fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim’s fraction, and then digest the residual victim’s DNA with a nuclease. Methods The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases. Results For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles. Conclusions In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods. PMID:23211019

Quantitative Comparison of Ternary Eutectic Phase-Field Simulations with Analytical 3D Jackson-Hunt Approaches

Science.gov (United States)

Steinmetz, Philipp; Kellner, Michael; Hötzer, Johannes; Nestler, Britta

2018-02-01

For the analytical description of the relationship between undercoolings, lamellar spacings and growth velocities during the directional solidification of ternary eutectics in 2D and 3D, different extensions based on the theory of Jackson and Hunt are reported in the literature. Besides analytical approaches, the phase-field method has been established to study the spatially complex microstructure evolution during the solidification of eutectic alloys. The understanding of the fundamental mechanisms controlling the morphology development in multiphase, multicomponent systems is of high interest. For this purpose, a comparison is made between the analytical extensions and three-dimensional phase-field simulations of directional solidification in an ideal ternary eutectic system. Based on the observed accordance in two-dimensional validation cases, the experimentally reported, inherently three-dimensional chain-like pattern is investigated in extensive simulation studies. The results are quantitatively compared with the analytical results reported in the literature, and with a newly derived approach which uses equal undercoolings. A good accordance of the undercooling-spacing characteristics between simulations and the analytical Jackson-Hunt apporaches are found. The results show that the applied phase-field model, which is based on the Grand potential approach, is able to describe the analytically predicted relationship between the undercooling and the lamellar arrangements during the directional solidification of a ternary eutectic system in 3D.

Statistical inference an integrated Bayesianlikelihood approach

CERN Document Server

Aitkin, Murray

2010-01-01

Filling a gap in current Bayesian theory, Statistical Inference: An Integrated Bayesian/Likelihood Approach presents a unified Bayesian treatment of parameter inference and model comparisons that can be used with simple diffuse prior specifications. This novel approach provides new solutions to difficult model comparison problems and offers direct Bayesian counterparts of frequentist t-tests and other standard statistical methods for hypothesis testing.After an overview of the competing theories of statistical inference, the book introduces the Bayes/likelihood approach used throughout. It pre

A Comparison of Approach and Avoidance Sexual Goals in Couples With Vulvodynia and Community Controls.

Science.gov (United States)

Dubé, Justin P; Bergeron, Sophie; Muise, Amy; Impett, Emily A; Rosen, Natalie O

2017-11-01

couples coping with PVD. Dubé JP, Bergeron S, Muise A, et al. A Comparison of Approach and Avoidance Sexual Goals in Couples With Vulvodynia and Community Controls. J Sex Med 2017;14:1412-1420. Copyright © 2017 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Fast and Frugal Framing Effects?

Science.gov (United States)

Mccloy, Rachel; Beaman, C. Philip; Frosch, Caren A.; Goddard, Kate

2010-01-01

Using 3 experiments, we examine whether simple pairwise comparison judgments, involving the "recognition heuristic" (Goldstein & Gigerenzer, 2002), are sensitive to implicit cues to the nature of the comparison required. In Experiments 1 and 2, we show that participants frequently choose the recognized option of a pair if asked to make "larger"…

An international comparison of models and approaches for the estimation of the radiological exposure of non-human biota

International Nuclear Information System (INIS)

Beresford, Nicholas A.; Balonov, Mikhail; Beaugelin-Seiller, Karine; Brown, Justin; Copplestone, David; Hingston, Joanne L.; Horyna, Jan; Hosseini, Ali; Howard, Brenda J.; Kamboj, Sunita; Nedveckaite, Tatjana; Olyslaegers, Geert; Sazykina, Tatiana; Vives i Batlle, Jordi; Yankovich, Tamara L.; Yu, Charley

2008-01-01

Over the last decade a number of models and approaches have been developed for the estimation of the exposure of non-human biota to ionising radiations. In some countries these are now being used in regulatory assessments. However, to date there has been no attempt to compare the outputs of the different models used. This paper presents the work of the International Atomic Energy Agency's EMRAS Biota Working Group which compares the predictions of a number of such models in model-model and model-data inter-comparisons

A systematic comparison of different approaches of density functional theory for the study of electrical double layers

International Nuclear Information System (INIS)

Yang, Guomin; Liu, Longcheng

2015-01-01

Based on the best available knowledge of density functional theory (DFT), the reference-fluid perturbation method is here extended to yield different approaches that well account for the cross correlations between the Columbic interaction and the hard-sphere exclusion in an inhomogeneous ionic hard-sphere fluid. In order to quantitatively evaluate the advantage and disadvantage of different approaches in describing the interfacial properties of electrical double layers, this study makes a systematic comparison against Monte Carlo simulations over a wide range of conditions. The results suggest that the accuracy of the DFT approaches is well correlated to a coupling parameter that describes the coupling strength of electrical double layers by accounting for the steric effect and that can be used to classify the systems into two regimes. In the weak-coupling regime, the approaches based on the bulk-fluid perturbation method are shown to be more accurate than the counterparts based on the reference-fluid perturbation method, whereas they exhibit the opposite behavior in the strong-coupling regime. More importantly, the analysis indicates that, with a suitable choice of the reference fluid, the weighted correlation approximation (WCA) to DFT gives the best account of the coupling effect of the electrostatic-excluded volume correlations. As a result, a piecewise WCA approach can be developed that is robust enough to describe the structural and thermodynamic properties of electrical double layers over both weak- and strong-coupling regimes

Optimization of approximate decision rules relative to number of misclassifications: Comparison of greedy and dynamic programming approaches

KAUST Repository

Amin, Talha

2013-01-01

In the paper, we present a comparison of dynamic programming and greedy approaches for construction and optimization of approximate decision rules relative to the number of misclassifications. We use an uncertainty measure that is a difference between the number of rows in a decision table T and the number of rows with the most common decision for T. For a nonnegative real number γ, we consider γ-decision rules that localize rows in subtables of T with uncertainty at most γ. Experimental results with decision tables from the UCI Machine Learning Repository are also presented. © 2013 Springer-Verlag.

Strategy-aligned fuzzy approach for market segment evaluation and selection: a modular decision support system by dynamic network process (DNP)

Science.gov (United States)

Mohammadi Nasrabadi, Ali; Hosseinpour, Mohammad Hossein; Ebrahimnejad, Sadoullah

2013-05-01

In competitive markets, market segmentation is a critical point of business, and it can be used as a generic strategy. In each segment, strategies lead companies to their targets; thus, segment selection and the application of the appropriate strategies over time are very important to achieve successful business. This paper aims to model a strategy-aligned fuzzy approach to market segment evaluation and selection. A modular decision support system (DSS) is developed to select an optimum segment with its appropriate strategies. The suggested DSS has two main modules. The first one is SPACE matrix which indicates the risk of each segment. Also, it determines the long-term strategies. The second module finds the most preferred segment-strategies over time. Dynamic network process is applied to prioritize segment-strategies according to five competitive force factors. There is vagueness in pairwise comparisons, and this vagueness has been modeled using fuzzy concepts. To clarify, an example is illustrated by a case study in Iran's coffee market. The results show that success possibility of segments could be different, and choosing the best ones could help companies to be sure in developing their business. Moreover, changing the priority of strategies over time indicates the importance of long-term planning. This fact has been supported by a case study on strategic priority difference in short- and long-term consideration.

A robust fuzzy possibilistic AHP approach for partner selection in international strategic alliance

Directory of Open Access Journals (Sweden)

Vahid Reza Salamat

2018-09-01

Full Text Available The international strategic alliance is an inevitable solution for making competitive advantage and reducing the risk in today’s business environment. Partner selection is an important part in success of partnerships, and meanwhile it is a complicated decision because of various dimensions of the problem and inherent conflicts of stockholders. The purpose of this paper is to provide a practical approach to the problem of partner selection in international strategic alliances, which fulfills the gap between theories of inter-organizational relationships and quantitative models. Thus, a novel Robust Fuzzy Possibilistic AHP approach is proposed for combining the benefits of two complementary theories of inter-organizational relationships named, (1 Resource-based view, and (2 Transaction-cost theory and considering Fit theory as the perquisite of alliance success. The Robust Fuzzy Possibilistic AHP approach is a novel development of Interval-AHP technique employing robust formulation; aimed at handling the ambiguity of the problem and let the use of intervals as pairwise judgments. The proposed approach was compared with existing approaches, and the results show that it provides the best quality solutions in terms of minimum error degree. Moreover, the framework implemented in a case study and its applicability were discussed.

Concentrations versus amounts of biomarkers in urine: a comparison of approaches to assess pyrethroid exposure

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Bouchard Michèle

2008-11-01

Full Text Available Abstract Background Assessment of human exposure to non-persistent pesticides such as pyrethroids is often based on urinary biomarker measurements. Urinary metabolite levels of these pesticides are usually reported in volume-weighted concentrations or creatinine-adjusted concentrations measured in spot urine samples. It is known that these units are subject to intra- and inter-individual variations. This research aimed at studying the impact of these variations on the assessment of pyrethroid absorbed doses at individual and population levels. Methods Using data obtained from various adult and infantile populations, the intra and inter-individual variability in the urinary flow rate and creatinine excretion rate was first estimated. Individual absorbed doses were then calculated using volume-weighted or creatinine-adjusted concentrations according to published approaches and compared to those estimated from the amounts of biomarkers excreted in 15- or 24-h urine collections, the latter serving as a benchmark unit. The effect of the units of measurements (volume-weighted or creatinine adjusted concentrations or 24-h amounts on results of the comparison of pyrethroid biomarker levels between two populations was also evaluated. Results Estimation of daily absorbed doses of permethrin from volume-weighted or creatinine-adjusted concentrations of biomarkers was found to potentially lead to substantial under or overestimation when compared to doses reconstructed directly from amounts excreted in urine during a given period of time (-70 to +573% and -83 to +167%, respectively. It was also shown that the variability in creatinine excretion rate and urinary flow rate may introduce a bias in the case of between population comparisons. Conclusion The unit chosen to express biomonitoring data may influence the validity of estimated individual absorbed dose as well as the outcome of between population comparisons.

Library fingerprints: a novel approach to the screening of virtual libraries.

Science.gov (United States)

Klon, Anthony E; Diller, David J

2007-01-01

We propose a novel method to prioritize libraries for combinatorial synthesis and high-throughput screening that assesses the viability of a particular library on the basis of the aggregate physical-chemical properties of the compounds using a naïve Bayesian classifier. This approach prioritizes collections of related compounds according to the aggregate values of their physical-chemical parameters in contrast to single-compound screening. The method is also shown to be useful in screening existing noncombinatorial libraries when the compounds in these libraries have been previously clustered according to their molecular graphs. We show that the method used here is comparable or superior to the single-compound virtual screening of combinatorial libraries and noncombinatorial libraries and is superior to the pairwise Tanimoto similarity searching of a collection of combinatorial libraries.

An approach to evaluate the topological significance of motifs and other patterns in regulatory networks

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Wingender Edgar

2009-05-01

Full Text Available Abstract Background The identification of network motifs as statistically over-represented topological patterns has become one of the most promising topics in the analysis of complex networks. The main focus is commonly made on how they operate by means of their internal organization. Yet, their contribution to a network's global architecture is poorly understood. However, this requires switching from the abstract view of a topological pattern to the level of its instances. Here, we show how a recently proposed metric, the pairwise disconnectivity index, can be adapted to survey if and which kind of topological patterns and their instances are most important for sustaining the connectivity within a network. Results The pairwise disconnectivity index of a pattern instance quantifies the dependency of the pairwise connections between vertices in a network on the presence of this pattern instance. Thereby, it particularly considers how the coherence between the unique constituents of a pattern instance relates to the rest of a network. We have applied the method exemplarily to the analysis of 3-vertex topological pattern instances in the transcription networks of a bacteria (E. coli, a unicellular eukaryote (S. cerevisiae and higher eukaryotes (human, mouse, rat. We found that in these networks only very few pattern instances break lots of the pairwise connections between vertices upon the removal of an instance. Among them network motifs do not prevail. Rather, those patterns that are shared by the three networks exhibit a conspicuously enhanced pairwise disconnectivity index. Additionally, these are often located in close vicinity to each other or are even overlapping, since only a small number of genes are repeatedly present in most of them. Moreover, evidence has gathered that the importance of these pattern instances is due to synergistic rather than merely additive effects between their constituents. Conclusion A new method has been proposed

Multi-country comparisons of energy performance: The index decomposition analysis approach

International Nuclear Information System (INIS)

Ang, B.W.; Xu, X.Y.; Su, Bin

2015-01-01

Index decomposition analysis (IDA) is a popular tool for studying changes in energy consumption over time in a country or region. This specific application of IDA, which may be called temporal decomposition analysis, has been extended by researchers and analysts to study variations in energy consumption or energy efficiency between countries or regions, i.e. spatial decomposition analysis. In spatial decomposition analysis, the main objective is often to understand the relative contributions of overall activity level, activity structure, and energy intensity in explaining differences in total energy consumption between two countries or regions. We review the literature of spatial decomposition analysis, investigate the methodological issues, and propose a spatial decomposition analysis framework for multi-region comparisons. A key feature of the proposed framework is that it passes the circularity test and provides consistent results for multi-region comparisons. A case study in which 30 regions in China are compared and ranked based on their performance in energy consumption is presented. - Highlights: • We conducted cross-regional comparisons of energy consumption using IDA. • We proposed two criteria for IDA method selection in spatial decomposition analysis. • We proposed a new model for regional comparison that passes the circularity test. • Features of the new model are illustrated using the data of 30 regions in China

Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota.

Directory of Open Access Journals (Sweden)

Xinli Wei

Full Text Available Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae. In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the "Automatic Barcode Gap Discovery" (ABGD, the Poisson tree process model (PTP, the General Mixed Yule Coalescent (GMYC, and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST. The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain

A comparison of fitness-case sampling methods for genetic programming

Science.gov (United States)

Martínez, Yuliana; Naredo, Enrique; Trujillo, Leonardo; Legrand, Pierrick; López, Uriel

2017-11-01

Genetic programming (GP) is an evolutionary computation paradigm for automatic program induction. GP has produced impressive results but it still needs to overcome some practical limitations, particularly its high computational cost, overfitting and excessive code growth. Recently, many researchers have proposed fitness-case sampling methods to overcome some of these problems, with mixed results in several limited tests. This paper presents an extensive comparative study of four fitness-case sampling methods, namely: Interleaved Sampling, Random Interleaved Sampling, Lexicase Selection and Keep-Worst Interleaved Sampling. The algorithms are compared on 11 symbolic regression problems and 11 supervised classification problems, using 10 synthetic benchmarks and 12 real-world data-sets. They are evaluated based on test performance, overfitting and average program size, comparing them with a standard GP search. Comparisons are carried out using non-parametric multigroup tests and post hoc pairwise statistical tests. The experimental results suggest that fitness-case sampling methods are particularly useful for difficult real-world symbolic regression problems, improving performance, reducing overfitting and limiting code growth. On the other hand, it seems that fitness-case sampling cannot improve upon GP performance when considering supervised binary classification.

Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family.

Science.gov (United States)

Kimura, M; Kimura, J; Hatakeyama, T

1988-11-21

The complete amino acid sequences of ribosomal proteins S11 from the Gram-positive eubacterium Bacillus stearothermophilus and of S19 from the archaebacterium Halobacterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein S11 family. Homologous proteins have previously been sequenced from Escherichia coli as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein S11 shares 68% identical residues with S11 from Escherichia coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45-49%) than to the eubacterial counterparts (35%).

Marketing through Social Media : Case: Comparison of Social Media Marketing Approaches of B2C Companies for Company X

OpenAIRE

Rantapelkonen Ahlberg, Jaana

2010-01-01

Rantapelkonen Ahlberg, Jaana. 2010. Social Media Marketing. Case: Comparison of Social Media Marketing Approaches of B2C Companies for Company X. Master’s Thesis. Kemi-Tornio University of Applied Sciences. Business and Culture. Pages 42 (74). The objective of this thesis is to provide insights on how Company X can use Social Media as a marketing and branding tool in consumer marketing in the Swedish market. More specifically, this study attempts to define what kinds of social media are u...

An experimental detrending approach to attributing change of pan evaporation in comparison with the traditional partial differential method

Science.gov (United States)

Wang, Tingting; Sun, Fubao; Xia, Jun; Liu, Wenbin; Sang, Yanfang

2017-04-01

In predicting how droughts and hydrological cycles would change in a warming climate, change of atmospheric evaporative demand measured by pan evaporation (Epan) is one crucial element to be understood. Over the last decade, the derived partial differential (PD) form of the PenPan equation is a prevailing attribution approach to attributing changes to Epan worldwide. However, the independency among climatic variables required by the PD approach cannot be met using long term observations. Here we designed a series of numerical experiments to attribute changes of Epan over China by detrending each climatic variable, i.e., an experimental detrending approach, to address the inter-correlation among climate variables, and made comparison with the traditional PD method. The results show that the detrending approach is superior not only to a complicate system with multi-variables and mixing algorithm like aerodynamic component (Ep,A) and Epan, but also to a simple case like radiative component (Ep,R), when compared with traditional PD method. The major reason for this is the strong and significant inter-correlation of input meteorological forcing. Very similar and fine attributing results have been achieved based on detrending approach and PD method after eliminating the inter-correlation of input through a randomize approach. The contribution of Rh and Ta in net radiation and thus Ep,R, which has been overlooked based on the PD method but successfully detected by detrending approach, provides some explanation to the comparing results. We adopted the control run from the detrending approach and applied it to made adjustment of PD method. Much improvement has been made and thus proven this adjustment an effective way in attributing changes to Epan. Hence, the detrending approach and the adjusted PD method are well recommended in attributing changes in hydrological models to better understand and predict water and energy cycle.

Application of analytic hierarchy process to extract the user's purpose of expert systems

International Nuclear Information System (INIS)

Gofuku, Akio; Wakabayashi, Jiro; Morimoto, Takashi.

1992-01-01

This paper deals with an application of analytic hierarchy process (AHP) to extract the user's purpose which must be input to expert systems. In the AHP, the process to obtain the weights for criteria by pairwise comparisons is interpreted as the extraction of the decision marker's idea about the importance of each criterion. With this interpretation, the analytic hierarchy process is applied to extract the analyst's idea of the weights of several factors to select constitutive equations suitable for a target analysis in a model selection support expert system under development for numerical simulation of nuclear thermal-hydraulics; the constitutive equations are ordinary introduced in a liquid-vapor two-phase flow analysis. Furthermore, an algorithm by applying the graph theory is shown to evaluate covering condition to obtain the weights from incomplete pairwise comparisons. (author)

Social relationships as a major determinant in the valuation of health states.

Science.gov (United States)

Frick, Ulrich; Irving, Hyacinth; Rehm, Jürgen

2012-03-01

To empirically determine the impact of the capacity to sustain social relationships on valuing health states. 68 clinical experts conducted a health state valuation exercise in five sites using pairwise comparison, ranking, and person trade-off as elicitation methods. 23,840 pairwise comparisons of a total of 379 health states were analyzed by conditional logistic regression. Social relationships had a clear monotonic association with perceived disability: the more limited the capacity to sustain social relationships, the more disabling the resulting health state valuations. The highest level of limitations with respect to social relationships was associated with slightly lower impact on health state valuations compared to the highest level of limitations in physical functioning. Social relationships showed an independent contribution to health state valuations and should be included in health state measures.

Comparison of community managed projects and conventional ...

African Journals Online (AJOL)

Comparison of community managed projects and conventional approaches in rural water supply of Ethiopia. ... African Journal of Environmental Science and Technology ... This study aimed to compare Community Managed Projects (CMP) approach with the conventional approaches (Non-CMP) in the case of Ethiopia.

Multi-Criteria Analysis of Laser Cut Surface Characteristics in CO2 Laser Cutting of Stainless Steel

Directory of Open Access Journals (Sweden)

M. Radovanović

2015-06-01

Full Text Available In this paper an approach for multi-criteria analysis of laser cut surface characteristics using multi-criteria decision making (MCDM approach was presented. Laser cutting experiment was conducted based on Taguchi’s L27 experimental design by varying laser power, cutting speed, assist gas pressure and focus position at three levels. Multi-criteria analysis was performed by using the weighted aggregated sum product assessment (WASPAS method while considering burr height, drag line separation, depth of separation line, surface roughness and perpendicularity of the cut as assessment criteria. Based on conducted experimental investigation the MCDM model with 27 alternatives (laser cuts and five criteria was developed. The relative importance of criteria was determined by using pair-wise comparison matrix and geometric mean method of the analytic hierarchy process (AHP method.

LEGAL CERTAINTY OF INDUSTRIAL DESIGN REVENUE IN INDONESIA BASED ON INTELLECTUAL PROPERTY APPROACH AND LEGAL COMPARISON

Directory of Open Access Journals (Sweden)

Ranti Fauza Mayana

2018-03-01

Full Text Available [Legal Certainty Of Industrial Design Revenue  In Indonesia Based On Intellectual Property Approach And Legal Comparison]  Protection of Industrial Designs, as well as intellectual property, is based on the ability of human creativity through creativity, taste and intention. According to Article 25 paragraph (1 TRIPs Protected Industrial Design Agreement is a new or original Industrial Design, this provision holds the principle that the novelty of a design is obtained when the design is differ from the previous, the novelty includes novelty and originality, the principal basis for the grant of Industrial Design, whereas this principle is not fully adopted in the provisions of Industrial Design. The Industrial Design Decree in Indonesia only requires novelty without clarifying how to interpret the novelty requirement so that a large number of Industrial Design Rights are obtained based on the Minor Change approach where slight differences in form and configuration have essentially demonstrated novelty. The minor change approach is considered to exclude the aspect of originality and is less able to provide legal certainty to the holder of the registered Industrial Design Rights. This paper aims to explore minor change approach as the basis for the evaluation of the novelty of Industrial Design in the perspective of comparative law in several countries of the world, namely the United States, Japan, the European Union and Australia as a study and reference material in an effort to establish protection of Industrial Design Rights in Indonesia that can provide legal certainty. Keywords: Industrial Design Revenue, Comparative Law.

A comparison of efficiency of mentoring and coaching the unemployed

OpenAIRE

Jagodnik, Sabina

2017-01-01

Master's thesis focuses on the comparison of mentoring and coaching of unemployed person entering labour market. Which approach is more siutable, considering unemployed person's needs, experience, knowledge and skills, which approach gives better results and what are advatages and disadvantages of both of them, are the questions anwsered by comparison between mentoring and coaching, based on three coaching and two mentoring process, using participatory action research approach. Effectiveness ...

A practical approach for writer-dependent symbol recognition using a writer-independent symbol recognizer.

Science.gov (United States)

LaViola, Joseph J; Zeleznik, Robert C

2007-11-01

We present a practical technique for using a writer-independent recognition engine to improve the accuracy and speed while reducing the training requirements of a writer-dependent symbol recognizer. Our writer-dependent recognizer uses a set of binary classifiers based on the AdaBoost learning algorithm, one for each possible pairwise symbol comparison. Each classifier consists of a set of weak learners, one of which is based on a writer-independent handwriting recognizer. During online recognition, we also use the n-best list of the writer-independent recognizer to prune the set of possible symbols and thus reduce the number of required binary classifications. In this paper, we describe the geometric and statistical features used in our recognizer and our all-pairs classification algorithm. We also present the results of experiments that quantify the effect incorporating a writer-independent recognition engine into a writer-dependent recognizer has on accuracy, speed, and user training time.

Emergent behaviors of the Schrödinger-Lohe model on cooperative-competitive networks

Science.gov (United States)

Huh, Hyungjin; Ha, Seung-Yeal; Kim, Dohyun

2017-12-01

We present several sufficient frameworks leading to the emergent behaviors of the coupled Schrödinger-Lohe (S-L) model under the same one-body external potential on cooperative-competitive networks. The S-L model was first introduced as a possible phenomenological model exhibiting quantum synchronization and its emergent dynamics on all-to-all cooperative networks has been treated via two distinct approaches, Lyapunov functional approach and the finite-dimensional reduction based on pairwise correlations. In this paper, we further generalize the finite-dimensional dynamical systems approach for pairwise correlation functions on cooperative-competitive networks and provide several sufficient frameworks leading to the collective exponential synchronization. For small systems consisting of three and four quantum subsystem, we also show that the system for pairwise correlations can be reduced to the Lotka-Volterra model with cooperative and competitive interactions, in which lots of interesting dynamical patterns appear, e.g., existence of closed orbits and limit-cycles.

A direct comparison of remote sensing approaches for high-throughput phenotyping in plant breeding

Directory of Open Access Journals (Sweden)

Maria Tattaris

2016-08-01

Full Text Available Remote sensing (RS of plant canopies permits non-intrusive, high-throughput monitoring of plant physiological characteristics. This study compared three RS approaches using a low flying UAV (unmanned aerial vehicle, with that of proximal sensing, and satellite-based imagery. Two physiological traits were considered, canopy temperature (CT and a vegetation index (NDVI, to determine the most viable approaches for large scale crop genetic improvement. The UAV-based platform achieves plot-level resolution while measuring several hundred plots in one mission via high-resolution thermal and multispectral imagery measured at altitudes of 30-100 m. The satellite measures multispectral imagery from an altitude of 770 km. Information was compared with proximal measurements using IR thermometers and an NDVI sensor at a distance of 0.5-1m above plots. For robust comparisons, CT and NDVI were assessed on panels of elite cultivars under irrigated and drought conditions, in different thermal regimes, and on un-adapted genetic resources under water deficit. Correlations between airborne data and yield/biomass at maturity were generally higher than equivalent proximal correlations. NDVI was derived from high-resolution satellite imagery for only larger sized plots (8.5 x 2.4 m due to restricted pixel density. Results support use of UAV-based RS techniques for high-throughput phenotyping for both precision and efficiency.

In silico local structure approach: a case study on outer membrane proteins.

Science.gov (United States)

Martin, Juliette; de Brevern, Alexandre G; Camproux, Anne-Claude

2008-04-01

The detection of Outer Membrane Proteins (OMP) in whole genomes is an actual question, their sequence characteristics have thus been intensively studied. This class of protein displays a common beta-barrel architecture, formed by adjacent antiparallel strands. However, due to the lack of available structures, few structural studies have been made on this class of proteins. Here we propose a novel OMP local structure investigation, based on a structural alphabet approach, i.e., the decomposition of 3D structures using a library of four-residue protein fragments. The optimal decomposition of structures using hidden Markov model results in a specific structural alphabet of 20 fragments, six of them dedicated to the decomposition of beta-strands. This optimal alphabet, called SA20-OMP, is analyzed in details, in terms of local structures and transitions between fragments. It highlights a particular and strong organization of beta-strands as series of regular canonical structural fragments. The comparison with alphabets learned on globular structures indicates that the internal organization of OMP structures is more constrained than in globular structures. The analysis of OMP structures using SA20-OMP reveals some recurrent structural patterns. The preferred location of fragments in the distinct regions of the membrane is investigated. The study of pairwise specificity of fragments reveals that some contacts between structural fragments in beta-sheets are clearly favored whereas others are avoided. This contact specificity is stronger in OMP than in globular structures. Moreover, SA20-OMP also captured sequential information. This can be integrated in a scoring function for structural model ranking with very promising results. (c) 2007 Wiley-Liss, Inc.

[Comparison of ablation of left-sided accessory pathway by atrial septal and retrograde arterial approach].

Science.gov (United States)

Zhu, J G; Bao, Z Y; Gu, X

2017-03-07

Objective: To compare the advantages and disadvantages of radiofrequency ablation of left-sided accessory pathways by via atrial septal approach with retrograde through aortic approach. Methods: A total of 184 patients of left-side accessory pathways were treated in Taizhou People's Hospital and the Subei People's Hospital from March 2012 to August 2015.A total of 103 cases were treated by aortic retrograde approach as through arterial group, 81 cases were treated by punctured atrial septal to left atrial for mapping and ablation as through atrial septal group.Comparison of ablation procedure time, total and pathways of different parts(subgroup) at instant success and relapse rates, safety (serious complications), and statistics other complications in operation and postoperative. Results: Through arterial group and through atrial septal group were no significant difference ( P >0.05) in the ablation procedure time((25±18 ) vs (22±15)min ), instant success(98.1% vs 97.5%) and relapse rates(1.0% vs 1.2%), security(1 vs 0 case). There was no statistical difference in septal part subgroups (all P >0.05) in the ablation procedure time((22±18)vs (25±19)min), instant success(91.7% vs 89.9 %) and relapse rates(0 vs 11.1%); posterior wall subgroup had no statistical difference in the ablation procedure time((18±15)vs (16±12)min), instant success(100% vs 100 %) and relapse rates(0 vs 0)(all P >0.05); side wall subgroup had no statistical difference in the ablation procedure time((29±20)vs (21±18) min), instant success (98.3% vs 98.1%)and relapse rates(1.7% vs 0%)(all P >0.05). Conclusion: Ablation of left-sided accessory pathways by transseptal approach and transaortic approach has no statistical difference in the procedure time, instant success and relapse rates, security.In a particular case, there is a certain complementarity between the two methods.

Transoral endoscopic thyroidectomy vestibular approach (TOETVA) for Graves' disease: a comparison of surgical results with open thyroidectomy.

Science.gov (United States)

Jitpratoom, Pornpeera; Ketwong, Khwannara; Sasanakietkul, Thanyawat; Anuwong, Angkoon

2016-12-01

Transoral endoscopic thyroidectomy vestibular approach (TOETVA) provides excellent cosmetic results from its potential for scar-free operation. The procedure has been applied successfully for Graves' disease by the authors of this work and compared with the standard open cervical approach to evaluate its safety and outcomes. From January 2014 to November 2016, a total of 97 patients with Graves' disease were reviewed retrospectively. Open thyroidectomy (OT) and TOETVA were performed in 49 patients and 46 patients, respectively. For TOETVA, a three-port technique through the oral vestibule was utilized. The thyroidectomy was done endoscopically using conventional laparoscopic instruments and an ultrasonic device. Patient demographics and surgical variables, including operative time, blood loss, and complications, were investigated and compared. TOETVA was performed successfully in all 45 patients, although conversion to open surgery was deemed necessary in one patient. All patient characteristics for both groups were similar. Operative time was shorter for the OT group compared to the TOETVA group, which totaled 101.97±24.618 and 134.11±31.48 minutes, respectively (PGraves' disease in comparison to the standard open cervical approach. It is considered a viable alternative for patients who have been indicated for surgery with excellent cosmetic results.

A spatial decision support system (SDSS) for sustainable tourism planning in Cameron Highlands, Malaysia

International Nuclear Information System (INIS)

Aminu, M; Yusof, K W; Matori, A N

2014-01-01

The study describes a methodological approach based on an integrated use of Geographic Information System (GIS) and Analytic Network Process (ANP) of Multi Criteria Evaluation (MCE) to determine nature conservation and tourism development priorities among the highland areas. A set of criteria and indicators were defined to evaluate the highlands biodiversity conservation and tourism development. Pair wise comparison technique was used in order to support solution of a decision problem by evaluating possible alternatives from different perspectives. After the weights have been derived from the pairwise comparison technique, the next step was to compute the unweighted supermatrix, weighted supermatrix and the limit matrix. The limit matrix was normalized to obtain the priorities and the results transferred into GIS environment. Elements evaluated and ranked were represented by criterion maps. Map layers reflecting the opinion of different experts involved were summed using the weighted overlay approach of GIS. Subsequently sustainable tourism development scenarios were generated. The generation of scenarios highlighted the critical issues of the decision problem because it allows one to gradually narrow down a problem

A spatial decision support system (SDSS) for sustainable tourism planning in Cameron Highlands, Malaysia

Science.gov (United States)

Aminu, M.; Matori, A. N.; Yusof, K. W.

2014-02-01

The study describes a methodological approach based on an integrated use of Geographic Information System (GIS) and Analytic Network Process (ANP) of Multi Criteria Evaluation (MCE) to determine nature conservation and tourism development priorities among the highland areas. A set of criteria and indicators were defined to evaluate the highlands biodiversity conservation and tourism development. Pair wise comparison technique was used in order to support solution of a decision problem by evaluating possible alternatives from different perspectives. After the weights have been derived from the pairwise comparison technique, the next step was to compute the unweighted supermatrix, weighted supermatrix and the limit matrix. The limit matrix was normalized to obtain the priorities and the results transferred into GIS environment. Elements evaluated and ranked were represented by criterion maps. Map layers reflecting the opinion of different experts involved were summed using the weighted overlay approach of GIS. Subsequently sustainable tourism development scenarios were generated. The generation of scenarios highlighted the critical issues of the decision problem because it allows one to gradually narrow down a problem.

Eigenvalue-eigenvector decomposition (EED) analysis of dissimilarity and covariance matrix obtained from total synchronous fluorescence spectral (TSFS) data sets of herbal preparations: Optimizing the classification approach

Science.gov (United States)

Tarai, Madhumita; Kumar, Keshav; Divya, O.; Bairi, Partha; Mishra, Kishor Kumar; Mishra, Ashok Kumar

2017-09-01

The present work compares the dissimilarity and covariance based unsupervised chemometric classification approaches by taking the total synchronous fluorescence spectroscopy data sets acquired for the cumin and non-cumin based herbal preparations. The conventional decomposition method involves eigenvalue-eigenvector analysis of the covariance of the data set and finds the factors that can explain the overall major sources of variation present in the data set. The conventional approach does this irrespective of the fact that the samples belong to intrinsically different groups and hence leads to poor class separation. The present work shows that classification of such samples can be optimized by performing the eigenvalue-eigenvector decomposition on the pair-wise dissimilarity matrix.

Ranking alternatives based on imprecise multi-criteria data and pairwise overlap dominance relations

DEFF Research Database (Denmark)

Franco de los Rios, Camilo Andres; Hougaard, Jens Leth; Nielsen, Kurt

illustrative example is given for comparison with standard methods like PROMETHEE. The proposed methodology takes into account the risk attitudes of decision makers, organizing the alternatives and ranking them according to their relevance. The whole interactive decision support allows understanding...

Comparison of the Remineralizing Effects of Sodium Fluoride and Bioactive Glass Using Bioerodible Gel Systems

Directory of Open Access Journals (Sweden)

Attiguppe Ramashetty Prabhakar

2009-12-01

Full Text Available Background and aims. A carious lesion is the accumulation of numerous episodes of de- and remineralization, rather than a unidirectional demineralization process. Tooth destruction can be arrested or reversed by the frequent delivery of fluoride or calcium/phosphorous ions to the tooth surface. The present study compared and evaluated the remineralization potential of sodium fluoride and bioactive glass delivered through a bioerodible gel system. Materials and methods. Longitudinal sections of artificial carious lesions, created at the gingivofacial surface of 64 primary maxillary incisors were photographed under a polarized light microscope and quantified for demineralization. The sections were repositioned into the tooth form and randomly mounted in sets of four that simulated an arch form. The teeth were divided into 4 groups: 1 sodium fluoride films, 2 bioactive glass films, 3 control films placed interproximally and 4 nontreatment group. Following exposure to artificial saliva for 30 days, the lesions were again photographed and quantified as above. The recorded values were statistically analyzed using Student’s paired t-test for intragroup comparison, one-way ANOVA and Post-Hoc Tukey’s test for pairwise comparison. Results. The sodium fluoride and bioactive gel groups showed significant remineralization compared with the control groups (P < 0.001. Conclusion. Bioerodible gel films can be used to deliver remineralizing agents to enhance remineralization.

Anaesthetic safety of the Macintosh® oral laryngeal spray device

African Journals Online (AJOL)

2013-01-14

Jan 14, 2013 ... is there a difference in the amount of local anaesthetic delivered when two ... pairwise comparisons were made among the factors using Student's t-test with Tukey's ... a dangerous outlier (Figure 1). This amount, inadvertently.

Metal Mixture Modeling Evaluation project: 2. Comparison of four modeling approaches

Science.gov (United States)

Farley, Kevin J.; Meyer, Joe; Balistrieri, Laurie S.; DeSchamphelaere, Karl; Iwasaki, Yuichi; Janssen, Colin; Kamo, Masashi; Lofts, Steve; Mebane, Christopher A.; Naito, Wataru; Ryan, Adam C.; Santore, Robert C.; Tipping, Edward

2015-01-01

As part of the Metal Mixture Modeling Evaluation (MMME) project, models were developed by the National Institute of Advanced Industrial Science and Technology (Japan), the U.S. Geological Survey (USA), HDR⎪HydroQual, Inc. (USA), and the Centre for Ecology and Hydrology (UK) to address the effects of metal mixtures on biological responses of aquatic organisms. A comparison of the 4 models, as they were presented at the MMME Workshop in Brussels, Belgium (May 2012), is provided herein. Overall, the models were found to be similar in structure (free ion activities computed by WHAM; specific or non-specific binding of metals/cations in or on the organism; specification of metal potency factors and/or toxicity response functions to relate metal accumulation to biological response). Major differences in modeling approaches are attributed to various modeling assumptions (e.g., single versus multiple types of binding site on the organism) and specific calibration strategies that affected the selection of model parameters. The models provided a reasonable description of additive (or nearly additive) toxicity for a number of individual toxicity test results. Less-than-additive toxicity was more difficult to describe with the available models. Because of limitations in the available datasets and the strong inter-relationships among the model parameters (log KM values, potency factors, toxicity response parameters), further evaluation of specific model assumptions and calibration strategies is needed.

Identifying functional reorganization of spelling networks: an individual peak probability comparison approach

Science.gov (United States)

Purcell, Jeremy J.; Rapp, Brenda

2013-01-01

Previous research has shown that damage to the neural substrates of orthographic processing can lead to functional reorganization during reading (Tsapkini et al., 2011); in this research we ask if the same is true for spelling. To examine the functional reorganization of spelling networks we present a novel three-stage Individual Peak Probability Comparison (IPPC) analysis approach for comparing the activation patterns obtained during fMRI of spelling in a single brain-damaged individual with dysgraphia to those obtained in a set of non-impaired control participants. The first analysis stage characterizes the convergence in activations across non-impaired control participants by applying a technique typically used for characterizing activations across studies: Activation Likelihood Estimate (ALE) (Turkeltaub et al., 2002). This method was used to identify locations that have a high likelihood of yielding activation peaks in the non-impaired participants. The second stage provides a characterization of the degree to which the brain-damaged individual's activations correspond to the group pattern identified in Stage 1. This involves performing a Mahalanobis distance statistics analysis (Tsapkini et al., 2011) that compares each of a control group's peak activation locations to the nearest peak generated by the brain-damaged individual. The third stage evaluates the extent to which the brain-damaged individual's peaks are atypical relative to the range of individual variation among the control participants. This IPPC analysis allows for a quantifiable, statistically sound method for comparing an individual's activation pattern to the patterns observed in a control group and, thus, provides a valuable tool for identifying functional reorganization in a brain-damaged individual with impaired spelling. Furthermore, this approach can be applied more generally to compare any individual's activation pattern with that of a set of other individuals. PMID:24399981

Knowledge-based biomedical word sense disambiguation: comparison of approaches

Directory of Open Access Journals (Sweden)

Aronson Alan R

2010-11-01

Full Text Available Abstract Background Word sense disambiguation (WSD algorithms attempt to select the proper sense of ambiguous terms in text. Resources like the UMLS provide a reference thesaurus to be used to annotate the biomedical literature. Statistical learning approaches have produced good results, but the size of the UMLS makes the production of training data infeasible to cover all the domain. Methods We present research on existing WSD approaches based on knowledge bases, which complement the studies performed on statistical learning. We compare four approaches which rely on the UMLS Metathesaurus as the source of knowledge. The first approach compares the overlap of the context of the ambiguous word to the candidate senses based on a representation built out of the definitions, synonyms and related terms. The second approach collects training data for each of the candidate senses to perform WSD based on queries built using monosemous synonyms and related terms. These queries are used to retrieve MEDLINE citations. Then, a machine learning approach is trained on this corpus. The third approach is a graph-based method which exploits the structure of the Metathesaurus network of relations to perform unsupervised WSD. This approach ranks nodes in the graph according to their relative structural importance. The last approach uses the semantic types assigned to the concepts in the Metathesaurus to perform WSD. The context of the ambiguous word and semantic types of the candidate concepts are mapped to Journal Descriptors. These mappings are compared to decide among the candidate concepts. Results are provided estimating accuracy of the different methods on the WSD test collection available from the NLM. Conclusions We have found that the last approach achieves better results compared to the other methods. The graph-based approach, using the structure of the Metathesaurus network to estimate the relevance of the Metathesaurus concepts, does not perform well

A Novel Pairwise Comparison-Based Method to Determine Radiation Dose Reduction Potentials of Iterative Reconstruction Algorithms, Exemplified Through Circle of Willis Computed Tomography Angiography.

Science.gov (United States)

Ellmann, Stephan; Kammerer, Ferdinand; Brand, Michael; Allmendinger, Thomas; May, Matthias S; Uder, Michael; Lell, Michael M; Kramer, Manuel

2016-05-01

The aim of this study was to determine the dose reduction potential of iterative reconstruction (IR) algorithms in computed tomography angiography (CTA) of the circle of Willis using a novel method of evaluating the quality of radiation dose-reduced images. This study relied on ReconCT, a proprietary reconstruction software that allows simulating CT scans acquired with reduced radiation dose based on the raw data of true scans. To evaluate the performance of ReconCT in this regard, a phantom study was performed to compare the image noise of true and simulated scans within simulated vessels of a head phantom. That followed, 10 patients scheduled for CTA of the circle of Willis were scanned according to our institute's standard protocol (100 kV, 145 reference mAs). Subsequently, CTA images of these patients were reconstructed as either a full-dose weighted filtered back projection or with radiation dose reductions down to 10% of the full-dose level and Sinogram-Affirmed Iterative Reconstruction (SAFIRE) with either strength 3 or 5. Images were marked with arrows pointing on vessels of different sizes, and image pairs were presented to observers. Five readers assessed image quality with 2-alternative forced choice comparisons. In the phantom study, no significant differences were observed between the noise levels of simulated and true scans in filtered back projection, SAFIRE 3, and SAFIRE 5 reconstructions.The dose reduction potential for patient scans showed a strong dependence on IR strength as well as on the size of the vessel of interest. Thus, the potential radiation dose reductions ranged from 84.4% for the evaluation of great vessels reconstructed with SAFIRE 5 to 40.9% for the evaluation of small vessels reconstructed with SAFIRE 3. This study provides a novel image quality evaluation method based on 2-alternative forced choice comparisons. In CTA of the circle of Willis, higher IR strengths and greater vessel sizes allowed higher degrees of radiation dose

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.

Science.gov (United States)

Dessimoz, Christophe; Boeckmann, Brigitte; Roth, Alexander C J; Gonnet, Gaston H

2006-01-01

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.

Comparing Diagnostic Accuracy of Cognitive Screening Instruments: A Weighted Comparison Approach

Directory of Open Access Journals (Sweden)

A.J. Larner

2013-03-01

Full Text Available Background/Aims: There are many cognitive screening instruments available to clinicians when assessing patients' cognitive function, but the best way to compare the diagnostic utility of these tests is uncertain. One method is to undertake a weighted comparison which takes into account the difference in sensitivity and specificity of two tests, the relative clinical misclassification costs of true- and false-positive diagnosis, and also disease prevalence. Methods: Data were examined from four pragmatic diagnostic accuracy studies from one clinic which compared the Mini-Mental State Examination (MMSE with the Addenbrooke's Cognitive Examination-Revised (ACE-R, the Montreal Cognitive Assessment (MoCA, the Test Your Memory (TYM test, and the Mini-Mental Parkinson (MMP, respectively. Results: Weighted comparison calculations suggested a net benefit for ACE-R, MoCA, and MMP compared to MMSE, but a net loss for TYM test compared to MMSE. Conclusion: Routine incorporation of weighted comparison or other similar net benefit measures into diagnostic accuracy studies merits consideration to better inform clinicians of the relative value of cognitive screening instruments.

Density-functional approaches to noncovalent interactions: a comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals.

Science.gov (United States)

Burns, Lori A; Vázquez-Mayagoitia, Alvaro; Sumpter, Bobby G; Sherrill, C David

2011-02-28

A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmark-quality evaluations of binding strength compiled for molecular complexes of diverse size and nature. In particular, the efficacy of functionals deliberately crafted to encompass long-range forces, a posteriori DFT+dispersion corrections (DFT-D2 and DFT-D3), and exchange-hole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 [revised in J. Chem. Phys. 132, 144104 (2010)] and JSCH test sets of minimum-energy structures, as well as collections of dispersion-bound (NBC10) and hydrogen-bonded (HBC6) dissociation curves and a pairwise decomposition of a protein-ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBE-D, BP86-D, B97-D, PBE0-D, B3LYP-D, B970-D, M05-2X, M06-2X, ωB97X-D, B2PLYP-D, XYG3, and B3LYP-XDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible double-ζ or robust triple-ζ basis set regimes and among hydrogen-bonded or dispersion-dominated complexes. For overall results, M05-2X, B97-D3, and B970-D2 yield superior values in conjunction with aug-cc-pVDZ, for a mean absolute deviation of 0.41 - 0.49 kcal/mol, and B3LYP-D3, B97-D3, ωB97X-D, and B2PLYP-D3 dominate with aug-cc-pVTZ, affording, together with XYG3/6-311+G(3df,2p), a mean absolute deviation of 0.33 - 0.38 kcal/mol.

Renewables in residential development. An integrated GIS-based multicriteria approach for decentralized micro-renewable energy production in new settlement development. A case study of the eastern metropolitan area of Cagliari, Sardinia, Italy

Energy Technology Data Exchange (ETDEWEB)

Palmas, Claudia; Haaren, Christina von [Hannover Univ. (Germany). Dept. of Environmental Planning; Abis, Emanuela [Cagliari Univ. (Italy). Dept. of Civil, Environmental Engineering and Architecture; Lovett, Andrew [East Anglia Univ., Norwich (United Kingdom). School of Environmental Sciences

2012-12-15

In recent years, there has been an increasing interest in using micro-renewable energy sources. However, planning has not yet developed methodological approaches (1) for spatially optimizing residential development according to the different renewable energy potentials and (2) for integrating objectives of optimized energy efficiency with other environmental requirements and concerns. This study addresses these topics by firstly presenting a new concept for the regional planning. The methodological approach for the evaluation of spatial variations in the available energy potential was based on the combination of existing methods adapted to the local scale and data availability. For assessing the bioenergy potential, a new method was developed. Other environmental criteria for deciding about sustainable locations were identified through a survey of more than 100 expert respondents. This survey involved pairwise comparisons of relevant factors, which were then translated into relative weights using the Analytical Hierarchy Process. Subsequently, these weights were applied to factor maps in a Geographical Information System using a weighted linear combination method. In the test region, the eastern metropolitan area of Cagliari, Sardinia, this analysis resulted in the designation of suitable areas for new settlements and preferred locations for microrenewable technologies. Based on expert preferences, a number of alternatives for future housing development were identified, which can be integrated in the early stages of land use or development plans. The method proposed can be an effective tool for planners to assess changes and to identify the best solution in terms of sustainable development. (orig.)

Learning radiological appearances of diseases: Does comparison help?

NARCIS (Netherlands)

Kok, Ellen M.; de Bruin, Anique B H; Robben, Simon C. F.; van Merrienboer, Jeroen J. G.

Comparison learning is a promising approach for learning complex real-life visual tasks. When medical students study radiological appearances of diseases, comparison of images showing diseases with images showing no abnormalities could help them learn to discriminate relevant, disease-related

Pairwise comparison of 89Zr- and 124I-labeled cG250 based on positron emission tomography imaging and nonlinear immunokinetic modeling: in vivo carbonic anhydrase IX receptor binding and internalization in mouse xenografts of clear-cell renal cell carcinoma

International Nuclear Information System (INIS)

Cheal, Sarah M.; Punzalan, Blesida; Doran, Michael G.; Osborne, Joseph R.; Evans, Michael J.; Lewis, Jason S.; Zanzonico, Pat; Larson, Steven M.

2014-01-01

The PET tracer, 124 I-cG250, directed against carbonic anhydrase IX (CAIX) shows promise for presurgical diagnosis of clear-cell renal cell carcinoma (ccRCC) (Divgi et al. in Lancet Oncol 8:304-310, 2007; Divgi et al. in J Clin Oncol 31:187-194, 2013). The radiometal 89 Zr, however, may offer advantages as a surrogate PET nuclide over 124 I in terms of greater tumor uptake and retention (Rice et al. in Semin Nucl Med 41:265-282, 2011). We have developed a nonlinear immunokinetic model to facilitate a quantitative comparison of absolute uptake and antibody turnover between 124 I-cG250 and 89 Zr-cG250 using a human ccRCC xenograft tumor model in mice. We believe that this unique model better relates quantitative imaging data to the salient biological features of tumor antibody-antigen binding and turnover. We conducted experiments with 89 Zr-cG250 and 124 I-cG250 using a human ccRCC cell line (SK-RC-38) to characterize the binding affinity and internalization kinetics of the two tracers in vitro. Serial PET imaging was performed in mice bearing subcutaneous ccRCC tumors to simultaneously detect and quantify time-dependent tumor uptake in vivo. Using the known specific activities of the two tracers, the equilibrium rates of antibody internalization and turnover in the tumors were derived from the PET images using nonlinear compartmental modeling. The two tracers demonstrated virtually identical tumor cell binding and internalization but showed markedly different retentions in vitro. Superior PET images were obtained using 89 Zr-cG250, owing to the more prolonged trapping of the radiolabel in the tumor and simultaneous washout from normal tissues. Estimates of cG250/CAIX complex turnover were 1.35 - 5.51 x 10 12 molecules per hour per gram of tumor (20 % of receptors internalized per hour), and the ratio of 124 I/ 89 Zr atoms released per unit time by tumor was 17.5. Pairwise evaluation of 89 Zr-cG250 and 124 I-cG250 provided the basis for a nonlinear immunokinetic

European Measurement Comparisons of Environmental Radioactivity

International Nuclear Information System (INIS)

Waetjen, Uwe

2008-01-01

The scheme of European measurement comparisons to verify radioactivity monitoring in the European Union is briefly explained. After a review of comparisons conducted during the years 1990, the approach of IRMM organising these comparisons since 2003 is presented. IRMM is providing comparison samples with a reference value traceable to the SI units and which is fully documented to all participants and national authorities after completion of the comparison. The sample preparation and determination of traceable reference values at IRMM, the sample treatment and measurement in the participating laboratories, as well as the evaluation of comparison results are described in some detail using the example of an air filter comparison. The results of a comparison to determine metabolised 40 K, 90 Sr and 137 Cs in milk powder are presented as well. The necessary improvements in the estimation of measurement uncertainty by the participating laboratories are discussed. The performance of individual laboratories which have participated in at least four comparison exercises over the years is studied in terms of observable trends

Investigation of the range of validity of the pairwise summation method applied to the calculation of the surface roughness correction to the van der Waals force

Science.gov (United States)

Gusso, André; Burnham, Nancy A.

2016-09-01

It has long been recognized that stochastic surface roughness can considerably change the van der Waals (vdW) force between interacting surfaces and particles. However, few analytical expressions for the vdW force between rough surfaces have been presented in the literature. Because they have been derived using perturbative methods or the proximity force approximation the expressions are valid when the roughness correction is small and for a limited range of roughness parameters and surface separation. In this work, a nonperturbative approach, the effective density method (EDM) is proposed to circumvent some of these limitations. The method simplifies the calculations of the roughness correction based on pairwise summation (PWS), and allows us to derive simple expressions for the vdW force and energy between two semispaces covered with stochastic rough surfaces. Because the range of applicability of PWS and, therefore, of our results, are not known a priori, we compare the predictions based on the EDM with those based on the multilayer effective medium model, whose range of validity can be defined more properly and which is valid when the roughness correction is comparatively large. We conclude that the PWS can be used for roughness characterized by a correlation length of the order of its rms amplitude, when this amplitude is of the order of or smaller than a few nanometers, and only for typically insulating materials such as silicon dioxide, silicon nitride, diamond, and certain glasses, polymers and ceramics. The results are relevant for the correct modeling of systems where the vdW force can play a significant role such as micro and nanodevices, for the calculation of the tip-sample force in atomic force microscopy, and in problems involving adhesion.

The Innovative Approaches to Packaging – Comparison Analysis of Intelligent and Active Packaging Perceptions in Slovakia

Directory of Open Access Journals (Sweden)

Loucanova Erika

2017-06-01

Full Text Available Packaging has always served a practical function - to hold goods together and protect it when moving toward the customer through distribution channel. Today packaging is also a container for promoting the product and making it easier and safer to use. The sheer importance of packaging functions is still growing and consequently the interest of the company is to access to the packaging more innovative and creative. The paper deals with the innovative approaches to packaging resulting in the creation of packaging with interactive active features in the form of active and intelligent packaging. Using comparative analysis, we monitored the perception of the active packaging functions in comparison to intelligent packaging function among different age categories. We identified the age categories which are most interested in these functions.

A Cross-Disciplinary Successful Aging Intervention and Evaluation: Comparison of Person-to-Person and Digital-Assisted Approaches

Directory of Open Access Journals (Sweden)

Hui-Chuan Hsu

2018-05-01

Full Text Available Background: Successful aging has been the paradigm of old-age life. The purpose of this study was to implement and evaluate a cross-disciplinary intervention program using two approaches for community-based older adults in Taichung, Taiwan. Methods: The content of the intervention included successful aging concepts and preparation, physical activity, chronic disease and health management, dietary and nutrition information, cognitive training, emotional awareness and coping skills, family relationship and resilience, legal concepts regarding financial protection, and Internet use. The traditional person-to-person (P2P intervention approach was implemented among participants at urban centers, and the personal-and-digital (P&D intervention approach was implemented among participants at rural centers; before the P&D group received the intervention, participants were assessed as the control group for comparison. Results: Healthy behavior and nutrition improved for the P2P group, although not significantly. Strategies for adapting to old age and reducing ineffective coping were significantly improved in the P2P group. The ability to search for health information improved in the P&D group, and knowledge of finance-related law increased in the P2P group. Conclusion: A continuous, well-designed and evidence-based intervention program is beneficial for improving the health of older adults, or at least delaying its decline.

A multivariate extension of mutual information for growing neural networks.

Science.gov (United States)

Ball, Kenneth R; Grant, Christopher; Mundy, William R; Shafer, Timothy J

2017-11-01

Recordings of neural network activity in vitro are increasingly being used to assess the development of neural network activity and the effects of drugs, chemicals and disease states on neural network function. The high-content nature of the data derived from such recordings can be used to infer effects of compounds or disease states on a variety of important neural functions, including network synchrony. Historically, synchrony of networks in vitro has been assessed either by determination of correlation coefficients (e.g. Pearson's correlation), by statistics estimated from cross-correlation histograms between pairs of active electrodes, and/or by pairwise mutual information and related measures. The present study examines the application of Normalized Multiinformation (NMI) as a scalar measure of shared information content in a multivariate network that is robust with respect to changes in network size. Theoretical simulations are designed to investigate NMI as a measure of complexity and synchrony in a developing network relative to several alternative approaches. The NMI approach is applied to these simulations and also to data collected during exposure of in vitro neural networks to neuroactive compounds during the first 12 days in vitro, and compared to other common measures, including correlation coefficients and mean firing rates of neurons. NMI is shown to be more sensitive to developmental effects than first order synchronous and nonsynchronous measures of network complexity. Finally, NMI is a scalar measure of global (rather than pairwise) mutual information in a multivariate network, and hence relies on less assumptions for cross-network comparisons than historical approaches. Copyright © 2017 Elsevier Ltd. All rights reserved.

Further investigations of the W-test for pairwise epistasis testing [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Richard Howey

2017-07-01

Full Text Available Background: In a recent paper, a novel W-test for pairwise epistasis testing was proposed that appeared, in computer simulations, to have higher power than competing alternatives. Application to genome-wide bipolar data detected significant epistasis between SNPs in genes of relevant biological function. Network analysis indicated that the implicated genes formed two separate interaction networks, each containing genes highly related to autism and neurodegenerative disorders. Methods: Here we investigate further the properties and performance of the W-test via theoretical evaluation, computer simulations and application to real data. Results: We demonstrate that, for common variants, the W-test is closely related to several existing tests of association allowing for interaction, including logistic regression on 8 degrees of freedom, although logistic regression can show inflated type I error for low minor allele frequencies,  whereas the W-test shows good/conservative type I error control. Although in some situations the W-test can show higher power, logistic regression is not limited to tests on 8 degrees of freedom but can instead be taylored to impose greater structure on the assumed alternative hypothesis, offering a power advantage when the imposed structure matches the true structure. Conclusions: The W-test is a potentially useful method for testing for association - without necessarily implying interaction - between genetic variants disease, particularly when one or more of the genetic variants are rare. For common variants, the advantages of the W-test are less clear, and, indeed, there are situations where existing methods perform better. In our investigations, we further uncover a number of problems with the practical implementation and application of the W-test (to bipolar disorder previously described, apparently due to inadequate use of standard data quality-control procedures. This observation leads us to urge caution in

Atmospheric Correction Inter-Comparison Exercise

Directory of Open Access Journals (Sweden)

Georgia Doxani

2018-02-01

Full Text Available The Atmospheric Correction Inter-comparison eXercise (ACIX is an international initiative with the aim to analyse the Surface Reflectance (SR products of various state-of-the-art atmospheric correction (AC processors. The Aerosol Optical Thickness (AOT and Water Vapour (WV are also examined in ACIX as additional outputs of AC processing. In this paper, the general ACIX framework is discussed; special mention is made of the motivation to initiate the experiment, the inter-comparison protocol, and the principal results. ACIX is free and open and every developer was welcome to participate. Eventually, 12 participants applied their approaches to various Landsat-8 and Sentinel-2 image datasets acquired over sites around the world. The current results diverge depending on the sensors, products, and sites, indicating their strengths and weaknesses. Indeed, this first implementation of processor inter-comparison was proven to be a good lesson for the developers to learn the advantages and limitations of their approaches. Various algorithm improvements are expected, if not already implemented, and the enhanced performances are yet to be assessed in future ACIX experiments.

Comparison of two anoxia models in rainbow trout cells by a 2-DE and MS/MS-based proteome approach

DEFF Research Database (Denmark)

Wulff, Tune; Hoffmann, E.K.; Roepstorff, P.

2008-01-01

In the literature, a variety of ways have been used to obtain anoxia, and most often results are compared between studies without taking into consideration how anoxia has been obtained. Here, we provide a comprehensive study of two types of anoxia, using a proteomics approach to compare changes...... and protein synthesis. It was also revealed that the level of a number of keratins was down-regulated. This study therefore provides a valuable comparison of two different anoxia models and shows that great care should be taken when comparing the effects of anoxia in studies that have used different types...

An estimation of the transformation value by means of the estimation function. Market Comparison Approach with abridged data chart

Directory of Open Access Journals (Sweden)

Maurizio d’Amato

2015-06-01

Full Text Available This essay suggests a re-elaboration of the Marketing Comparison Approach in order to set the value of properties subject to transformation. The essay focuses on identifying the property valuation following a certain transformation and is aimed at determining the land value by means of the extraction method. The outcome, based on trading data and a study case in the province of Bari may also be applied to under construction properties valuation and to the identification of the value of properties under construction, (investment property under construction by means of the Future Value method.

Performance comparisons between PCA-EA-LBG and PCA-LBG-EA approaches in VQ codebook generation for image compression

Science.gov (United States)

Tsai, Jinn-Tsong; Chou, Ping-Yi; Chou, Jyh-Horng

2015-11-01

The aim of this study is to generate vector quantisation (VQ) codebooks by integrating principle component analysis (PCA) algorithm, Linde-Buzo-Gray (LBG) algorithm, and evolutionary algorithms (EAs). The EAs include genetic algorithm (GA), particle swarm optimisation (PSO), honey bee mating optimisation (HBMO), and firefly algorithm (FF). The study is to provide performance comparisons between PCA-EA-LBG and PCA-LBG-EA approaches. The PCA-EA-LBG approaches contain PCA-GA-LBG, PCA-PSO-LBG, PCA-HBMO-LBG, and PCA-FF-LBG, while the PCA-LBG-EA approaches contain PCA-LBG, PCA-LBG-GA, PCA-LBG-PSO, PCA-LBG-HBMO, and PCA-LBG-FF. All training vectors of test images are grouped according to PCA. The PCA-EA-LBG used the vectors grouped by PCA as initial individuals, and the best solution gained by the EAs was given for LBG to discover a codebook. The PCA-LBG approach is to use the PCA to select vectors as initial individuals for LBG to find a codebook. The PCA-LBG-EA used the final result of PCA-LBG as an initial individual for EAs to find a codebook. The search schemes in PCA-EA-LBG first used global search and then applied local search skill, while in PCA-LBG-EA first used local search and then employed global search skill. The results verify that the PCA-EA-LBG indeed gain superior results compared to the PCA-LBG-EA, because the PCA-EA-LBG explores a global area to find a solution, and then exploits a better one from the local area of the solution. Furthermore the proposed PCA-EA-LBG approaches in designing VQ codebooks outperform existing approaches shown in the literature.

Mild Traumatic Brain Injury and Dynamic Simulated Shooting Performance

Science.gov (United States)

2016-02-01

differences between tasks. All pairwise comparisons were adjusted with a Sidak correction for multiple comparisons. TLX scores 0 5 10 15 20 25 30 35...research at multiple sites. Specific to the question of MTBI-related balance, we recommend that future studies seek, when feasible, to quantify body sway...higher ratings of perceived workload. In addition, the alternate analyses yielded some preliminary evidence of shooting performance decrements

Eigenvalue-eigenvector decomposition (EED) analysis of dissimilarity and covariance matrix obtained from total synchronous fluorescence spectral (TSFS) data sets of herbal preparations: Optimizing the classification approach.

Science.gov (United States)

Tarai, Madhumita; Kumar, Keshav; Divya, O; Bairi, Partha; Mishra, Kishor Kumar; Mishra, Ashok Kumar

2017-09-05

The present work compares the dissimilarity and covariance based unsupervised chemometric classification approaches by taking the total synchronous fluorescence spectroscopy data sets acquired for the cumin and non-cumin based herbal preparations. The conventional decomposition method involves eigenvalue-eigenvector analysis of the covariance of the data set and finds the factors that can explain the overall major sources of variation present in the data set. The conventional approach does this irrespective of the fact that the samples belong to intrinsically different groups and hence leads to poor class separation. The present work shows that classification of such samples can be optimized by performing the eigenvalue-eigenvector decomposition on the pair-wise dissimilarity matrix. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantification of uncertainties in turbulence modeling: A comparison of physics-based and random matrix theoretic approaches

International Nuclear Information System (INIS)

Wang, Jian-Xun; Sun, Rui; Xiao, Heng

2016-01-01

Highlights: • Compared physics-based and random matrix methods to quantify RANS model uncertainty. • Demonstrated applications of both methods in channel ow over periodic hills. • Examined the amount of information introduced in the physics-based approach. • Discussed implications to modeling turbulence in both near-wall and separated regions. - Abstract: Numerical models based on Reynolds-Averaged Navier-Stokes (RANS) equations are widely used in engineering turbulence modeling. However, the RANS predictions have large model-form uncertainties for many complex flows, e.g., those with non-parallel shear layers or strong mean flow curvature. Quantification of these large uncertainties originating from the modeled Reynolds stresses has attracted attention in the turbulence modeling community. Recently, a physics-based Bayesian framework for quantifying model-form uncertainties has been proposed with successful applications to several flows. Nonetheless, how to specify proper priors without introducing unwarranted, artificial information remains challenging to the current form of the physics-based approach. Another recently proposed method based on random matrix theory provides the prior distributions with maximum entropy, which is an alternative for model-form uncertainty quantification in RANS simulations. This method has better mathematical rigorousness and provides the most non-committal prior distributions without introducing artificial constraints. On the other hand, the physics-based approach has the advantages of being more flexible to incorporate available physical insights. In this work, we compare and discuss the advantages and disadvantages of the two approaches on model-form uncertainty quantification. In addition, we utilize the random matrix theoretic approach to assess and possibly improve the specification of priors used in the physics-based approach. The comparison is conducted through a test case using a canonical flow, the flow past

Effect of air turbulence on gas transport in soil; comparison of approaches

Science.gov (United States)

Pourbakhtiar, Alireza; Papadikis, Konstantinos; Poulsen, Tjalfe; Bridge, Jonathan; Wilkinson, Stephen

2017-04-01

Greenhouse gases are playing the key role in global warming. Soil is a source of greenhouse gases such as methane (CH4). Radon (Rn) which is a radioactive gas can emit form subsurface into the atmosphere and leads to health concerns in urban areas. Temperature, humidity, air pressure and vegetation of soil can affect gas emissions inside soil (Oertel et al., 2016). It's shown in many cases that wind induced fluctuations is an important factor in transport of gas through soil and other porous media. An example is: landfill gas emissions (Poulsen et al., 2001). We applied an experimental equipment for measuring controlled air turbulence on gas transport in soil in relation to the depth of sample. Two approaches for measurement of effect of wind turbulence on gas transport were applied and compared. Experiments were carried out with diffusion of CO2 and air as tracer gases with average vertical wind speeds of 0 to 0.83 m s-1. In approach A, Six different sample thicknesses from 5 to 30 cm were selected and total of 4 different wind conditions with different speed and fluctuations were applied. In approach B, a sample with constant depth was used. Five oxygen sensors were places inside sample at different depths. Total of 111 experiments were carried out. Gas transport is described by advection-dispersion equation. Gas transport is quantified as a dispersion coefficient. Oxygen breakthrough curves as a function of distance to the surface of the sample exposed to wind were derived numerically with an explicit forward time, central space finite-difference based model to evaluate gas transport. We showed that wind turbulence-induced fluctuations is an important factor in gas transport that can increase gas transport with average of 45 times more than molecular diffusion under zero wind condition. Comparison of two strategies for experiments, indicated that, constant deep samples (Approach B) are more reliable for measurement of gas transport under influence of wind

Template-based protein-protein docking exploiting pairwise interfacial residue restraints

NARCIS (Netherlands)

Xue, Li C; Garcia Lopes Maia Rodrigues, João; Dobbs, Drena; Honavar, Vasant; Bonvin, Alexandre M J J

2016-01-01

Although many advanced and sophisticatedab initioapproaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to

Identifying the dominating perceptual differences in headphone reproduction

DEFF Research Database (Denmark)

Volk, Christer Peter; Lavandier, Mathieu; Bech, Søren

2016-01-01

The perceptual differences between the sound reproductions of headphones were investigated in a pair-wise comparison study. Two musical excerpts were reproduced over 21 headphones positioned on a mannequin and recorded. The recordings were then processed and reproduced over one set of headphones ...

Milk production of dairy cows as affected by the length of the ...

African Journals Online (AJOL)

Useni , Alain

2014-08-22

Aug 22, 2014 ... Differences between means were obtained using the pair-wise comparison of ... Furthermore, cows produced less (P <0.05) milk with a high protein content when .... Effets de la reduction de la durée de la periode seche ou.

Statistical evaluation of SAGE libraries: consequences for experimental design

NARCIS (Netherlands)

Ruijter, Jan M.; van Kampen, Antoine H. C.; Baas, Frank

2002-01-01

Since the introduction of serial analysis of gene expression (SAGE) as a method to quantitatively analyze the differential expression of genes, several statistical tests have been published for the pairwise comparison of SAGE libraries. Testing the difference between the number of specific tags

A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks

DEFF Research Database (Denmark)

Larsen, Simon; Alkærsig, Frederik G.; Ditzel, Henrik

2016-01-01

Network alignment is a challenging computational problem that identifies node or edge mappings between two or more networks, with the aim to unravel common patterns among them. Pairwise network alignment is already intractable, making multiple network comparison even more difficult. Here, we intr...

Cultivar identification by means of isoenzymes 2. Genetic variation at 4 enzyme loci in diploid ryegrass lolium-spp

DEFF Research Database (Denmark)

Nielsen, G.; Østergaard, H.; Johansen, Henrik

1985-01-01

gel electrophoresis. Cultivars were pairwise compared by means of allelic frequencies assuming Hardy-Weinberg proportions. At first, the comparisons were carried out for each locus separately. The 2 loci Pgi-2 and Got-3 distinguished perennial ryegrass cultivars fairly well, but the discrimination...

Analysis of 49 autosomal SNPs in an Iraqi population

DEFF Research Database (Denmark)

Tomas Mas, Carmen; Diez, Isabel E; Moncada, Enrique

2013-01-01

(ST) values were statistically significant when pairwise comparisons were performed between the 18 populations. The Iraqi population did not show significant difference from the population in Turkey and it grouped together with other Middle-Eastern populations when a multidimensional scaling plot was drawn...

Recursive nearest neighbor search in a sparse and multiscale domain for comparing audio signals

DEFF Research Database (Denmark)

Sturm, Bob L.; Daudet, Laurent

2011-01-01

We investigate recursive nearest neighbor search in a sparse domain at the scale of audio signals. Essentially, to approximate the cosine distance between the signals we make pairwise comparisons between the elements of localized sparse models built from large and redundant multiscale dictionaries...

A linear programming approach to max-sum problem: a review.

Science.gov (United States)

Werner, Tomás

2007-07-01

The max-sum labeling problem, defined as maximizing a sum of binary (i.e., pairwise) functions of discrete variables, is a general NP-hard optimization problem with many applications, such as computing the MAP configuration of a Markov random field. We review a not widely known approach to the problem, developed by Ukrainian researchers Schlesinger et al. in 1976, and show how it contributes to recent results, most importantly, those on the convex combination of trees and tree-reweighted max-product. In particular, we review Schlesinger et al.'s upper bound on the max-sum criterion, its minimization by equivalent transformations, its relation to the constraint satisfaction problem, the fact that this minimization is dual to a linear programming relaxation of the original problem, and the three kinds of consistency necessary for optimality of the upper bound. We revisit problems with Boolean variables and supermodular problems. We describe two algorithms for decreasing the upper bound. We present an example application for structural image analysis.

A comparison of top-down and bottom-up approaches to benthic habitat mapping to inform offshore wind energy development

Science.gov (United States)

LaFrance, Monique; King, John W.; Oakley, Bryan A.; Pratt, Sheldon

2014-07-01

Recent interest in offshore renewable energy within the United States has amplified the need for marine spatial planning to direct management strategies and address competing user demands. To assist this effort in Rhode Island, benthic habitat classification maps were developed for two sites in offshore waters being considered for wind turbine installation. Maps characterizing and representing the distribution and extent of benthic habitats are valuable tools for improving understanding of ecosystem patterns and processes, and promoting scientifically-sound management decisions. This project presented the opportunity to conduct a comparison of the methodologies and resulting map outputs of two classification approaches, “top-down” and “bottom-up” in the two study areas. This comparison was undertaken to improve understanding of mapping methodologies and their applicability, including the bottom-up approach in offshore environments where data density tends to be lower, as well as to provide case studies for scientists and managers to consider for their own areas of interest. Such case studies can offer guidance for future work for assessing methodologies and translating them to other areas. The traditional top-down mapping approach identifies biological community patterns based on communities occurring within geologically defined habitat map units, under the concept that geologic environments contain distinct biological assemblages. Alternatively, the bottom-up approach aims to establish habitat map units centered on biological similarity and then uses statistics to identify relationships with associated environmental parameters and determine habitat boundaries. When applied to the two study areas, both mapping approaches produced habitat classes with distinct macrofaunal assemblages and each established statistically strong and significant biotic-abiotic relationships with geologic features, sediment characteristics, water depth, and/or habitat

ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.

Science.gov (United States)

Zhu, Lin; Guo, Wei-Li; Deng, Su-Ping; Huang, De-Shuang

2016-01-01

In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.

The comparison of various approach to evaluation erosion risks and design control erosion measures

Science.gov (United States)

Kapicka, Jiri

2015-04-01

In the present is in the Czech Republic one methodology how to compute and compare erosion risks. This methodology contain also method to design erosion control measures. The base of this methodology is Universal Soil Loss Equation (USLE) and their result long-term average annual rate of erosion (G). This methodology is used for landscape planners. Data and statistics from database of erosion events in the Czech Republic shows that many troubles and damages are from local episodes of erosion events. An extent of these events and theirs impact are conditional to local precipitation events, current plant phase and soil conditions. These erosion events can do troubles and damages on agriculture land, municipally property and hydro components and even in a location is from point of view long-term average annual rate of erosion in good conditions. Other way how to compute and compare erosion risks is episodes approach. In this paper is presented the compare of various approach to compute erosion risks. The comparison was computed to locality from database of erosion events on agricultural land in the Czech Republic where have been records two erosion events. The study area is a simple agriculture land without any barriers that can have high influence to water flow and soil sediment transport. The computation of erosion risks (for all methodology) was based on laboratory analysis of soil samples which was sampled on study area. Results of the methodology USLE, MUSLE and results from mathematical model Erosion 3D have been compared. Variances of the results in space distribution of the places with highest soil erosion where compared and discussed. Other part presents variances of design control erosion measures where their design was done on based different methodology. The results shows variance of computed erosion risks which was done by different methodology. These variances can start discussion about different approach how compute and evaluate erosion risks in areas

Suitability analysis for rice growing sites using a multicriteria evaluation and GIS approach in great Mwea region, Kenya.

Science.gov (United States)

Kihoro, Joseph; Bosco, Njoroge J; Murage, Hunja

2013-12-01

Land suitability analysis is a prerequisite to achieving optimum utilization of the available land resources. Lack of knowledge on best combination of factors that suit production of rice has contributed to the low production. The aim of this study was to develop a suitability map for rice crop based on physical and climatic factors of production using a Multi-Criteria Evaluation (MCE) & GIS approach. The study was carried out in Kirinyaga, Embu and Mberee counties in Kenya. Biophysical variables of soil, climate and topography were considered for suitability analysis. All data were stored in ArcGIS 9.3 environment and the factor maps were generated. For MCE, Pairwise Comparison Matrix was applied and the suitable areas for rice crop were generated and graduated. The current land cover map of the area was developed from a scanned survey map of the rice growing areas. According to the present land cover map, the rice cultivated area was 13,369 ha. Finally, we overlaid the land cover map with the suitability map to identify variances between the present and potential land use. The crop-land evaluation results of the present study showed that, 75% of total area currently being used was under highly suitable areas and 25% was under moderately suitable areas. The results showed that the potential area for rice growing is 86,364 ha and out of this only 12% is under rice cultivation. This research provided information at local level that could be used by farmers to select cropping patterns and suitability.

Comparison of high-speed transportation systems in special consideration of investment costs

Directory of Open Access Journals (Sweden)

R. Schach

2007-10-01

Full Text Available In this paper a substantial comparison of different high-speed transportation systems and an approach to stochastic cost estimations are provided. Starting from the developments in Europe, the high-speed traffic technical characteristics of high-speed railways and Maglev systems are compared. But for a comprehensive comparison more criterions must be included and led to a wider consideration and the development of a multi-criteria comparison of high-speed transportation systems. In the second part a stochastic approach to cost estimations of infrastructure projects is encouraged. Its advantages in comparison with the traditional proceeding are presented and exemplify the practical implementation.

Landscape characteristics influencing the genetic structure of greater sage-grouse within the stronghold of their range: a holistic modeling approach

Science.gov (United States)

Row, Jeff R; Oyler-McCance, Sara J.; Fike, Jennifer; O'Donnell, Michael; Doherty, Kevin E.; Aldridge, Cameron L.; Bowen, Zachary H.; Fedy, Brad C.

2015-01-01

Given the significance of animal dispersal to population dynamics and geographic variability, understanding how dispersal is impacted by landscape patterns has major ecological and conservation importance. Speaking to the importance of dispersal, the use of linear mixed models to compare genetic differentiation with pairwise resistance derived from landscape resistance surfaces has presented new opportunities to disentangle the menagerie of factors behind effective dispersal across a given landscape. Here, we combine these approaches with novel resistance surface parameterization to determine how the distribution of high- and low-quality seasonal habitat and individual landscape components shape patterns of gene flow for the greater sage-grouse (Centrocercus urophasianus) across Wyoming. We found that pairwise resistance derived from the distribution of low-quality nesting and winter, but not summer, seasonal habitat had the strongest correlation with genetic differentiation. Although the patterns were not as strong as with habitat distribution, multivariate models with sagebrush cover and landscape ruggedness or forest cover and ruggedness similarly had a much stronger fit with genetic differentiation than an undifferentiated landscape. In most cases, landscape resistance surfaces transformed with 17.33-km-diameter moving windows were preferred, suggesting small-scale differences in habitat were unimportant at this large spatial extent. Despite the emergence of these overall patterns, there were differences in the selection of top models depending on the model selection criteria, suggesting research into the most appropriate criteria for landscape genetics is required. Overall, our results highlight the importance of differences in seasonal habitat preferences to patterns of gene flow and suggest the combination of habitat suitability modeling and linear mixed models with our resistance parameterization is a powerful approach to discerning the effects of landscape

Stima del valore di trasformazione utilizzando la funzione di stima. Il Market Comparison Approach a tabella dei dati ridotta

Directory of Open Access Journals (Sweden)

Maurizio d’Amato

2015-06-01

Full Text Available Il contributo propone l’utilizzo di una rielaborazione dell’uso del Market Comparison Approach per la determinazione del valore di beni immobili che sono stati oggetto di una trasformazione. Esso è focalizzato sulla determinazione valore di un bene immobile in seguito a una trasformazione finalizzato alla determinazione del valore di un suolo nell’ambito dell’applicazione dell’extraction method. I risultati, basati su dati di compravendita e riferiti a un caso reale in provincia di Bari, possono essere estesi anche alla valutazione degli immobili in costruzione e alla determinazione del valore di beni immobili in costruzione (investment property under construction con il metodo del valore futuro.

Spike sorting for polytrodes: a divide and conquer approach

Directory of Open Access Journals (Sweden)

Nicholas V. Swindale

2014-02-01

Full Text Available In order to determine patterns of neural activity, spike signals recorded by extracellular electrodes have to be clustered (sorted with the aim of ensuring that each cluster represents all the spikes generated by an individual neuron. Many methods for spike sorting have been proposed but few are easily applicable to recordings from polytrodes which may have 16 or more recording sites. As with tetrodes, these are spaced sufficiently closely that signals from single neurons will usually be recorded on several adjacent sites. Although this offers a better chance of distinguishing neurons with similarly shaped spikes, sorting is difficult in such cases because of the high dimensionality of the space in which the signals must be classified. This report details a method for spike sorting based on a divide and conquer approach. Clusters are initially formed by assigning each event to the channel on which it is largest. Each channel-based cluster is then sub-divided into as many distinct clusters as possible. These are then recombined on the basis of pairwise tests into a final set of clusters. Pairwise tests are also performed to establish how distinct each cluster is from the others. A modified gradient ascent clustering (GAC algorithm is used to do the clustering. The method can sort spikes with minimal user input in times comparable to real time for recordings lasting up to 45 minutes. Our results illustrate some of the difficulties inherent in spike sorting, including changes in spike shape over time. We show that some physiologically distinct units may have very similar spike shapes. We show that RMS measures of spike shape similarity are not sensitive enough to discriminate clusters that can otherwise be separated by principal components analysis. Hence spike sorting based on least-squares matching to templates may be unreliable. Our methods should be applicable to tetrodes and scaleable to larger multi-electrode arrays (MEAs.

Investigating design: A comparison of manifest and latent approaches

DEFF Research Database (Denmark)

Cash, Philip; Snider, Chris

2014-01-01

This paper contributes to the on-going focus on improving design research methods, by exploring and synthesising two key interrelated research approaches e manifest and latent. These approaches are widely used individually in design research, however, this paper represents the first work bringing...

Dissimilarity-based classification of anatomical tree structures

DEFF Research Database (Denmark)

Sørensen, Lauge; Lo, Pechin Chien Pau; Dirksen, Asger

2011-01-01

A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment betw...

Dissimilarity-based classification of anatomical tree structures

DEFF Research Database (Denmark)

Sørensen, Lauge Emil Borch Laurs; Lo, Pechin Chien Pau; Dirksen, Asger

2011-01-01

A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment...

randomised double blind study to compare effectiveness of honey

African Journals Online (AJOL)

2014-02-02

Feb 2, 2014 ... EAsT AFRICAN MEDICAL JOURNAL. February 2014 .... based randomised double- blinded clinical trial evaluating effectiveness of ... study drugs was undertaken following a random ... included sodium citrate, citric acid monohydrate, ... post-hoc test to carry out pair-wise comparisons of .... self-care market.

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

Science.gov (United States)

Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

2017-01-21

RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA

Comparison of effective Hough transform-based fingerprint alignment approaches

CSIR Research Space (South Africa)

Mlambo, CS

2014-08-01

Full Text Available points set with larger rotation and small number of points. The DRBA approach was found to perform better with minutiae points with large amount of translation, and the computational time was less than that of LMBA approach. However, the memory usage...

Comparison of Traditional and Constructivist Teaching Approaches ...

African Journals Online (AJOL)

The second section of students had 47 students and was taught using traditional teaching approach. Learning strategy inventory questionnaire which was adapted from strategy inventory for language learning (SILL) L2 students of English, (Oxford, 1990) was employed before and after students were taught using two ...

The Pennsylvania Phosphorus Index and TopoSWAT: A comparison of transport components and approaches

Science.gov (United States)

The regional Chesapeake Bay Conservation Innovation Grant Initiative includes comparison of TopoSWAT results and Phosphorus Index (P Index) evaluations of eight study watersheds throughout the Chesapeake Bay watershed. While similarities exist between the P Index and TopoSWAT, further comparison of ...

Fluoroscopically-Guided Posterior Approach for Shoulder Magnetic Resonance Arthrography: Comparison with Conventional Anterior Approach

International Nuclear Information System (INIS)

Yoo, Koun J.; Ha, Doo Hoe; Lee, Sang Min

2011-01-01

To prospectively evaluate the usefulness of the fluoroscopically-guided posterior approach compared with the anterior approach for shoulder magnetic resonance(MR) arthrography. Institutional review board approval and informed consent were obtained. Among 60 shoulder MR arthrographies performed on 59 patients with symptomatic shoulders, an intra-articular injection was performed (30 cases using the anterior approach and 30 using the posterior approach). Procedure-related pain was assessed by using a 5 score visual analogue scale (VAS). Depth of the puncture and standardized depth of puncture by body mass index (BMI) were recorded. The contrast leakage along the course of the puncture was evaluated by reviewing the MR. The statistical analyses included the Mann-Whitney U and Kruskal-Wallis test. There was no significant difference in VAS scores between the anterior and posterior groups (1.77 ± 1.10 vs. 1.80 ± 0.96). Depth of puncture and standardized depth of puncture by BMI were significantly shorter in the posterior group than those in the anterior group (4.4 ± 0.8 cm and 1.8 ± 0.3 cm vs. 6.6 ± 0.9 cm and 2.8 ± 0.4 cm, p < 0.001), respectively. The incidence of contrast leakage was more frequent in the posterior group (p = 0.003). The posterior approach will be useful in shoulder MR arthrography with a suspected anterior pathology, a postoperative follow-up study or obese patient.

Hong Kong Students' Approaches to Learning: Cross-Cultural Comparisons

Science.gov (United States)

Dasari, Bhoomiah

2009-01-01

Anecdotal evidence abounds in Hong Kong to the effect that students entering tertiary education are predisposed to a "rote" learning approach. With the internalisation of higher education in many countries, there is still insufficient understanding of how Chinese students approach their learning. Except few studies were conducted…

Pairwise comparison of {sup 89}Zr- and {sup 124}I-labeled cG250 based on positron emission tomography imaging and nonlinear immunokinetic modeling: in vivo carbonic anhydrase IX receptor binding and internalization in mouse xenografts of clear-cell renal cell carcinoma

Energy Technology Data Exchange (ETDEWEB)

Cheal, Sarah M.; Punzalan, Blesida; Doran, Michael G.; Osborne, Joseph R. [Memorial Sloan-Kettering Cancer Center, Department of Radiology, New York, NY (United States); Evans, Michael J. [Memorial Sloan-Kettering Cancer Center, Human Oncology and Pathogenesis Program, New York, NY (United States); Lewis, Jason S. [Memorial Sloan-Kettering Cancer Center, Department of Radiology, New York, NY (United States); Memorial Sloan-Kettering Cancer Center, Program in Molecular Pharmacology and Chemistry, New York, NY (United States); Memorial Sloan-Kettering Cancer Center, Radiochemistry and Imaging Sciences Service, New York, NY (United States); Zanzonico, Pat [Memorial Sloan-Kettering Cancer Center, Department of Radiology, New York, NY (United States); Memorial Sloan-Kettering Cancer Center, Molecular Pharmacology and Therapy Service, New York, NY (United States); Memorial-Sloan Kettering Cancer Center, New York, NY (United States); Larson, Steven M. [Memorial Sloan-Kettering Cancer Center, Department of Radiology, New York, NY (United States); Memorial Sloan-Kettering Cancer Center, Program in Molecular Pharmacology and Chemistry, New York, NY (United States); Memorial Sloan-Kettering Cancer Center, Molecular Pharmacology and Therapy Service, New York, NY (United States)

2014-05-15

The PET tracer, {sup 124}I-cG250, directed against carbonic anhydrase IX (CAIX) shows promise for presurgical diagnosis of clear-cell renal cell carcinoma (ccRCC) (Divgi et al. in Lancet Oncol 8:304-310, 2007; Divgi et al. in J Clin Oncol 31:187-194, 2013). The radiometal {sup 89}Zr, however, may offer advantages as a surrogate PET nuclide over {sup 124}I in terms of greater tumor uptake and retention (Rice et al. in Semin Nucl Med 41:265-282, 2011). We have developed a nonlinear immunokinetic model to facilitate a quantitative comparison of absolute uptake and antibody turnover between {sup 124}I-cG250 and {sup 89}Zr-cG250 using a human ccRCC xenograft tumor model in mice. We believe that this unique model better relates quantitative imaging data to the salient biological features of tumor antibody-antigen binding and turnover. We conducted experiments with {sup 89}Zr-cG250 and {sup 124}I-cG250 using a human ccRCC cell line (SK-RC-38) to characterize the binding affinity and internalization kinetics of the two tracers in vitro. Serial PET imaging was performed in mice bearing subcutaneous ccRCC tumors to simultaneously detect and quantify time-dependent tumor uptake in vivo. Using the known specific activities of the two tracers, the equilibrium rates of antibody internalization and turnover in the tumors were derived from the PET images using nonlinear compartmental modeling. The two tracers demonstrated virtually identical tumor cell binding and internalization but showed markedly different retentions in vitro. Superior PET images were obtained using {sup 89}Zr-cG250, owing to the more prolonged trapping of the radiolabel in the tumor and simultaneous washout from normal tissues. Estimates of cG250/CAIX complex turnover were 1.35 - 5.51 x 10{sup 12} molecules per hour per gram of tumor (20 % of receptors internalized per hour), and the ratio of {sup 124}I/{sup 89}Zr atoms released per unit time by tumor was 17.5. Pairwise evaluation of {sup 89}Zr-cG250 and {sup

A Quantitative Comparison of Semantic Web Page Segmentation Approaches

NARCIS (Netherlands)

Kreuzer, Robert; Hage, J.; Feelders, A.J.

2015-01-01

We compare three known semantic web page segmentation algorithms, each serving as an example of a particular approach to the problem, and one self-developed algorithm, WebTerrain, that combines two of the approaches. We compare the performance of the four algorithms for a large benchmark of modern

Comparison of two novel approaches to model fibre reinforced concrete

NARCIS (Netherlands)

Radtke, F.K.F.; Simone, A.; Sluys, L.J.

2009-01-01

We present two approaches to model fibre reinforced concrete. In both approaches, discrete fibre distributions and the behaviour of the fibre-matrix interface are explicitly considered. One approach employs the reaction forces from fibre to matrix while the other is based on the partition of unity

A comparison of two instructional methods for drawing Lewis Structures

Science.gov (United States)

Terhune, Kari

Two instructional methods for teaching Lewis structures were compared -- the Direct Octet Rule Method (DORM) and the Commonly Accepted Method (CAM). The DORM gives the number of bonds and the number of nonbonding electrons immediately, while the CAM involves moving electron pairs from nonbonding to bonding electrons, if necessary. The research question was as follows: Will high school chemistry students draw more accurate Lewis structures using the DORM or the CAM? Students in Regular Chemistry 1 (N = 23), Honors Chemistry 1 (N = 51) and Chemistry 2 (N = 15) at an urban high school were the study participants. An identical pretest and posttest was given before and after instruction. Students were given instruction with either the DORM (N = 45), the treatment method, or the CAM (N = 44), the control for two days. After the posttest, 15 students were interviewed, using a semistructured interview process. The pretest/posttest consisted of 23 numerical response questions and 2 to 6 free response questions that were graded using a rubric. A two-way ANOVA showed a significant interaction effect between the groups and the methods, F (1, 70) = 10.960, p = 0.001. Post hoc comparisons using the Bonferroni pairwise comparison showed that Reg Chem 1 students demonstrated larger gain scores when they had been taught the CAM (Mean difference = 3.275, SE = 1.324, p Chemistry 1 students performed better with the DORM, perhaps due to better math skills, enhanced working memory, and better metacognitive skills. Regular Chemistry 1 students performed better with the CAM, perhaps because it is more visual. Teachers may want to use the CAM or a direct-pairing method to introduce the topic and use the DORM in advanced classes when a correct structure is needed quickly.

Visual comparison for information visualization

KAUST Repository

Gleicher, M.; Albers, D.; Walker, R.; Jusufi, I.; Hansen, C. D.; Roberts, J. C.

2011-01-01

Data analysis often involves the comparison of complex objects. With the ever increasing amounts and complexity of data, the demand for systems to help with these comparisons is also growing. Increasingly, information visualization tools support such comparisons explicitly, beyond simply allowing a viewer to examine each object individually. In this paper, we argue that the design of information visualizations of complex objects can, and should, be studied in general, that is independently of what those objects are. As a first step in developing this general understanding of comparison, we propose a general taxonomy of visual designs for comparison that groups designs into three basic categories, which can be combined. To clarify the taxonomy and validate its completeness, we provide a survey of work in information visualization related to comparison. Although we find a great diversity of systems and approaches, we see that all designs are assembled from the building blocks of juxtaposition, superposition and explicit encodings. This initial exploration shows the power of our model, and suggests future challenges in developing a general understanding of comparative visualization and facilitating the development of more comparative visualization tools. © The Author(s) 2011.

Visual comparison for information visualization

KAUST Repository

Gleicher, M.

2011-09-07

Data analysis often involves the comparison of complex objects. With the ever increasing amounts and complexity of data, the demand for systems to help with these comparisons is also growing. Increasingly, information visualization tools support such comparisons explicitly, beyond simply allowing a viewer to examine each object individually. In this paper, we argue that the design of information visualizations of complex objects can, and should, be studied in general, that is independently of what those objects are. As a first step in developing this general understanding of comparison, we propose a general taxonomy of visual designs for comparison that groups designs into three basic categories, which can be combined. To clarify the taxonomy and validate its completeness, we provide a survey of work in information visualization related to comparison. Although we find a great diversity of systems and approaches, we see that all designs are assembled from the building blocks of juxtaposition, superposition and explicit encodings. This initial exploration shows the power of our model, and suggests future challenges in developing a general understanding of comparative visualization and facilitating the development of more comparative visualization tools. © The Author(s) 2011.

High-throughput detection of prostate cancer in histological sections using probabilistic pairwise Markov models.

Science.gov (United States)

Monaco, James P; Tomaszewski, John E; Feldman, Michael D; Hagemann, Ian; Moradi, Mehdi; Mousavi, Parvin; Boag, Alexander; Davidson, Chris; Abolmaesumi, Purang; Madabhushi, Anant

2010-08-01

In this paper we present a high-throughput system for detecting regions of carcinoma of the prostate (CaP) in HSs from radical prostatectomies (RPs) using probabilistic pairwise Markov models (PPMMs), a novel type of Markov random field (MRF). At diagnostic resolution a digitized HS can contain 80Kx70K pixels - far too many for current automated Gleason grading algorithms to process. However, grading can be separated into two distinct steps: (1) detecting cancerous regions and (2) then grading these regions. The detection step does not require diagnostic resolution and can be performed much more quickly. Thus, we introduce a CaP detection system capable of analyzing an entire digitized whole-mount HS (2x1.75cm(2)) in under three minutes (on a desktop computer) while achieving a CaP detection sensitivity and specificity of 0.87 and 0.90, respectively. We obtain this high-throughput by tailoring the system to analyze the HSs at low resolution (8microm per pixel). This motivates the following algorithm: (Step 1) glands are segmented, (Step 2) the segmented glands are classified as malignant or benign, and (Step 3) the malignant glands are consolidated into continuous regions. The classification of individual glands leverages two features: gland size and the tendency for proximate glands to share the same class. The latter feature describes a spatial dependency which we model using a Markov prior. Typically, Markov priors are expressed as the product of potential functions. Unfortunately, potential functions are mathematical abstractions, and constructing priors through their selection becomes an ad hoc procedure, resulting in simplistic models such as the Potts. Addressing this problem, we introduce PPMMs which formulate priors in terms of probability density functions, allowing the creation of more sophisticated models. To demonstrate the efficacy of our CaP detection system and assess the advantages of using a PPMM prior instead of the Potts, we alternately

Automatic Genre Classification of Musical Signals

Science.gov (United States)

Barbedo, Jayme Garcia sArnal; Lopes, Amauri

2006-12-01

We present a strategy to perform automatic genre classification of musical signals. The technique divides the signals into 21.3 milliseconds frames, from which 4 features are extracted. The values of each feature are treated over 1-second analysis segments. Some statistical results of the features along each analysis segment are used to determine a vector of summary features that characterizes the respective segment. Next, a classification procedure uses those vectors to differentiate between genres. The classification procedure has two main characteristics: (1) a very wide and deep taxonomy, which allows a very meticulous comparison between different genres, and (2) a wide pairwise comparison of genres, which allows emphasizing the differences between each pair of genres. The procedure points out the genre that best fits the characteristics of each segment. The final classification of the signal is given by the genre that appears more times along all signal segments. The approach has shown very good accuracy even for the lowest layers of the hierarchical structure.

Acupuncture-Related Techniques for Psoriasis: A Systematic Review with Pairwise and Network Meta-Analyses of Randomized Controlled Trials.

Science.gov (United States)

Yeh, Mei-Ling; Ko, Shu-Hua; Wang, Mei-Hua; Chi, Ching-Chi; Chung, Yu-Chu

2017-12-01

There has be a large body of evidence on the pharmacological treatments for psoriasis, but whether nonpharmacological interventions are effective in managing psoriasis remains largely unclear. This systematic review conducted pairwise and network meta-analyses to determine the effects of acupuncture-related techniques on acupoint stimulation for the treatment of psoriasis and to determine the order of effectiveness of these remedies. This study searched the following databases from inception to March 15, 2016: Medline, PubMed, Cochrane Central Register of Controlled Trials, EBSCO (including Academic Search Premier, American Doctoral Dissertations, and CINAHL), Airiti Library, and China National Knowledge Infrastructure. Randomized controlled trials (RCTs) on the effects of acupuncture-related techniques on acupoint stimulation as intervention for psoriasis were independently reviewed by two researchers. A total of 13 RCTs with 1,060 participants were included. The methodological quality of included studies was not rigorous. Acupoint stimulation, compared with nonacupoint stimulation, had a significant treatment for psoriasis. However, the most common adverse events were thirst and dry mouth. Subgroup analysis was further done to confirm that the short-term treatment effect was superior to that of the long-term effect in treating psoriasis. Network meta-analysis identified acupressure or acupoint catgut embedding, compared with medication, and had a significant effect for improving psoriasis. It was noted that acupressure was the most effective treatment. Acupuncture-related techniques could be considered as an alternative or adjuvant therapy for psoriasis in short term, especially of acupressure and acupoint catgut embedding. This study recommends further well-designed, methodologically rigorous, and more head-to-head randomized trials to explore the effects of acupuncture-related techniques for treating psoriasis.

Improving the modelling of redshift-space distortions - I. A bivariate Gaussian description for the galaxy pairwise velocity distributions

Science.gov (United States)

Bianchi, Davide; Chiesa, Matteo; Guzzo, Luigi

2015-01-01

As a step towards a more accurate modelling of redshift-space distortions (RSD) in galaxy surveys, we develop a general description of the probability distribution function of galaxy pairwise velocities within the framework of the so-called streaming model. For a given galaxy separation r, such function can be described as a superposition of virtually infinite local distributions. We characterize these in terms of their moments and then consider the specific case in which they are Gaussian functions, each with its own mean μ and dispersion σ. Based on physical considerations, we make the further crucial assumption that these two parameters are in turn distributed according to a bivariate Gaussian, with its own mean and covariance matrix. Tests using numerical simulations explicitly show that with this compact description one can correctly model redshift-space distortions on all scales, fully capturing the overall linear and non-linear dynamics of the galaxy flow at different separations. In particular, we naturally obtain Gaussian/exponential, skewed/unskewed distribution functions, depending on separation as observed in simulations and data. Also, the recently proposed single-Gaussian description of RSD is included in this model as a limiting case, when the bivariate Gaussian is collapsed to a two-dimensional Dirac delta function. We also show how this description naturally allows for the Taylor expansion of 1 + ξS(s) around 1 + ξR(r), which leads to the Kaiser linear formula when truncated to second order, explicating its connection with the moments of the velocity distribution functions. More work is needed, but these results indicate a very promising path to make definitive progress in our programme to improve RSD estimators.

A comparison and assessment of approaches for modelling flow over in-line tube banks

International Nuclear Information System (INIS)

Iacovides, Hector; Launder, Brian; West, Alastair

2014-01-01

Highlights: • We present wall-resolved LES and URANS simulations of periodic flow in heated in-line tube banks. • Simulations of flow in a confined in-line tube-bank are compared with experimental data. • When pitch-to-diameter (P/D) ratio becomes less than 1.6, the periodic flow becomes skewed. • URANS tested here unable to mimic the periodic flow at P/D = 1.6. • In confined tube banks URANS suggest alternate, in the axial direction, flow deflection. - Abstract: The paper reports experiences from applying alternative strategies for modelling turbulent flow and local heat-transfer coefficients around in-line tube banks. The motivation is the simulation of conditions in the closely packed cross-flow heat exchangers used in advanced gas-cooled nuclear reactors (AGRs). The main objective is the flow simulation in large-scale tube banks with confining walls. The suitability and accuracy of wall-resolved large-eddy simulation (LES) and Unsteady Reynolds-Averaged Navier–Stokes (URANS) approaches are examined for generic, square, in-line tube banks, where experimental data are limited but available. Within the latter approach, both eddy-viscosity and Reynolds-stress-transport models have been tested. The assumption of flow periodicity in all three directions is investigated by varying the domain size. It is found that the path taken by the fluid through the tube-bank configuration differs according to the treatment of turbulence and whether the flow is treated as two- or three-dimensional. Finally, the important effect of confining walls has been examined by making direct comparison with the experiments of the complete test rig of Aiba et al. (1982)

The optimal hormonal replacement modality selection for multiple organ procurement from brain-dead organ donors.

Science.gov (United States)

Mi, Zhibao; Novitzky, Dimitri; Collins, Joseph F; Cooper, David Kc

2015-01-01

The management of brain-dead organ donors is complex. The use of inotropic agents and replacement of depleted hormones (hormonal replacement therapy) is crucial for successful multiple organ procurement, yet the optimal hormonal replacement has not been identified, and the statistical adjustment to determine the best selection is not trivial. Traditional pair-wise comparisons between every pair of treatments, and multiple comparisons to all (MCA), are statistically conservative. Hsu's multiple comparisons with the best (MCB) - adapted from the Dunnett's multiple comparisons with control (MCC) - has been used for selecting the best treatment based on continuous variables. We selected the best hormonal replacement modality for successful multiple organ procurement using a two-step approach. First, we estimated the predicted margins by constructing generalized linear models (GLM) or generalized linear mixed models (GLMM), and then we applied the multiple comparison methods to identify the best hormonal replacement modality given that the testing of hormonal replacement modalities is independent. Based on 10-year data from the United Network for Organ Sharing (UNOS), among 16 hormonal replacement modalities, and using the 95% simultaneous confidence intervals, we found that the combination of thyroid hormone, a corticosteroid, antidiuretic hormone, and insulin was the best modality for multiple organ procurement for transplantation.

A Comparison of Five Alternative Approaches to Information Systems Development

Directory of Open Access Journals (Sweden)

Rudy Hirschheim

1997-11-01

Full Text Available The field of information systems (IS has grown dramatically over the past three decades. Recent trends have transformed the IS landscape. These trends include: the evolution of implementation technology from centralized mainframe environments towards distributed client-server architectures, embracing the internet and intranets; changes in user interface technology from character-based to graphical user interfaces, multimedia, and the World Wide Web; changes in applications from transaction processing systems towards systems supporting collaborative work; and the use of information technology as an enabler of business process reengineering and redesign. These technology changes coupled with changes in organizations and their operating environment, such as the growth of the network and virtual organization, internationalization and globalization of many organizations, intensified global competition, changes in values such as customer orientation (service quality and Quality of Working Life, have imposed new demands on the development of information systems. These changes have led to an increasing discussion about information systems development (ISO, and in particular, the various methods, tools, methodologies, and approaches for ISD. We believe such discussion has opened the door for new, alternative IS development approaches and methodologies. Our paper takes up this theme by describing five alternative ISD approaches, namely the Interactionist approach, the Speech Act-based approach, Soft Systems Methodology, the Trade Unionist approach, and the Professional Work Practices approach. Despite the fact that most of these approaches have a history of over 15 years, their relevance to IS development is not well recognized in the mainstream of IS practice and research, nor is their institutional status comparable to traditional approaches such as structured analysis and design methods. Therefore we characterize the five approaches as 'alternative' in

Association of lens vault with narrow angles among different ethnic groups.

Science.gov (United States)

Lee, Roland Y; Huang, Guofu; Cui, Qi N; He, Mingguang; Porco, Travis C; Lin, Shan C

2012-06-01

To compare lens vault between open-angle and narrow-angle eyes in African-, Caucasian-, Hispanic-, Chinese- and Filipino-Americans. In this prospective study, 436 patients with open angle and narrow angle based on the Shaffer gonioscopic grading classification underwent anterior-segment optical coherence tomography. The Zhongshan Angle Assessment Program was used to calculate lens vault. The narrow-angle group included 32 Chinese-Americans, 22 Filipino-Americans, 26 African-Americans, 24 Hispanic-Americans and 73 Caucasian-Americans. The open-angle group included 56 Chinese-Americans, 29 Filipino-Americans, 45 African-Americans, 27 Hispanic-Americans and 102 Caucasian-Americans. Linear mixed effect regression models, accounting for the use of both eyes and adjusting for age, sex, pupil diameter and spherical equivalent, were used to test for the ethnicity and angle coefficients. Tukey's multiple comparison test was used for pairwise comparisons among the open-angle racial groups. Significant difference in lens vault was found among the open-angle racial groups (P = 0.022). For the open-angle patients, mean values for the lens vault measurements were 265 ± 288 µm for Chinese-Americans, 431 ± 248 µm for Caucasian-Americans, 302 ± 213 µm for Filipino-Americans, 304 ± 263 µm for Hispanic-Americans and 200 ± 237 µm for African-Americans. Using Tukey's multiple comparison for pairwise comparisons among the open-angle racial groups, a significant difference was found between African-American and Caucasian-Americans groups (P values for the rest of the pairwise comparisons were not statistically significant. No significant difference was found among the narrow-angle racial groups (P = 0.14). Comparison between the open angle and narrow angle within each racial group revealed significant difference for all racial groups (P < 0.05). Among all the ethnicities included in this study, narrow-angle eyes have greater lens vault compared to open

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

International Nuclear Information System (INIS)

Hearin, Andrew P.; Campbell, Duncan; Tollerud, Erik

2017-01-01

Here, we present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution (HOD), the conditional luminosity function (CLF), abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos, or to follow custom number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. Here, the package has an optimized toolkit to make mock observations on a synthetic galaxy population, including galaxy clustering, galaxy-galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others, allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation.

A canonical approach to forces in molecules

Energy Technology Data Exchange (ETDEWEB)

Walton, Jay R. [Department of Mathematics, Texas A& M University, College Station, TX 77843-3368 (United States); Rivera-Rivera, Luis A., E-mail: rivera@chem.tamu.edu [Department of Chemistry, Texas A& M University, College Station, TX 77843-3255 (United States); Lucchese, Robert R.; Bevan, John W. [Department of Chemistry, Texas A& M University, College Station, TX 77843-3255 (United States)

2016-08-02

Highlights: • Derivation of canonical representation of molecular force. • Correlation of derivations with accurate results from Born–Oppenheimer potentials. • Extension of methodology to Mg{sub 2}, benzene dimer, and water dimer. - Abstract: In previous studies, we introduced a generalized formulation for canonical transformations and spectra to investigate the concept of canonical potentials strictly within the Born–Oppenheimer approximation. Data for the most accurate available ground electronic state pairwise intramolecular potentials in H{sub 2}{sup +}, H{sub 2}, HeH{sup +}, and LiH were used to rigorously establish such conclusions. Now, a canonical transformation is derived for the molecular force, F(R), with H{sub 2}{sup +} as molecular reference. These transformations are demonstrated to be inherently canonical to high accuracy but distinctly different from those corresponding to the respective potentials of H{sub 2}, HeH{sup +}, and LiH. In this paper, we establish the canonical nature of the molecular force which is key to fundamental generalization of canonical approaches to molecular bonding. As further examples Mg{sub 2}, benzene dimer and to water dimer are also considered within the radial limit as applications of the current methodology.

Complementation of Escherichia coli uncD mutant strains by a chimeric F1-beta subunit constructed from E. coli and spinach chloroplast F1-beta

NARCIS (Netherlands)

Burkovski, Andreas; Lill, H; Engelbrecht, Siegfried

1994-01-01

ATP-synthesizing F0F1-ATPases are complex enzymes consisting of at least eight different subunits. These subunits are conserved during evolution to a very variable degree ranging in pairwise comparison between, for example, Escherichia coli and spinach chloroplast from 20% to 66% identical residues.

Watershed to Local Scale Characteristics and Function of Intermittent and Ephemeral Streams on Military Lands

Science.gov (United States)

2015-07-31

stream types in riparian plant community composition ( PerMANOVA ) and compositional variance (PermDISP...111 Table 5-3. Pairwise comparisons for differences in riparian plant community composition ( PerMANOVA ) among...multidimensional scaling ordination PerManova = permutational multivariate analysis of variance PC-Ord = computer program for multivariate statistics

Using Analytic Hierarchy Process in Textbook Evaluation

Science.gov (United States)

Kato, Shigeo

2014-01-01

This study demonstrates the application of the analytic hierarchy process (AHP) in English language teaching materials evaluation, focusing in particular on its potential for systematically integrating different components of evaluation criteria in a variety of teaching contexts. AHP is a measurement procedure wherein pairwise comparisons are made…

Developmental Changes in Children’s Processing of Redundant Modifiers in Definite Object Descriptions

NARCIS (Netherlands)

Koolen, Ruud; Krahmer, Emiel; Swerts, Marc

2016-01-01

This paper investigates developmental changes in children’s processing of redundant information in definite object descriptions. In two experiments, children of two age groups (6 or 7, and 9 or 10 years old) were presented with pictures of sweets. In the first experiment (pairwise comparison), two

Elaboration likelihood and the perceived value of labels

DEFF Research Database (Denmark)

Poulsen, Carsten Stig; Juhl, Hans Jørn

2001-01-01

In this paper the increasingly popular method of choice based on conjoint analysis is used and data are collected by pairwise comparisons. A latent class model is formulated allowing that the resulting data can be analyzed with segmentation in mind. The empirical study is on food labeling...

Designing experiments and analyzing data a model comparison perspective

CERN Document Server

Maxwell, Scott E

2013-01-01

Through this book's unique model comparison approach, students and researchers are introduced to a set of fundamental principles for analyzing data. After seeing how these principles can be applied in simple designs, students are shown how these same principles also apply in more complicated designs. Drs. Maxwell and Delaney believe that the model comparison approach better prepares students to understand the logic behind a general strategy of data analysis appropriate for various designs; and builds a stronger foundation, which allows for the introduction of more complex topics omitt

Genetic analysis on three South Indian sympatric hipposiderid bats (Chiroptera, Hipposideridae

Directory of Open Access Journals (Sweden)

Kanagaraj, C

2010-12-01

Full Text Available In mitochondrial DNA, variations in the sequence of 16S rRNA region were analyzed to infer the genetic relationship and population history of three sympatric hipposiderid bats, Hipposideros speoris, H. fulvus and H. ater. Based on the DNA sequence data, we observed relatively lower haplotype and higher nucleotide diversity in H. speoris than in the other two species. The pairwise comparisons of the genetic divergence inferred a genetic relationship between the three hipposiderid bats. We used haplotype sequences to construct a phylogenetic tree. Maximum parsimony and Bayesian inference analysis generated a tree with similar topology. H. fulvus and H. ater formed one cluster and H. speoris formed another cluster. Analysis of the demographic history of populations using Jajima’s D test revealed past changes in populations. Comparison of the observed distribution of pairwise differences in the nucleotides with expected sudden expansion model accepts for H. fulvus and H. ater but not for H. speoris populations.

WEIGHTING OF STUDENTS’ PREFERENCES OF TEACHER’S COMPETENCIES

Directory of Open Access Journals (Sweden)

BROŽOVÁ, Helena

2011-12-01

Full Text Available The aim of this article is to describe the proposed methodology of identification of the students’ weights or preferences of teacher’s managerial competencies at the Faculty of Economics, Czech University of Life Sciences in Prague (CULS. The goal of this article is not to evaluate the teacher’s scientific ability but describe the evaluation of the teacher’s managerial competencies weights from students’ point of view. For setting of weights there are many different methods that varied in the proportion of including the subjective and objective judgement. Commonly diffused method is the Analytic Hierarchy or Network Process by prof. Saaty (AHP or ANP. Because it is not possible to see or to evaluate teacher’s competencies in complexity, we proposed the questionnaires for pairwise comparisons of various teacher’s managerial characteristics and competencies. These answers are then analysed using the AHP method. The AHP is a method deriving global weights from partial weights received as result of pairwise comparisons.

Software Tool Implementing the Fuzzy AHP Method in Ecological Risk Assessment

Directory of Open Access Journals (Sweden)

Radionovs Andrejs

2017-12-01

Full Text Available Due to the increased spread of invasive animals and plants in the territory of Latvia, the necessity of ecological risk assessment related to such kind of spread has grown lately. In cases with sufficient statistical data, the risk assessment may be successfully performed on the basis of statistical methods. The amount of statistical data in the context of spread of invasive animals and plants is pretty poor; therefore, the only method of ecological risk assessment remains subjective judgements of experts. The present paper proposes using a programming tool for ecological risk analysis elaborated by the authors. With the help of this programming tool the method of Fuzzy Analytical Hierarchical Process is implemented. The elements of the pairwise comparison matrix are allowed to be expressed by triangular and trapezoidal fuzzy sets. The presented tool makes it possible to design the fuzzy pair-wise comparison matrix and process the results in a user-friendly way.

StAR: a simple tool for the statistical comparison of ROC curves

Directory of Open Access Journals (Sweden)

Melo Francisco

2008-06-01

Full Text Available Abstract Background As in many different areas of science and technology, most important problems in bioinformatics rely on the proper development and assessment of binary classifiers. A generalized assessment of the performance of binary classifiers is typically carried out through the analysis of their receiver operating characteristic (ROC curves. The area under the ROC curve (AUC constitutes a popular indicator of the performance of a binary classifier. However, the assessment of the statistical significance of the difference between any two classifiers based on this measure is not a straightforward task, since not many freely available tools exist. Most existing software is either not free, difficult to use or not easy to automate when a comparative assessment of the performance of many binary classifiers is intended. This constitutes the typical scenario for the optimization of parameters when developing new classifiers and also for their performance validation through the comparison to previous art. Results In this work we describe and release new software to assess the statistical significance of the observed difference between the AUCs of any two classifiers for a common task estimated from paired data or unpaired balanced data. The software is able to perform a pairwise comparison of many classifiers in a single run, without requiring any expert or advanced knowledge to use it. The software relies on a non-parametric test for the difference of the AUCs that accounts for the correlation of the ROC curves. The results are displayed graphically and can be easily customized by the user. A human-readable report is generated and the complete data resulting from the analysis are also available for download, which can be used for further analysis with other software. The software is released as a web server that can be used in any client platform and also as a standalone application for the Linux operating system. Conclusion A new software for

How Well Does LCA Model Land Use Impacts on Biodiversity?--A Comparison with Approaches from Ecology and Conservation.

Science.gov (United States)

Curran, Michael; de Souza, Danielle Maia; Antón, Assumpció; Teixeira, Ricardo F M; Michelsen, Ottar; Vidal-Legaz, Beatriz; Sala, Serenella; Milà i Canals, Llorenç

2016-03-15

The modeling of land use impacts on biodiversity is considered a priority in life cycle assessment (LCA). Many diverging approaches have been proposed in an expanding literature on the topic. The UNEP/SETAC Life Cycle Initiative is engaged in building consensus on a shared modeling framework to highlight best-practice and guide model application by practitioners. In this paper, we evaluated the performance of 31 models from both the LCA and the ecology/conservation literature (20 from LCA, 11 from non-LCA fields) according to a set of criteria reflecting (i) model completeness, (ii) biodiversity representation, (iii) impact pathway coverage, (iv) scientific quality, and (v) stakeholder acceptance. We show that LCA models tend to perform worse than those from ecology and conservation (although not significantly), implying room for improvement. We identify seven best-practice recommendations that can be implemented immediately to improve LCA models based on existing approaches in the literature. We further propose building a "consensus model" through weighted averaging of existing information, to complement future development. While our research focuses on conceptual model design, further quantitative comparison of promising models in shared case studies is an essential prerequisite for future informed model choice.

Assessing repetitive negative thinking using categorical and transdiagnostic approaches: A comparison and validation of three Polish language adaptations of self-report questionnaires

Directory of Open Access Journals (Sweden)

Monika eKornacka

2016-03-01

Full Text Available Repetitive negative thinking (RNT is a transdiagnostic process involved in the risk, maintenance, and relapse of serious conditions including mood disorders, anxiety, eating disorders, and addictions. Processing mode theory provides a theoretical model to assess, research, and treat RNT using a transdiagnostic approach. Clinical researchers also often employ categorical approaches to RNT, including a focus on depressive rumination or worry, for similar purposes. Three widely used self-report questionnaires have been developed to assess these related constructs: the Ruminative Response Scale (RRT, the Perseverative Thinking Questionnaire (PTQ, and the Mini-Cambridge Exeter Repetitive Thought Scale (Mini-CERTS. Yet these scales have not previously been used in conjunction, despite useful theoretical distinctions only available in Mini-CERTS. The present validation of the methods in a Polish speaking population provides psychometric parameters estimates that contribute to current efforts to increase reliable replication of theoretical outcomes. Moreover, the following study aims to present particular characteristics and a comparison of the three methods. Although there has been some exploration of the categorical approach, the comparison of transdiagnostic methods is still lacking. These methods are particularly relevant for developing and evaluating theoretically based interventions like concreteness training, an emerging field of increasing interest, which can be used to address the maladaptive processing mode in RNT that can lead to depression and other disorders. Furthermore, the translation of these measures enables the examination of possible cross-cultural structural differences that may lead to important theoretical progress in the measurement and classification of RNT. The results support the theoretical hypothesis. As expected, the dimensions of brooding, general Repetitive Negative Thinking and Abstract Analytic Thinking, can all be

Classroom EFL Writing: The Alignment-Oriented Approach

Science.gov (United States)

Haiyan, Miao; Rilong, Liu

2016-01-01

This paper outlines the alignment-oriented approach in classroom EFL writing. Based on a review of the characteristics of the written language and comparison between the product-focused approach and the process-focused approach, the paper proposes a practical classroom procedure as to how to teach EFL writing. A follow-up empirical study is…

Perfluoroalkyl substances in aquatic environment-comparison of fish and passive sampling approaches.

Science.gov (United States)

Cerveny, Daniel; Grabic, Roman; Fedorova, Ganna; Grabicova, Katerina; Turek, Jan; Kodes, Vit; Golovko, Oksana; Zlabek, Vladimir; Randak, Tomas

2016-01-01

The concentrations of seven perfluoroalkyl substances (PFASs) were investigated in 36 European chub (Squalius cephalus) individuals from six localities in the Czech Republic. Chub muscle and liver tissue were analysed at all sampling sites. In addition, analyses of 16 target PFASs were performed in Polar Organic Chemical Integrative Samplers (POCISs) deployed in the water at the same sampling sites. We evaluated the possibility of using passive samplers as a standardized method for monitoring PFAS contamination in aquatic environments and the mutual relationships between determined concentrations. Only perfluorooctane sulphonate was above the LOQ in fish muscle samples and 52% of the analysed fish individuals exceeded the Environmental Quality Standard for water biota. Fish muscle concentration is also particularly important for risk assessment of fish consumers. The comparison of fish tissue results with published data showed the similarity of the Czech results with those found in Germany and France. However, fish liver analysis and the passive sampling approach resulted in different fish exposure scenarios. The total concentration of PFASs in fish liver tissue was strongly correlated with POCIS data, but pollutant patterns differed between these two matrices. The differences could be attributed to the metabolic activity of the living organism. In addition to providing a different view regarding the real PFAS cocktail to which the fish are exposed, POCISs fulfil the Three Rs strategy (replacement, reduction, and refinement) in animal testing. Copyright © 2015 Elsevier Inc. All rights reserved.

Phylogenetic rooting using minimal ancestor deviation.

Science.gov (United States)

Tria, Fernando Domingues Kümmel; Landan, Giddy; Dagan, Tal

2017-06-19

Ancestor-descendent relations play a cardinal role in evolutionary theory. Those relations are determined by rooting phylogenetic trees. Existing rooting methods are hampered by evolutionary rate heterogeneity or the unavailability of auxiliary phylogenetic information. Here we present a rooting approach, the minimal ancestor deviation (MAD) method, which accommodates heterotachy by using all pairwise topological and metric information in unrooted trees. We demonstrate the performance of the method, in comparison to existing rooting methods, by the analysis of phylogenies from eukaryotes and prokaryotes. MAD correctly recovers the known root of eukaryotes and uncovers evidence for the origin of cyanobacteria in the ocean. MAD is more robust and consistent than existing methods, provides measures of the root inference quality and is applicable to any tree with branch lengths.

Psychoeducation for hypochondriasis : A comparison of a cognitive-behavioural approach and a problem-solving approach

NARCIS (Netherlands)

Buwalda, Femke M.; Bouman, Theo. K.; van Duijn, Marijtje A. J.; Van der Duin, M.

In this study, two 6-week psychoeducational courses for hypochondriasis are compared, one based on the cognitive-behavioural approach, and the other on the problem-solving approach. Effects of both courses on hypochondriacal complaints, depression, trait anxiety, and number of problems encountered

Comparison of chemical washing and physical cell-disruption approaches to assess the surface adsorption and internalization of cadmium by Cupriavidus metallidurans CH34

Energy Technology Data Exchange (ETDEWEB)

Desaunay, Aurélien; Martins, Jean M.F., E-mail: jean.martins@ujf-grenoble.fr

2014-05-01

Highlights: • Subcellular distribution of cadmium in Cupriavidus metallidurans CH34 cells. • Comparison of a chemical (EDTA washing) and a physical method (physical disruption). • EDTA washings strongly overestimated membrane-bound Cd concentrations. • The physical method revealed surprisingly over 80% of Cd internalization in the cells. • Metal biosorption by bacteria cannot be considered as a surface complexation process. - Abstract: Bacterial biosorption of heavy metals is often considered as a surface complexation process, without considering other retention compartments than cell walls. Although this approach gives a good description of the global biosorption process, it hardly permits the prediction of the fate of biosorbed metals in the environment. This study examines the subcellular distribution of cadmium (Cd) in the metal-tolerant bacterium Cupriavidus metallidurans CH34 through the comparison of an indirect chemical method (washing cells with EDTA) and a direct physical method (physical disruption of cells). The chemical washing approach presented strong experimental biases leading to the overestimation of washed amount of Cd, supposedly bound to cell membranes. On the contrary, the physical disruption approach gave reproducible and robust results of Cd subcellular distribution. Unexpectedly, these results showed that over 80% of passively biosorbed Cd is internalized in the cytoplasm. In disagreement with the common concept of surface complexation of metals onto bacteria the cell wall was poorly reactive to Cd. Our results indicate that metal sorption onto bacterial surfaces is only a first step in metal management by bacteria and open new perspectives on metal biosorption by bacteria in the environment, with implications for soil bioremediation or facilitated transport of metals by bacteria.

[Comparison of film-screen combination in a contrast detail diagram and with interactive image analysis. 1: Contrast detail diagram].

Science.gov (United States)

Hagemann, G; Eichbaum, G

1997-07-01

The following three film-screen combinations were compared: a) a combination of anticrossover film and UV-light emitting screens, b) a combination of blue-light emitting screens and film, and c) a conventional green fluorescing screen film combination. Radiographs of a specially designed plexiglass phantom (0.2 x 0.2 x 0.12 m3) were obtained that contained bar patterns of lead and plaster (calcium sulfate) to test high and intermediate contrast resolution and bar patterns of air to test low contrast resolution, respectively. An aluminum step wedge was integrated to evaluate dose-density curves of the radiographs. The dose values for the various step thicknesses were measured as percentage of the dose value in air for 60, 81, and 117 kV. Exposure conditions were the following: 12 pulse generator, 0.6 mm focus size, 4.7 mm aluminum prefilter, a grid with 40 lines/cm (12:1), and a focus-detector distance of 1.15 m. The thresholds of visible bars of the various pattern materials were assessed by seven radiologists, one technician, and the authors. The resulting contrast detail diagram could not prove any significant differences between the three tested screen film combinations. The pairwise comparison, however, found 8 of the 18 paired differences to be statistically significant between the conventional and the two new screen-film combinations. The authors concluded that subjective visual assessment of the threshold in a contrast detail study alone is of only limited value to grade image quality if no well-defined criteria are used (BIR report 20 [1989] 137-139). The statistical approach of paired differences of the estimated means appeared to be more appropriate.

Comparison of quantum-mechanical and semiclassical approaches for an analysis of spin dynamics in quantum dots

International Nuclear Information System (INIS)

Petrov, M. Yu.; Yakovlev, S. V.

2012-01-01

Two approaches to the description of spin dynamics of electron-nuclear system in quantum dots are compared: the quantum-mechanical one is based on direct diagonalization of the model Hamiltonian and semiclassical one is based on coupled equations for precession of mean electron spin and mean spin of nuclear spin fluctuations. The comparison was done for a model problem describing periodic excitation of electron-nuclear system by optical excitation. The computation results show that scattering of parameters related to fluctuation of the nuclear spin system leads to appearance of an ordered state in the system caused by periodic excitation and to the effect of electron-spin mode locking in an external magnetic field. It is concluded that both models can qualitatively describe the mode-locking effect, however give significantly different quantitative results. This may indicate the limited applicability of the precession model for describing the spin dynamics in quantum dots in the presence of optical pumping.

Assessing doses to terrestrial wildlife at a radioactive waste disposal site: Inter-comparison of modelling approaches

Energy Technology Data Exchange (ETDEWEB)

Johansen, M.P., E-mail: mathew.johansen@ansto.gov.au [Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW, 2232 (Australia); Barnett, C.L., E-mail: clb@ceh.ac.uk [Centre for Ecology and Hydrology, Lancaster (United Kingdom); Beresford, N.A., E-mail: nab@ceh.ac.uk [Centre for Ecology and Hydrology, Lancaster (United Kingdom); Brown, J.E., E-mail: justin.brown@nrpa.no [Norwegian Radiation Protection Authority, Oesteraas (Norway); Cerne, M., E-mail: marko.cerne@ijs.si [Jozef Stefan Institute, Ljubljana (Slovenia); Howard, B.J., E-mail: bjho@ceh.ac.uk [Centre for Ecology and Hydrology, Lancaster (United Kingdom); Kamboj, S., E-mail: skamboj@anl.gov [Argonne National Laboratory, IL (United States); Keum, D.-K., E-mail: dkkeum@kaeri.re.kr [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Smodis, B. [Jozef Stefan Institute, Ljubljana (Slovenia); Twining, J.R., E-mail: jrt@ansto.gov.au [Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW, 2232 (Australia); Vandenhove, H., E-mail: hvandenh@sckcen.be [Belgian Nuclear Research Centre, Mol (Belgium); Vives i Batlle, J., E-mail: jvbatll@sckcen.be [Belgian Nuclear Research Centre, Mol (Belgium); Wood, M.D., E-mail: m.d.wood@salford.ac.uk [University of Salford, Manchester (United Kingdom); Yu, C., E-mail: cyu@anl.gov [Argonne National Laboratory, IL (United States)

2012-06-15

Radiological doses to terrestrial wildlife were examined in this model inter-comparison study that emphasised factors causing variability in dose estimation. The study participants used varying modelling approaches and information sources to estimate dose rates and tissue concentrations for a range of biota types exposed to soil contamination at a shallow radionuclide waste burial site in Australia. Results indicated that the dominant factor causing variation in dose rate estimates (up to three orders of magnitude on mean total dose rates) was the soil-to-organism transfer of radionuclides that included variation in transfer parameter values as well as transfer calculation methods. Additional variation was associated with other modelling factors including: how participants conceptualised and modelled the exposure configurations (two orders of magnitude); which progeny to include with the parent radionuclide (typically less than one order of magnitude); and dose calculation parameters, including radiation weighting factors and dose conversion coefficients (typically less than one order of magnitude). Probabilistic approaches to model parameterisation were used to encompass and describe variable model parameters and outcomes. The study confirms the need for continued evaluation of the underlying mechanisms governing soil-to-organism transfer of radionuclides to improve estimation of dose rates to terrestrial wildlife. The exposure pathways and configurations available in most current codes are limited when considering instances where organisms access subsurface contamination through rooting, burrowing, or using different localised waste areas as part of their habitual routines. - Highlights: Black-Right-Pointing-Pointer Assessment of modelled dose rates to terrestrial biota from radionuclides. Black-Right-Pointing-Pointer The substantial variation among current approaches is quantifiable. Black-Right-Pointing-Pointer The dominant variable was soil

Assessing doses to terrestrial wildlife at a radioactive waste disposal site: inter-comparison of modelling approaches.

Science.gov (United States)

Johansen, M P; Barnett, C L; Beresford, N A; Brown, J E; Černe, M; Howard, B J; Kamboj, S; Keum, D-K; Smodiš, B; Twining, J R; Vandenhove, H; Vives i Batlle, J; Wood, M D; Yu, C

2012-06-15

Radiological doses to terrestrial wildlife were examined in this model inter-comparison study that emphasised factors causing variability in dose estimation. The study participants used varying modelling approaches and information sources to estimate dose rates and tissue concentrations for a range of biota types exposed to soil contamination at a shallow radionuclide waste burial site in Australia. Results indicated that the dominant factor causing variation in dose rate estimates (up to three orders of magnitude on mean total dose rates) was the soil-to-organism transfer of radionuclides that included variation in transfer parameter values as well as transfer calculation methods. Additional variation was associated with other modelling factors including: how participants conceptualised and modelled the exposure configurations (two orders of magnitude); which progeny to include with the parent radionuclide (typically less than one order of magnitude); and dose calculation parameters, including radiation weighting factors and dose conversion coefficients (typically less than one order of magnitude). Probabilistic approaches to model parameterisation were used to encompass and describe variable model parameters and outcomes. The study confirms the need for continued evaluation of the underlying mechanisms governing soil-to-organism transfer of radionuclides to improve estimation of dose rates to terrestrial wildlife. The exposure pathways and configurations available in most current codes are limited when considering instances where organisms access subsurface contamination through rooting, burrowing, or using different localised waste areas as part of their habitual routines. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

A kernel regression approach to gene-gene interaction detection for case-control studies.

Science.gov (United States)

Larson, Nicholas B; Schaid, Daniel J

2013-11-01

Gene-gene interactions are increasingly being addressed as a potentially important contributor to the variability of complex traits. Consequently, attentions have moved beyond single locus analysis of association to more complex genetic models. Although several single-marker approaches toward interaction analysis have been developed, such methods suffer from very high testing dimensionality and do not take advantage of existing information, notably the definition of genes as functional units. Here, we propose a comprehensive family of gene-level score tests for identifying genetic elements of disease risk, in particular pairwise gene-gene interactions. Using kernel machine methods, we devise score-based variance component tests under a generalized linear mixed model framework. We conducted simulations based upon coalescent genetic models to evaluate the performance of our approach under a variety of disease models. These simulations indicate that our methods are generally higher powered than alternative gene-level approaches and at worst competitive with exhaustive SNP-level (where SNP is single-nucleotide polymorphism) analyses. Furthermore, we observe that simulated epistatic effects resulted in significant marginal testing results for the involved genes regardless of whether or not true main effects were present. We detail the benefits of our methods and discuss potential genome-wide analysis strategies for gene-gene interaction analysis in a case-control study design. © 2013 WILEY PERIODICALS, INC.

Multivariate determinants of self-management in Health Care: assessing Health Empowerment Model by comparison between structural equation and graphical models approaches

Directory of Open Access Journals (Sweden)

Filippo Trentini

2015-03-01

Full Text Available Backgroung. In public health one debated issue is related to consequences of improper self-management in health care.  Some theoretical models have been proposed in Health Communication theory which highlight how components such general literacy and specific knowledge of the disease might be very important for effective actions in healthcare system.  Methods. This  paper aims at investigating the consistency of Health Empowerment Model by means of both graphical models approach, which is a “data driven” method and a Structural Equation Modeling (SEM approach, which is instead “theory driven”, showing the different information pattern that can be revealed in a health care research context.The analyzed dataset provides data on the relationship between the Health Empowerment Model constructs and the behavioral and health status in 263 chronic low back pain (cLBP patients. We used the graphical models approach to evaluate the dependence structure in a “blind” way, thus learning the structure from the data.Results. From the estimation results dependence structure confirms links design assumed in SEM approach directly from researchers, thus validating the hypotheses which generated the Health Empowerment Model constructs.Conclusions. This models comparison helps in avoiding confirmation bias. In Structural Equation Modeling, we used SPSS AMOS 21 software. Graphical modeling algorithms were implemented in a R software environment.

Comparison of topic extraction approaches and their results

NARCIS (Netherlands)

Velden, Theresa; Boyack, Kevin W.; Gläser, Jochen; Koopman, Rob; Scharnhorst, Andrea; Wang, Shenghui

2017-01-01

This is the last paper in the Synthesis section of this special issue on ‘Same Data, Different Results’. We first provide a framework of how to describe and distinguish approaches to topic extraction

Linear VSS and Distributed Commitments Based on Secret Sharing and Pairwise Checks

DEFF Research Database (Denmark)

Fehr, Serge; Maurer, Ueli M.

2002-01-01

. VSS and DC are main building blocks for unconditional secure multi-party computation protocols. This general approach covers all known linear VSS and DC schemes. The main theorem states that the security of a scheme is equivalent to a pure linear-algebra condition on the linear mappings (e.......g. described as matrices and vectors) describing the scheme. The security of all known schemes follows as corollaries whose proofs are pure linear-algebra arguments, in contrast to some hybrid arguments used in the literature. Our approach is demonstrated for the CDM DC scheme, which we generalize to be secure...

A comparison of low-carbohydrate vs. high-carbohydrate diets: energy restriction, nutrient quality and correlation to body mass index.

Science.gov (United States)

Bowman, Shanthy A; Spence, Joseph T

2002-06-01

To evaluate free-living adults' diets that ranged from very low to high amounts of carbohydrate for their energy content, nutritional quality and correlation to Body Mass Index. Adults ages 19 years and older, who had complete dietary intake data on day-1 of the USDA's 1994 to 1996 Continuing Survey of Food Intakes by Individuals (CSFII 1994-1996), were divided into four groups--very low, low, moderate and high carbohydrate--based on the percent total energy from carbohydrate. Mean energy, nutrient, food intakes and Body Mass Index values were compared among the groups. SUDAAN software package was used for the data analysis and pair-wise mean comparisons (p low-fat foods, grain products and fruits. This group also had the lowest sodium intake. Adults eating a high-carbohydrate diet are more likely to have Body Mass Index values below 25. A study of diets of free-living adults in the U.S. showed that diets high in carbohydrate were both energy restrictive and nutritious and may be adopted for successful weight management.

A comparison of the palatability of flavored oral contrasts.

Science.gov (United States)

Arya, Rajiv; Hansen, Allison; Taira, Breena R; Packy, Theodore; Singer, Adam J

2009-09-01

The aim of this study was to compare the taste of computed tomography (CT) oral contrast diluted with various flavored drinks. We performed a prospective, blinded, controlled trial in healthy adult volunteers. Subjects were assigned to ingest four 250-mL aliquots of oral contrast media diluted in water, Crystal Light Lemonade (Kraft Food, Northfield, Ill), Tropical Punch Kool-Aid (Kraft Food), and Tropicana orange juice (Pepsi Bottling Company, Sommers, NY) in random order; and the taste of the solution was measured with a 100-mm visual analogue scale and 5-point Likert scale from very worst to best. Between-group comparison of the taste scores was performed with repeated-measures analysis of variance and pairwise t tests. The study had 80% power to detect an effect size 0.75 SDs. There were 23 subjects; mean (SD) age was 33 (7.7) and 30% were female. The mean (SD) taste scores were water 12 (5), lemonade 37 (21), Kool-Aid 44 (20), and orange juice 40 (20) (P < .05). The proportion of subjects completely ingesting the contrast in water (65%) was significantly less than that with other 3 study solutions (100% each, P < .001). Dilution of oral contrast media with lemonade, fruit punch, or orange juice is tastier than with water. The choice of the specific juice used to dilute the oral contrast should be individualized based on patient preferences and availability.

Surgically induced astigmatism after phacoemulsification by temporal clear corneal and superior clear corneal approach: a comparison

Directory of Open Access Journals (Sweden)

Nikose AS

2018-01-01

Full Text Available Archana Sunil Nikose, Dhrubojyoti Saha, Pradnya Mukesh Laddha, Mayuri Patil Department of Ophthalmology, N.K.P. Salve Institute and LMH, Nagpur, Maharashtra, India Introduction: Cataract surgery has undergone various advances since it was evolved from ancient couching to the modern phacoemulsification cataract surgery. Surgically induced astigmatism (SIA remains one of the most common complications. The introduction of sutureless clear corneal incision has gained increasing popularity worldwide because it offers several advantages over the traditional sutured limbal incision and scleral tunnel. A clear corneal incision has the benefit of being bloodless and having an easy approach, but SIA is still a concern.Purpose: In this study, we evaluated the SIA in clear corneal incisions with temporal approach and superior approach phacoemulsification. Comparisons between the two incisions were done using keratometric readings of preoperative and postoperative refractive status.Methodology: It was a hospital-based prospective interventional comparative randomized control trial of 261 patients conducted in a rural-based tertiary care center from September 2012 to August 2014. The visual acuity and detailed anterior segment and posterior segment examinations were done and the cataract was graded according to Lens Opacification Classification System II. Patients were divided for phacoemulsification into two groups, group A and group B, who underwent temporal and superior clear corneal approach, respectively. The patients were followed up on day 1, 7, 30, and 90 postoperatively. The parameters recorded were uncorrected visual acuity, best-corrected visual acuity, slit lamp examination, and keratometry. The mean difference of SIA between 30th and 90th day was statistically evaluated using paired t-test, and all the analyses were performed using SPSS 18.0 (SPSS Inc. software.Results: The mean postoperative SIA in group A was 0.998 D on the 30th day, which

Inappropriate use of the quasi-reversible electrode kinetic model in simulation-experiment comparisons of voltammetric processes that approach the reversible limit.

Science.gov (United States)

Simonov, Alexandr N; Morris, Graham P; Mashkina, Elena A; Bethwaite, Blair; Gillow, Kathryn; Baker, Ruth E; Gavaghan, David J; Bond, Alan M

2014-08-19

Many electrode processes that approach the "reversible" (infinitely fast) limit under voltammetric conditions have been inappropriately analyzed by comparison of experimental data and theory derived from the "quasi-reversible" model. Simulations based on "reversible" and "quasi-reversible" models have been fitted to an extensive series of a.c. voltammetric experiments undertaken at macrodisk glassy carbon (GC) electrodes for oxidation of ferrocene (Fc(0/+)) in CH3CN (0.10 M (n-Bu)4NPF6) and reduction of [Ru(NH3)6](3+) and [Fe(CN)6](3-) in 1 M KCl aqueous electrolyte. The confidence with which parameters such as standard formal potential (E(0)), heterogeneous electron transfer rate constant at E(0) (k(0)), charge transfer coefficient (α), uncompensated resistance (Ru), and double layer capacitance (CDL) can be reported using the "quasi-reversible" model has been assessed using bootstrapping and parameter sweep (contour plot) techniques. Underparameterization, such as that which occurs when modeling CDL with a potential independent value, results in a less than optimal level of experiment-theory agreement. Overparameterization may improve the agreement but easily results in generation of physically meaningful but incorrect values of the recovered parameters, as is the case with the very fast Fc(0/+) and [Ru(NH3)6](3+/2+) processes. In summary, for fast electrode kinetics approaching the "reversible" limit, it is recommended that the "reversible" model be used for theory-experiment comparisons with only E(0), Ru, and CDL being quantified and a lower limit of k(0) being reported; e.g., k(0) ≥ 9 cm s(-1) for the Fc(0/+) process.

Inappropriate Use of the Quasi-Reversible Electrode Kinetic Model in Simulation-Experiment Comparisons of Voltammetric Processes That Approach the Reversible Limit

KAUST Repository

Simonov, Alexandr N.

2014-08-19

Many electrode processes that approach the "reversible" (infinitely fast) limit under voltammetric conditions have been inappropriately analyzed by comparison of experimental data and theory derived from the "quasi-reversible" model. Simulations based on "reversible" and "quasi-reversible" models have been fitted to an extensive series of a.c. voltammetric experiments undertaken at macrodisk glassy carbon (GC) electrodes for oxidation of ferrocene (Fc0/+) in CH3CN (0.10 M (n-Bu)4NPF6) and reduction of [Ru(NH 3)6]3+ and [Fe(CN)6]3- in 1 M KCl aqueous electrolyte. The confidence with which parameters such as standard formal potential (E0), heterogeneous electron transfer rate constant at E0 (k0), charge transfer coefficient (α), uncompensated resistance (Ru), and double layer capacitance (CDL) can be reported using the "quasi- reversible" model has been assessed using bootstrapping and parameter sweep (contour plot) techniques. Underparameterization, such as that which occurs when modeling CDL with a potential independent value, results in a less than optimal level of experiment-theory agreement. Overparameterization may improve the agreement but easily results in generation of physically meaningful but incorrect values of the recovered parameters, as is the case with the very fast Fc0/+ and [Ru(NH3)6]3+/2+ processes. In summary, for fast electrode kinetics approaching the "reversible" limit, it is recommended that the "reversible" model be used for theory-experiment comparisons with only E0, R u, and CDL being quantified and a lower limit of k 0 being reported; e.g., k0 ≥ 9 cm s-1 for the Fc0/+ process. © 2014 American Chemical Society.

Inappropriate Use of the Quasi-Reversible Electrode Kinetic Model in Simulation-Experiment Comparisons of Voltammetric Processes That Approach the Reversible Limit

KAUST Repository

Simonov, Alexandr N.; Morris, Graham P.; Mashkina, Elena A.; Bethwaite, Blair; Gillow, Kathryn; Baker, Ruth E.; Gavaghan, David J.; Bond, Alan M.

2014-01-01

Many electrode processes that approach the "reversible" (infinitely fast) limit under voltammetric conditions have been inappropriately analyzed by comparison of experimental data and theory derived from the "quasi-reversible" model. Simulations based on "reversible" and "quasi-reversible" models have been fitted to an extensive series of a.c. voltammetric experiments undertaken at macrodisk glassy carbon (GC) electrodes for oxidation of ferrocene (Fc0/+) in CH3CN (0.10 M (n-Bu)4NPF6) and reduction of [Ru(NH 3)6]3+ and [Fe(CN)6]3- in 1 M KCl aqueous electrolyte. The confidence with which parameters such as standard formal potential (E0), heterogeneous electron transfer rate constant at E0 (k0), charge transfer coefficient (α), uncompensated resistance (Ru), and double layer capacitance (CDL) can be reported using the "quasi- reversible" model has been assessed using bootstrapping and parameter sweep (contour plot) techniques. Underparameterization, such as that which occurs when modeling CDL with a potential independent value, results in a less than optimal level of experiment-theory agreement. Overparameterization may improve the agreement but easily results in generation of physically meaningful but incorrect values of the recovered parameters, as is the case with the very fast Fc0/+ and [Ru(NH3)6]3+/2+ processes. In summary, for fast electrode kinetics approaching the "reversible" limit, it is recommended that the "reversible" model be used for theory-experiment comparisons with only E0, R u, and CDL being quantified and a lower limit of k 0 being reported; e.g., k0 ≥ 9 cm s-1 for the Fc0/+ process. © 2014 American Chemical Society.

Green Infrastructure and German Landscape Planning: A Comparison of Approaches

Directory of Open Access Journals (Sweden)

Catalina VIEIRA MEJÍA

2015-11-01

Full Text Available A variety of similarities between green infrastructure and the German landscape planning can be found in comparing the approaches of the two planning instruments. Principles of green infrastructure such as multifunctionality, the multi-scale approach and connectivity show correspondences with landscape planning elements. However, some differences are apparent. The objective of this paper is to determine whether the main aims of these two frameworks overlap. It also seeks to deduce what benefits from ecosystem services could be provided by integrating the green infrastructure approach into the German landscape planning system. The results show that the green infrastructure concept is not well-known in German planning practice, although its principles are generally implemented through traditional landscape planning. Nevertheless, green infrastructure could act as a supplementary approach to current landscape planning practices by improving public acceptance and strengthening the social focus of the current landscape planning system.

Report on EUROMET.RI(I)-K1 and EUROMET.RI(I)-K4 (EUROMET project no. 813): Comparison of air kerma and absorbed dose to water measurements of 60Co radiation beams for radiotherapy

International Nuclear Information System (INIS)

Csete, I.; Leiton, A.G.; Sochor, V.; Lapenas, A.; Grindborg, J.E.; Jokelainen, I.; Bjerke, H.; Dobrovodsky, J.; Megzifene, A.; Hourdakis, C.J.; Ivanov, R.; Vekic, B.; Kokocinski, J.; Cardoso, J.; Buermann, L.; Tiefenboeck, W.; Stucki, G.; Van Dijk, E.; Toni, M.P.; Minniti, R.; McCaffrey, J.P.; Silva, C.N.M.; Kharitonov, I.; Webb, D.; Saravi, M.; Delaunay, F.

2010-01-01

The results of an unprecedented international effort involving 26 countries are reported. The EUROMET.RI(I)-K1 and EUROMET.RI(I)-K4 key comparisons were conducted with the goal of supporting the relevant calibration and measurement capabilities (CMC) planned for publication by the participant laboratories. The measured quantities were the air kerma (K air ) and the absorbed dose to water (Dw) in 60 Co radiotherapy beams. The comparison was conducted by the pilot laboratory MKEH (Hungary), in a star-shaped arrangement from January 2005 to December 2008. The calibration coefficients of four transfer ionization chambers were measured using two electrometers. The largest deviation between any two calibration coefficients for the four chambers in terms of air kerma and absorbed dose to water was 2.7% and 3.3% respectively. An analysis of the participant uncertainty budgets enabled the calculation of degrees of equivalence (DoE), in terms of the deviations of the results and their associated uncertainties. As a result of this EUROMET project 813 comparison, the BIPM key comparison database (KCDB) will include eleven new Kair and fourteen new D w DoE values of European secondary standard dosimetry laboratories (SSDLs), and the KCDB will be updated with the new DoE values of the other participant laboratories. The pair-wise degrees of equivalence of participants were also calculated. In addition to assessing calibration techniques and uncertainty calculations of the participants, these comparisons enabled the experimental determinations of N Dw /N Kair ratios in the 60 Co gamma radiation beam for the four radiotherapy transfer chambers. (authors)